Hhmi-narrative

From Earlham CS Department
Jump to: navigation, search

Narrative

  • Notes
    • 7000 words double-spaced

Part I: Introduction:

Under the guidance provided in BIO2010 and How People Learn and in accordance with our mission to deliver inquiry-based and student-centered science education experiences, we provide the following major objectives:

  • 1. Expose students to inquiry-based, open-ended research endeavors throughout their academic careers;
  • 2. Excite and retain students, notably underrepresented groups, in the natural and biomedical sciences;
  • 3. Develop in-class student research experiences and course modules that integrate the physical sciences into the Biology and Chemistry curriculum;
  • 4. Engage students in contemporary bioinformatics and computational biology congruent with modern approaches in studying the Central Dogma of Molecular Biology;
  • 5. Build on the Earlham College tradition of excellence in international education;
  • 6. Train current faculty in the pedagogical utility of modern technical instrumentation;
  • 7. Become regional and national leaders in access to genomic, proteomic, and computational techniques;
  • 8. Expose students to numerous pre-health educational experiences embracing the trend of interest in Public Health;
  • 9. Evaluate and update the science curriculum with emphasis on the integration of quantitative reasoning, statistics, and computational approaches; and
  • 10. Provide local science outreach and health-related service to the local community.

To reach these goals, we plan the following strategies of implementation, combining past HHMI-funded programming and novel endeavors:

  • 1. Continue our summer science education program creating 20 research placements for current students; 10 on campus, and 10 off-campus;
  • 2. Maintain our successful Bridge to Excellence program to retain and recruit students, targeting underrepresented groups, in the biological and biomedical sciences;
  • 3. Acquire contemporary computational-based instrumentation currently paving the modern revolution in high-throughput genomics/proteomics;
  • 4. Attend and provide workshops to broaden the incorporation of utilizing this equipment in laboratory course modules;
  • 5. Integrate applications using these instruments directly into our classes exposing students to these technologies from their first year through graduation;
  • 6. Develop into an active and leading member of the growing Genome Consortium of Active Teaching (GCAT) through becoming a microarray scanning center;
  • 7. Promote pre-health education through an innovative program connecting local/regional and international Public Health
  • 8. Formally evaluate the curriculum of our increasingly popular Biochemistry interdepartmental major focusing on student quantitative and statistical prowess;
  • 9. Create new computational-based laboratory course modules directly integrating Mathematics and Computer Science Faculty; and
  • 10. Extend the science education outreach services and enhance the curricular aims of the Joseph Moore Museum of Natural History.

Part II: Institutional Setting

Earlham College is a four-year, private, coeducational institution providing a liberal arts education for 1200 undergraduates. Guided by its original 1847 founders, the Religious Society of Friends, Earlham emphasizes the search for truth through lack of coercion, letting the evidence lead the search. The educational philosophy of the College promotes the learning process of awakening the ‘teacher within’, so that our students become active, involved life-long learners. These Quaker principles shape our philosophy regarding science education where students are full and active participants in evidence-directed, hands-on, inquiry-based educational experiences. We are constantly integrating valuable student experiences throughout our curricula, intentionally building student competence and confidence towards the capstone experiences provided by intimate student-faculty mentoring and research endeavors. Earlham strives to educate students in becoming engaged global citizens. Not only is the Earlham student body a diverse community (12% being international), more than 65% of the students, including those on pre-health trajectories, participate in an off-campus international experience. This is incomparable to the national average of less than 3%. Notably, every off-campus venture is organized and led by current Earlham Faculty and not by oversees host institutions. The novel PHILTER program (see Page ##) proposed herein hopes to extend our international success in the rising field of Public Health. The Natural Science Division (NSD) includes 25 faculty members and offers majors in Biology, Biochemistry (interdepartmental major), Chemistry, Computer Science, Geosciences, Mathematics, Physics, Psychobiology (interdepartmental major). The department shares a complex, approaching 76,000 square feet, that includes molecular biology teaching and research laboratories, animal care facilities, greenhouse, planetarium, natural history museum, science library, SEM, 400 MHz NMR, automated DNA sequencer, and numerous computer laboratories. In Colleges that Change Lives (2006), noted education reporter, Loren Pope, states that, ‘If every college and university sharpened young minds and consciences as effectively as Earlham does, this country would approach utopia’. We feel this no more evident than in our student success in the Sciences. The Biology Department ranks impressively high in the percent of graduates achieving Ph.D.s; Biology ranks 8th among 1302 institutions nationally in the Life Sciences. In the past five years, greater than 90% of our pre-health graduates have matriculated into medical schools, including University of Pennsylvania, Johns Hopkins, and University of Chicago. Our students have been and will be supported by recent grants, of the past two years, by many of the key personnel contributing to this proposal: Dr. Deibel is program director, with John Iverson and Charlie Peck are contributing to the funded Keck Foundation Grant which targets multidisciplinary education (see grant objectives PFO##) across all departments of the NSD, Dr. Stocksdale is funded by the USDA, Dr. Blair’s bioinformatics-based methods of revising malaria genomes funded by an NIH AREA grant. We believe are successes can be attributed, in part, to our emphases on student-centered learning via our commitment to help students develop to their full academic and personal potential in today’s world. To this end, the current proposal combines acclaimed initiatives of the past with new innovative and contemporary approaches to teaching and recruiting/retaining students of all backgrounds into science.

Part III: Broadening the Access to Science:

Earlham requires students take part in hands-on and complete research experiences where students participate at every stage of the scientific process. This includes a focused attention to: 1) informational technology and bibliographic searching, 2) literature and data guided hypothesis generation, 3) experimental design including pre-planned statistics and knowledge of techniques/instrumentation, 4) proper experimentation and data acquisition, 5) synthesis and interpretation of data, 6) conclusion drawing, and 7) effective written and oral dissemination of findings. A scientific experience void of any of the above practices is marked as lacking. The three major components described in this section will actively engage students, of various skill and backgrounds, in science, each involving complete student research experiences. The novel PHILTER and modified Bridge to Excellence programming have been designed for continuance even after HHMI funding as part of our May-term offerings. May-terms are optional 3-4 week academic/research and credit-earning opportunities for students.

Summer Undergraduate Research Experience: We will resume our active HHMI-funded summer student-faculty research program for 20 students per summer. We intend to place half of these student researchers with faculty at Earlham and the remainder in research settings with alumni and friends of the college. Anticipated on-campus research topics, research mentors, and years of participation are listed below:

  • Peter Blair (Biology, 2009-2012): Bioinformatics approaches to refining annotations of malaria genomes.
  • Michael Deibel (Chemistry, 2009-2012): Isolation and characterization of antioxidant compounds in natural products
  • Corinne Deibel (Chemistry, 2010-2011): Determination of atrazine and its metabolites in local waters
  • John Iverson (JMMNH, 2009-2012): Physiological ecology of hatchling turtles in their nests
  • David Matlack (Biology, 2009-2012): the study of spatial and temporal expression of genes involved in neural crest specification
  • Amy Mulnix (Biology, 2011-2012): analyzing differential gene expression in tree leaves exposed to direct sunlight versus those in the more shaded interior using microarray and proteomic techniques.
  • Charlie Peck (Computer Science, 2009-2012): Analysis of gene prediction software on AT-rich genomes. Improved algorithms could better support malaria genomes.
  • Olen Stephens (Chemistry, 2009-2012): Improving solubility and helicity of b3-peptide 14-helices
  • Mark Stocksdale (Chemistry, 2010-2012): Chemical synthesis of biologically interesting molecules including phytosiderophores.

The attached CVs of key personnel involved in summer research demonstrate our success in providing substantial student research experiences, including publication and presentation of their work at regional and national meetings. In the past five years, 77 students (51% women and 21% international) have conducted science research on- or off- campus.

Past secured HHMI funding has assisted in the opportunity of our students to engage in research experiences off-campus. We are seeking continued support for off-campus student placement since this allows us to increase both the numbers of student participants in summer research and the project topics available to them. Our alumni and other collaborators enthusiastically welcome and supervise our students. Please refer the letters of support and personal commitment attached (joint letter from Drs. Ksander and Gregory, and alumnus Dr. Sean Crosson).

A short list of off-campus laboratory commitments include:

  • Dr. Bruce Ksander and Dr. Meredith Gregory, Schepens Eye Institute, affiliate of Harvard Medical School
  • (Mark will Provide name), Eli Lilly
  • (Corrine and Mike are considering administrative hassles that might complicate this inclusion), Oak Ridge National Laboratories
  • Dr. Sean Crosson and Dr. Aretha Crosson, University of Chicago
  • Dr. John Adams, Global Health Infectious Disease Program, University of South Florida
  • Dr. Peter Beal, University of California, Davis
  • Dr. Nathan Luedtke, University of Zurich
  • Dr. Tamara Hershey, Washington University School of Medicine
  • Dr. Steven Mennerick, Washington University School of Medicine
  • Prof. Joseph J. Falke, Director, Molecular Biophysics Program
  • Dr. Carter Van Waes, NIH/NIDCD
  • Dr. Cindy Buhse (contact Loretta Saey), Director, DPA at the FDA in St. Louis

To promote interdisciplinary discussion and collaboration, the on-campus HHMI research scholars will live in the same hall of a student dormitory. Weekly meetings of all on-campus researchers during the summer (including those projects funded by other sources) will contribute to the interdisciplinary nature of the projects and provide greater opportunities for mentoring relationships that extend beyond the faculty member directly involved with a given student researcher. Earlham will also host an Undergraduate Research Conference, providing an opportunity for our student researchers to present their work to their peers, while also serving as a recruiting vehicle to attract future scientists.

Support is requested for student stipends, supply money, travel support for students at off-campus research locations and for student travel to regional or national scientific meetings to present research findings, and for miscellaneous materials for group meetings and social activities. Faculty honoraria are not being requested rather will be contributed by Earlham as an indication of the institute’s commitment to the irreplaceable value of student research.

Student selection will follow our current format for summer research experiences. In the prior Fall semester student experiences are publicly advertised with pertinent information including the duration and description of all research opportunities (on- and off-campus). Students complete a written application where research opportunities are prioritized. The summer science research committee meets and negotiates the targeting of students with the ‘best-fit’ laboratory. The Program Director will facilitate the meeting ensuring the HHMI-funded experiences are upheld among the non-HHMI supported experiences.

Bridge for Excellence:

NEED TO ADD (Mark is the champion)

Public Health Initiative: Local/Tanzania Experience and Research (PHILTER): A national trend, visible with our current and recent student pursuits, is a growth in the field of Public Health. A rapid increase in undergraduate interest has created the ‘supply’ for 127 domestic institutes to offer an undergraduate major in Public Health. Of the 39 accredited post-baccalaureate schools of public health, the majority showed increase interest and enrollment in 2006 (communicated by Bill Harvey, Earlham emeritus faculty and National Association of Advisors for the Health Professions liaison to the Association of Schools of Public Health). In fact, some schools are reporting as high as 35% increases in program matriculation and together the accredited schools educate more than 19,000 students annually (from SOPHAS.org). Earlham has recently graduated students now enrolled at distinctive programs in Public Health including Johns Hopkins University, need more here. Based on the growth and interest in the field, we now propose a two-armed student experience in Public Health in the form of a connected program in local/regional public health and international (Tanzania) health. The cohesive PHILTER program design purposefully mixes the two student cohorts at the beginning and end of their May research experiences. Both the local and international program will share introductory lectures and course readings prior to the departure of the Tanzania group. Upon returning from abroad, both groups will have significant time to share experiences resulting in overall program synthesis and for maximizing student exposure to the field of Public Health. Both branches of the program would include active student exposure to the five core and interdisciplinary public health areas of biostatistics, epidemiology, environmental health, health services administration and behavioral sciences/health education. The research embedded in the programming would also serve as the research requirement for the Biochemistry interdepartmental major. The following sections provide programming detail of both arms of the PHILTER program.

Local: HHMI would fund an initial pilot program with 12 academically talented rising sophomore and junior participants each year with interest in the medical and allied health fields. This 4-week program in May facilitated by two Earlham faculty members would include both a local public health project on a topic which has been identified by a combined group of community health leaders and program faculty, as well as a formal opportunity for students to explore different aspects of medical practice. This second goal, exposure to the medical field, would continue in the form of a fall internship in a community health care setting. Students would receive academic credit for their participation in this program. At the end of the grant period, we would hope to transition this program into a regularly offered May-term course and Health Careers Internship program.

Earlham College students and faculty will participate in a project to address pertinent public health issues in the local Richmond/Wayne County area. Initial topics with potential to study include smoking cessation, weight loss (affiliated with STOP), and prenatal care. One example of a student research experience would be using existing data and possibly further data collection (in collaboration with the Wayne County Health Department) to determine patterns and causes of lower than average rates of prenatal care in the local area. Students will then work with the community alongside local physicians and health administration to design and implement educational and media materials for use in secondary schools and community based centers. Students will utilize statistics to assess the effects of these targeted programs to measure intended improvement.

Specific curricular activities early in the course would include data mining of WHO, CDC, Health and Human Services, and Indiana data with statistical and meaningful analysis.

This project would be carried out during May for the four years of the grant period (beginning May 2009); work on aspects of this project during the academic year is also possible. Each year, students would be responsible for writing a final summary report of their work and presenting it in a public forum, like the URC.

The 12 rising sophomores and juniors above would participate in a series of experiences designed to increase their awareness and exposure to a wide array of medical fields. These experiences might take the form of tours, observations, presentations given by medical professionals, or other activities agreed on by all parties. We anticipate that much of this would take place at Reid Hospital and the Wayne County Health Department, with other community resources added as needed. Possible departments may include: Radiology, Surgery, Primary Care, Pathology, Toxicology, Rehabilitation, Hospital Administration, Obstetrics, Dentistry, Optometry, or Veterinary Medicine. Please see letters of support and commitment from Dr. Paul Rider, Director of Medical Education, Reid Hospital; and Barry McDowell, President of Reid Hospital).

Earlham faculty, using community members as resources where appropriate, will design and facilitate a number of lectures and discussions with the students on cross-cultural medicine, bioethics, and current healthcare practices (i.e. regulations regarding medical confidentiality). These experiences will employ written texts and case studies where appropriate. Students would be asked to complete a reflection on their experience in the health care setting, as well as complete other assignments related to the Humanity in Medicine and Bioethics components.

Participants in the local PHILTER program, and potentially several of the international cohort, would participate in a fall internship in a health care setting in the community. These students would be expected to commit several hours weekly to the experience. While the exact nature of the internship will differ depending on the setting, we would hope that each student both be provided opportunities to observe health care delivery as well as participate in some project of use to the office or clinic to which they are assigned (for example, statistical analysis of a group of patients for a variable of interest, design and implementation of Health Education programs, etc.). Available internships would be based on interest of clinics in the Richmond/Wayne county area and may include: Radiology, Adult and Pediatric Primary Care, Pathology, Toxicology, Rehabilitation, Hospital Administration, Obstetrics, Dentistry, Optometry, Mental Health, or Veterinary Medicine.

Tanzania: Earlham’s tradition in international education is almost unparalleled. Recently celebrating 50 years of off-campus programming, Earlham is committed for these student-centered opportunities to be sustained. Providing one example, Earlham has offered Faculty-led, semester-long, student experiences in East Africa for three decades. Based on travel advisories, the program shifted from Kenya to Tanzania in 2003. One alumnus transformed by her own experiences in Africa, and indicative of student global citizenry and service, is contributing back to local Tanzania populations. Jessica Castleberry ’05 initiated a middle-school fundraiser to support an AIDS hospital in Tanzania. (visit http://www.earlham.edu/publicaffairs/content/pressroom/archive/2006/march/060314s-castleberry.php). In coordination with the previously described local public health experience, and utilizing our experience and established international contacts, we are requesting support for a 4-week public health focused student experience in Tanzania. With the presence of the three most devastating infectious diseases – HIV, Malaria, and AIDS-Tanzania offers a unique student-experience to witness and participate in local education, treatments, prevention, epidemiology, and international outreach (MIM, Roll Back Malaria).


NEED TO ADD (Sara is the champion)

The student participants of the three May programs described above will live in a communal dormitory where experiences can be shared outside the laboratory and classroom. The Bridge students, those targeted for science retention and personal growth, will be able to live and socialize with successful peer mentors, the PHILTER students. In fact, we foresee Bridge graduates to be inspired to become future PHILTER participants due the close association and integrated nature of the programming. This will be assessed as Bridge graduates are monitored after the experience.

Part IV: New, Current, and Future Faculty Development:

Workshops: We request support to expand the technical expertise of our current faculty given the contemporary emergence of informatics-based, post-genomic, analytical, and forensic technologies within the Sciences. As once cemented canons get reworked by modern technological advances, such as the evolving nonlinear view of the Central Dogma of Molecular Biology – DNA ⇔ RNA ⇔Protein (as supported by the preliminary ENCODE Project), we propose our faculty must be trained in the pedagogical use of these modern tools. We propose our faculty attend workshops for training and application use for the following:

  • LICOR 4300L DNA Analyzer: The recently (2006) acquired automated sequencer has already proved educational dividends in Dr. Blair’s courses and research specifically through DNA sequencing, yet we would like to maximize its use in our curriculum by attending the AFLP and SNP training workshops held at LICOR’s headquarters in Lincoln, Nebraska. Incorporating these techniques demonstrating species relatedness and phylogeny into our courses would serve students well given the current complexities with taxonomy.
  • GenePix 4200A Microarray Scanner: The requested microarray scanner serves a dual role: as a tool for student access to large-scale gene expression studies and as the featured instrument to our outreach commitment in becoming a GCAT scanning facility (see GCAT component PP##). GCAT has NSF support for workshops on application use and data/statistical analysis for microarrays. We are requesting three Faculty attend one of these workshops in summer 2009. Support is also requested for scanning facility training from GCAT founder, Dr. Malcolm Cambell (Davidson College).
  • JMS-T100DART AccuTOF-D Mass Spectrometer: The requested mass spectrometer brings immense teaching utility to our laboratory courses across disciplines (see Equipment pp##). JEOL offers off-site training for two individuals (free tuition). We propose to send four individuals representing Biology and Chemistry for instrument training in Peabody, MA.

The requested support for off-campus workshops will train our faculty in the use of the aforementioned technologies. To further maximize the utility of the instruments across the NSD and regionally, we will host an on-campus workshop to further train existing Earlham and regional Faculty (from Ivy Tech, Indiana University East, and …). In becoming a regional leader in biotechnological capacity, we hope to share our knowledge in hopes students at adjacent campuses can be exposed to the same technological advances as our own students.

Part V: Curriculum, Equipment, and Laboratory Development

Building laboratory-based scientific inquiry into our curricula makes lab work more interesting and instruction more effective, thus attracting and retaining students. Earlham’s history of students doing science is still evident in the student-organized and independent project assignments incorporated in the core curricula. This coupled with a focus on scientific literacy has proven attractive to majors and non-majors enrolled in these first-year courses. For instance, students are expected to think critically about concepts and examples; integrate their original thoughts to propose new experiments or explain unexpected results; and communicate precisely, both orally and in writing.

While the set of practices detailed above and on p. ## are still in place at Earlham, we are devoted to adapting the scientific process based on emerging trends in our field, notably genomic and post-genomic technologies. The large-scale and computationally heavy data sets generated by these technologies have changed how we approach scientific problems. In a relatively short amount of experimentation immense and sophisticated data sets emerge. The conceptual ability to grasp and analyze these data sets, with quantitative prowess and proper analytical reasoning, is a challenge to students. We propose that students can and will embrace these changes in the field due to repeated and purposefully developed curricular exposure to these computationally-driven, statistically-powered, instrumentation-guided modern practices. This intended process of repeated, non-redundant, exposure to these research technologies embraces the directives of ‘learning scaffolding’, real-world problem solving, and interactive interfaces, as detailed in How People Learn.

Equipment and computers:

Acquisition of instrumentation is a centerpiece to the overall mission of the proposal and to the curricular revisions described herein. For it is the integration of these technologies in laboratory modules, that will expose students to modern day trends in problem solving, hypothesis-crafting, and data interpretation/analysis.

As part of this proposal, we are requesting a JMS-T100 DART with HPLC and nano-ESI. This instrument is a high resolution mass spectrometer which we will equip with two different interfaces: a direct analysis in real time (DART) interface and a nanospray electrospray HPLC interface. While the result of having this high resolution and multiple interfaces is a relatively large cost, we believe the benefits to our students, courses and research are tremendous and outweigh these costs. Although we currently have GC-MS, it is limited in application to small volatile molecules and its resolution is also limited to 1 amu. This system will allow us to analyze nonvolatile compounds (such as drug metabolites) and larger compounds (such as peptides) with a much higher resolution. In fact, the accuracy of both the mass and isotopic abundances is such that the elemental composition of an unknown can be determined directly (JEOL lit). This type of analysis is very important in both the Organic II course as well as research.

The DART interface allows analysis of compounds directly off of a surface without the need for extensive preparation. It is extremely fast, simple and easy to use. This allows its incorporation into laboratories with larger numbers of students, such as General Chemistry. Because of its simplicity, students at all levels of experience can operate this instrument first hand, rather than handing a sample to a teaching assistant or instructor to analyze. In addition, the speed of analysis gives students almost instantaneous results, limiting wait time and increasing the time students can spend actually evaluating and understanding the data. With the use of internal standards, this technique can not only give qualitative identification of compounds, but also quantify them. The HPLC with nanospray-ESI will be utilized when trace analysis is being performed on a complex matrix or when a sample analysis is too complicated for the simpler DART interface(for example when used for proteomics work). An example of this is proteomic work (expand here with new information).

The impact of this instrument would be significant across the Biology and Chemistry curricula, with impeccable student exposure over their undergraduate career (Table 1). This instrument would be incorporated into projects into four biology courses as well as four chemistry courses reaching >180 different individuals (15% of the entire student body). Overall, student contact per academic year, including multiple use by the same individual, will approach 332 students. A typical Biochemistry interdepartmental major would utilize the mass spectrometer a minimum of six times prior to graduation (minimum of 3 for Biology and 4 for Chemistry majors). Because the instrument will be used in our introductory courses (BIOL112 and CHEM111), which also meet College-wide general education requirements, non-majors would be significantly impacted as well.

The projects using the instrument are planned to increase in sophistication and student independence as they rise through the core curricula. Often our courses include a self-designed independent research project imbedded in our laboratories. This type of project allows students to take ownership of the experiment they are doing in laboratory and to explore interests of their own, often addressing real-world problems. This allows them to more fully appreciate and understand the scientific process by experiencing it first hand. Here is a brief description of planned projects or examples of student-derived independent experiments:

  • CHEM111: Principles of Chemistry; As a complement to our neutron activation experiment, students will direct measure isotopic ratio patterns in compounds. Because of the ease and speed of the DART interface, students can take their own data for a variety of compounds and direct determine isotopic ratios and use those to understand isotopic abundances.
  • CHEM221: Organic Chemistry: Currently, this course has a laboratory on the isolation of limonene in oranges. Using the DART interface, students can first determine experimentally which part of the orange contains the limonene and later determine the purity of their isolated limonene.
  • CHEM 321 Organic Chemistry II: Early in the semester, this will be used to obtain MS data for unknown structure elucidation (coupled with NMR and IR). Routinely throughout the semester (including the student selected synthesis or isolation projects), the students will acquire MS data as part of their standard molecular characterization.
  • CHEM331: Equilibrium and Analysis: One of the highlights of this course is a 4 week (8 laboratory periods) independent project. Utilizing both the ability to analyze nonvolatile compounds and the high mass resolution, students will now be able to truly design projects that complement their individual interests.
  • CHEM351: Biochemistry: The direct-detection MS will be used to monitor chemical modification of purified proteins. Fluorescein and Biotin labeled proteins will be used in substrate binding assays and ligand capture experiments.
  • CHEM371: Environmental Chemistry and Toxicology: (MIKE WILL ADD)
  • BIOL341: Cell Physiology:
  • BIOL347: Anatomy and Physiology: Endocrinology and Metabolism: Independent, student-designed, semester-long physiology projects are an essential component of this popular course. The MS could be used to identify metabolites of nutritional supplements, hormones, or endogenous compounds in a number of body fluids. Dr. Matlack is also interested in the identification of human pheromones, which would be greatly facilitated by MS.
  • BIOL362: Parasitology: Dr. Blair would integrate a proteomics module into his semester-long research project on human malaria. Currently, he trains students on the free on-line genomics resource, PlasmoDB (www.plasmodb.org, University of Pennsylvania), to harness microarray expression data and provide genome sequences for students to target novel vaccine targets. Students couple this bioinformatics knowledge with wet-lab techniques of RNA extraction, primer design of student selected target sequences, RT-PCR, and gel electrophoresis to visualize their amplified products. The DART mass spectrometer would be used to confirm protein expression in blood-stage parasites and compared to the original malaria proteome literature (Florens et al, Nature 2002). Thus students witness genome, transcript, and protein analysis representing each step of the Central Dogma.

We also seek support for the purchase of a GenePix 4200A microarray scanner. Already in possession and actively using our automated DNA sequencer, we wish to incorporate gene expression and high-throughput studies into additional laboratory modules (Table 1). Students will be exposed to the scanner in their first year, including Biology/Biochemistry majors and non-majors as part of our BIOL112: Cells, Genes, and Inheritance course. The majority of Biology students would receive an upper level experience with the scanner in Advanced Cell Physiology Laboratory and/or Microbiology. Transcriptional analysis or metagenomic projects include:

  • BIOL112: Cells, Genes, and Inheritance: Student experiences in CGI already include a student-driven, literature-guided study of microbial populations in local environmental samples. Secondly, students close the semester with a genetic disease project using on-line informatics (NCBI, GenBank, GeneCards, and the like) culminating in a formal poster presentation. We propose to create and include and intermediate/bridging module where students use available microarrays (analagous to PhyloChips) in metagenomic studies to reveal bacterial species populations in their soil samples. A knowledge of microarray techniques would prepare students for large-scale expression content often arising from their genetic disease project while also be consistent and well-timed with existing lecture material.
  • BIOL461: Microbiology: As an active member of GCAT, Dr. Blair would obtain free E. coli microarrays to engage students in inquiry-based expression projects. Students, in groups of 4, would design an experiment, to alter, due to stress or nutrient availability, etc., gene expression of the bacteria compared to controls.

The scanner will serve a dual role as a mode of outreach as part of our initiative to become a GCAT scanning facility (see Outreach pp##.). The model, capable of detecting both Red/Green fluorescence, is recommended by Malcolm Campbell (GCAT Director, see attached letter).

In addition to having a transformative effect on our curriculum, particularly in courses with self-designed independent lab components, these instruments will also tremendously impact the student-faculty collaborative research at Earlham. The proposed research of eight out of the nine faculty will utilize one or both of the proposed instruments. (any chance we can get a “turtle chip” so that we can make it 9 for 9?). Both the sophistication and ease of use of these instruments are crucial.

These instruments fit perfectly with the experiential nature of how we “do science” at Earlham College. The small size of our laboratory sections utilizing this equipment, typically 12-15 students, rarely surpassing 20, provides significant student contact with the technology and with faculty mentors. As a statement of institutional commitment to the educational reward provided by these two instruments, the College will provide $100,000 of matching money for their acquisition.

Biochemistry Major Review/Course Module Development:

Shaped from previous HHMI support (see PFO), our Biochemistry major has flourished with the number of majors increasing four-fold from its inception as a faculty-approved major in 1999. This increase is also attributable to an increase of enrolled students with interest in pre-health careers. Being one of the most rigorous majors in terms of credit demands (56 major requirements, out of 120 needed for graduation), the interdisciplinary major also includes a research requirement and oral/written comprehensive capstone examinations. Approaching ten years as a major, we propose a complete review of our Biochemistry curricula using the directives of BIO2010 (Chapter 2: A New Biology Curriculum) as our guide. Simply stated, we will use BIO2010 as a checklist to review course syllabi and content to assure that all recommendations are met in at least one required course. A second objective will be a comparison of our interdisciplinary major course content and load to comparable, traditional Biochemistry majors of our peer institutes. We request support for an internal review committee, including all members of the Biochemistry teaching faculty, to participate in two August review sessions over the four year funding period. During the second review session, we will seek an external reviewer to assess our programming.

An included aim of a review is to modernize our course content to better represent technological and computational advances in the field. This has direct connections with the proposed equipment requested and use in the core curriculum and the wide use of these instruments will be reviewed concurrently. To this end, in the review process we will also include the development of new class modules integrating biology with our mathematics and computer science faculty. An emphasis will also be the quantitative reasoning prowess of our students, including experimental design and statistics. Two course module additions already with developmental momentum include:

  • Charlie Peck (Computer Science): Mr. Peck and Dr. Blair will engage students in the analysis of gene prediction software (e.g. FullPhat, GlimmerM, GeneFinder) in pursuit of training these algorithms for improved annotation of A-T-rich genomes (such as for malaria and slime molds). This module could be placed in a combined laboratory session joining Parasitology and Computer Applications students. This would serve to mix biology and computer student populations exposing them to real-world applications.
  • Anand Pardhanani (Mathematics): Dr. Pardhanani, a recent tenure-track addition, brings expertise of mathematical modeling of biological systems to Earlham. Specifically, Dr. Pardhanani would engage upper-level Biology/Biochemistry students in comprehension of k-means clustering analysis involved in gene function prediction based on expression patterns. This method has been pivotal in gene function prediction in malaria and yeast systems. Module would be relevant in Molecular Genetics, Parasitology, and Microbiology classes and maximizes the return of microarray experiments.


Part IV: Precollege and Other Outreach:

Genome Consortium for Active Teaching (GCAT):

(Initiate an active membership and become scanning facility for the Genome Consortium for Active Teaching)

The Genome Consortium for Active Teaching (GCAT) is a success story for both the integration of and access to computational biology, bioinformatics and genomics within undergraduate education. Briefly, GCAT provides affordable microarray slides, off-site scanning services, free analytical software, faculty workshops, and technical support for interested undergraduate institutes (currently totaling 141 faculty on 134 campuses). In doing so, GCAT meets many of the goals of BIO2010. Under the supervision of founder Dr. Malcolm Campbell (Davidson College), the Consortium now has six years of supportive and positive assessment and a projection for continued growth (Campbell et al, Life Sciences Education 2007). In fact, member institutes have placed requests for 1,156 microarrays slides for the 2007-08 academic year correlating to a 30% increase from the prior year (Malcolm Campbell, personal communication). With great respect to the success to this program, and the need to sustain it for the future, Earlham College seeks to become an active member of this consortium.

We propose to become the fourth scanning center, joining Davidson College, Pomona College, and Niagara University, to assist in managing the increased GCAT scanning needs. Dr. Peter Blair, who has experience with microarray technology, including RNA preparation, and analysis (see CV publications), is committed to become the program director. He will supervise two undergraduate ‘work study’ students per semester in the scheduling, scanning, and maintenance of the facility. Students that have completed the Bridge to Excellence Program, thus potentially exposed to microarray technologies and experimentation, will be the target group for these student positions. The receiving of hybridized glass slides, scanning, and the dissemination of data to GCAT participating institutes will be governed through the established GCAT methodologies (http://www.bio.davidson.edu/projects/gcat/GCAT.html#mission). Charlie Peck and computer science students will oversee the management of the ISB FTP server for data delivery.

We feel Earlham is an attractive addition to the team of GCAT scanning facilities. Currently, the existing facilities are geographically located on either the east or west coasts. We would provide proximal access to institutes in the Midwest region (approximately 40 colleges/universities) and become only the second institute in Indiana to gain GCAT membership. What are the advantages of having a facility in closer location? First, less time for postal handling lends itself to rewarding and successful experimentation. Furthermore, similar to the Earlham College mission to provide full hands-on research, in which students conduct research from initial hypothesis to analysis, we will offer this same opportunity to our GCAT neighbors. Upon a funded HHMI proposal, Dr. Blair would communicate to regional institutes (including both GCAT members and non-members) to encourage active GCAT participation on-site at our facility. External students and instructors could visit the facility and run samples firsthand. To our knowledge, Earlham would become the sole microarray scanning facility in Eastern Indiana.

Enhancing Elementary Science Education: B. Joseph Moore Museum

NEED TO ADD (John is the Champion)

PART V: Program Administration, Assessment, and Dissemination:

Earlham College designates Dr. Peter Blair, Assistant Professor of Biology, as Program Director. Dr. Blair will be assisted by an HHMI advisory committee (AC) consisting of the five key personnel (all attached CVs) and Barbara Gregg, Director of Foundation Relations. Members of the AC have extensive experience in administering our previous HHMI awards including Dr. Amy Mulnix, HHMI-00 Program Director. The AC will oversee the grant and make policy decisions in consultation with the Academic Dean, Dr. Gregory Mahler, and the Associate Academic Dean for Program Development, Dr. Alice Shrock. The Program Director will conduct daily management of all program elements, recruit/interact with faculty program participants/leaders, maintain regular contact with the aforementioned key personnel/consults, oversee allocation and accounting of all funds, and supervise the assessment program. In times when Dr. Blair is leading an international program (Spring 2010) or on sabbatical (Fall 2010), Dr. Mike Deibel, Associate Professor of Chemistry/Chief Health Careers Advisory Committee, will take leadership responsibilities. From experience on the demands of the Program Director, we are seeking approximately 1/5 release time annually. Dr. Blair will be supported by an administrative assistant with a strong track record of clerical duties with past HHMI programming including correspondence, accounting, filing, student housing, and assessment. We are seeking five additional hours for her per week annually with additional time during peak programming (May-July). We also request support for a stockroom administrator for 25/hours per week for a period of 10 weeks in each summer. This administrator will be responsible for ordering materials, maintaining equipment, and overseeing laboratory technicians.

Amy to champion assessment