Hhmi-narrative - Revision history

Deibemi at 19:04, 20 September 2007

2007-09-20T19:04:04Z

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	*3. Develop in-class student research experiences and course modules that integrate the physical sciences into the Biology and Chemistry curriculum;		*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;		*4. Engage students in contemporary bioinformatics and computational biology congruent with modern approaches in studying the Central Dogma of Molecular Biology;
	*5. ~~Sustain~~ the Earlham College tradition of excellence in international education;		*5. Build on the Earlham College tradition of excellence in international education;
	*6. Train current faculty in the pedagogical utility of modern technical instrumentation;		*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;		*7. Become regional and national leaders in access to genomic, proteomic, and computational techniques;
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	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:		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.		*Peter Blair (Biology, 2009-2012): Bioinformatics approaches to refining annotations of malaria genomes.
	*~~Mike~~ Deibel (Chemistry, 2009-2012):		*Michael Deibel (Chemistry, 2009-2012): Isolation and characterization of antioxidant compounds in natural products
	*Corinne Deibel (Chemistry, 2010-2011): ~~Metabolic products~~ of ~~atrazines~~		*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		*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		*David Matlack (Biology, 2009-2012): the study of spatial and temporal expression of genes involved in neural crest specification
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	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.		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. An example of this is proteomic work (expand here with new information).		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 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.
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	Here is a brief description of planned projects or examples of student-derived independent experiments:		Here is a brief description of planned projects or examples of student-derived independent experiments:

	*CHEM111: ~~General~~ Chemistry;		*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:		*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.
	*CHEM331: Equilibrium and Analysis:		*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.		*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:		*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.		*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.
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	*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.		*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),		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 â€œturtle chipâ€ 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 â€œdo scienceâ€ 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.		These instruments fit perfectly with the experiential nature of how we â€œdo scienceâ€ 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.

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2007-09-20T13:58:47Z

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	* Prof. Joseph J. Falke, Director, Molecular Biophysics Program		* Prof. Joseph J. Falke, Director, Molecular Biophysics Program
	* Dr. Carter Van Waes, NIH/NIDCD		* 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.		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.

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2007-09-19T21:02:20Z

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	These instruments fit perfectly with the experiential nature of how we â€œdo scienceâ€ 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.		These instruments fit perfectly with the experiential nature of how we â€œdo scienceâ€ 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.

	Course Module Development:		Biochemistry Major Review/Course Module Development:

	~~NEED TO ADD~~ (~~Peter~~)		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.

	~~Biochemistry Major Review~~:		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:

	~~NEED TO ADD~~ (~~Peter~~)		*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:		Part IV: Precollege and Other Outreach:

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2007-09-19T20:59:35Z

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	NEED TO ADD (John is the Champion)		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

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2007-09-18T18:51:39Z

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	*John Iverson (JMMNH, 2009-2012): Physiological ecology of hatchling turtles in their nests		*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		*David Matlack (Biology, 2009-2012): the study of spatial and temporal expression of genes involved in neural crest specification
	*Amy Mulnix (Biology, 2011-2012): ~~Functional plant genomics~~.		*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.		*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		*Olen Stephens (Chemistry, 2009-2012): Improving solubility and helicity of b3-peptide 14-helices

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2007-09-17T19:41:47Z

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	* Dr. Steven Mennerick, Washington University School of Medicine		* Dr. Steven Mennerick, Washington University School of Medicine
	* Prof. Joseph J. Falke, Director, Molecular Biophysics Program		* Prof. Joseph J. Falke, Director, Molecular Biophysics Program
			* Dr. Carter Van Waes, NIH/NIDCD

	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.		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.

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2007-09-17T16:51:12Z

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	* Dr. Tamara Hershey, Washington University School of Medicine		* Dr. Tamara Hershey, Washington University School of Medicine
	* Dr. Steven Mennerick, Washington University School of Medicine		* Dr. Steven Mennerick, Washington University School of Medicine
			* Prof. Joseph J. Falke, Director, Molecular Biophysics Program

	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.		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.

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2007-09-16T15:36:09Z

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2007-09-14T14:16:18Z

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2007-09-11T19:11:48Z

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	purified proteins. Fluorescein and Biotin labeled proteins will be used in substrate binding assays and ligand capture experiments.		purified proteins. Fluorescein and Biotin labeled proteins will be used in substrate binding assays and ligand capture experiments.
	*BIOL341: Cell Physiology:		*BIOL341: Cell Physiology:
	*BIOL347: Anatomy and Physiology: Endocrinology and Metabolism:		*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.		*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.

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	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:		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.		*Peter Blair (Biology, 2009-2012): Bioinformatics approaches to refining annotations of malaria genomes.
	*Mike Deibel (Chemistry, 2009-2012): ~~Iron-regulating metalloproteins using molecular cloning techniques.~~		*Mike Deibel (Chemistry, 2009-2012):
	*Corinne Deibel (Chemistry, 2010-2011):		*Corinne Deibel (Chemistry, 2010-2011): Metabolic products of atrazines
	*John Iverson (JMMNH, 2009-2012): Physiological ecology of hatchling turtles in their nests		*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		*David Matlack (Biology, 2009-2012): the study of spatial and temporal expression of genes involved in neural crest specification
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	*Dr. Bruce Ksander and Dr. Meredith Gregory, Schepens Eye Institute, affiliate of Harvard Medical School		*Dr. Bruce Ksander and Dr. Meredith Gregory, Schepens Eye Institute, affiliate of Harvard Medical School
	* , Eli Lilly		* (Mark will Provide name), Eli Lilly
	* , Oak Ridge National Laboratories		* (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. Sean Crosson and Dr. Aretha Crosson, University of Chicago
	* Dr. John Adams, Global Health Infectious Disease Program, University of South Florida		* Dr. John Adams, Global Health Infectious Disease Program, University of South Florida
	* Dr. Peter Beal, University of California, Davis		* Dr. Peter Beal, University of California, Davis
	* Dr. Nathan Luedtke, University of Zurich		* Dr. Nathan Luedtke, University of Zurich
			* Dr. Tamara Hershey, Washington University School of Medicine
			* Dr. Steven Mennerick, Washington University School of Medicine

	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.		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.

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	Part I: Introduction:		Part I: Introduction:

	Under the guidance ~~and framework~~ provided in BIO2010 and How People Learn and in accordance of our mission to deliver inquiry-based and student-centered science education experiences, we provide the following major objectives:		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;		*1. Expose students to inquiry-based, open-ended research endeavors throughout their academic careers;
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	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.		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.		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.
	~~As one of the 2006~~ Colleges that Change Lives, ~~author and~~ noted education reporter Loren Pope states, â€˜If every college and university sharpened young minds and consciences as effectively as Earlham does, this country would approach utopiaâ€™. 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. Blairâ€™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 todayâ€™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.		In Colleges that Change Lives (2006), noted education reporter, Loren Pope, states that, â€˜If every college and university sharpened young minds and consciences as effectively as Earlham does, this country would approach utopiaâ€™. 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. Blairâ€™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 todayâ€™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:		Part III: Broadening the Access to Science:

	Earlham ~~demands~~ 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.		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:		Summer Undergraduate Research Experience:
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	*Mike Deibel (Chemistry, 2009-2012): Iron-regulating metalloproteins using molecular cloning techniques.		*Mike Deibel (Chemistry, 2009-2012): Iron-regulating metalloproteins using molecular cloning techniques.
	*Corinne Deibel (Chemistry, 2010-2011):		*Corinne Deibel (Chemistry, 2010-2011):
	*John Iverson (JMMNH, ~~2008~~-2012): Physiological ecology of hatchling turtles in their nests		*John Iverson (JMMNH, 2009-2012): Physiological ecology of hatchling turtles in their nests
	*David Matlack (Biology, 2009-2012):		*David Matlack (Biology, 2009-2012): the study of spatial and temporal expression of genes involved in neural crest specification
	*Amy Mulnix (Biology, 2011-2012): Functional plant genomics.		*Amy Mulnix (Biology, 2011-2012): Functional plant genomics.
	*Charlie Peck (Computer Science, 2009-2012): Analysis of gene prediction software on AT-rich genomes. Improved algorithms could better support malaria genomes.		*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):		*Olen Stephens (Chemistry, 2009-2012): Improving solubility and helicity of b3-peptide 14-helices
	*Mark Stocksdale (Chemistry, ~~2009~~-2012): Chemical synthesis of biologically interesting molecules including phytosiderophores.		*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.		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.
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	* Dr. Sean Crosson and Dr. Aretha Crosson, University of Chicago		* Dr. Sean Crosson and Dr. Aretha Crosson, University of Chicago
	* Dr. John Adams, Global Health Infectious Disease Program, University of South Florida		* Dr. John Adams, Global Health Infectious Disease Program, University of South Florida
	* ~~OTHERS~~		* Dr. Peter Beal, University of California, Davis
			* Dr. Nathan Luedtke, University of Zurich

	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.		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 ~~yet~~ will be contributed by Earlham as an indication of the instituteâ€™s commitment to the irreplaceable value of student research.		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 instituteâ€™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 â€˜best-fitâ€™ laboratory. The Program Director will facilitate the meeting ensuring the HHMI-funded experiences are upheld among the non-HHMI supported experiences.		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 â€˜best-fitâ€™ laboratory. The Program Director will facilitate the meeting ensuring the HHMI-funded experiences are upheld among the non-HHMI supported experiences.
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	*CHEM221: Organic Chemistry:		*CHEM221: Organic Chemistry:
	*CHEM331: Equilibrium and Analysis:		*CHEM331: Equilibrium and Analysis:
	*CHEM351: Biochemistry: The direct-detection MS will be used to monitor chemical modification of		*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.
	purified proteins. Fluorescein and Biotin labeled proteins will be used in substrate binding assays and ligand capture experiments.
	*BIOL341: Cell Physiology:		*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.		*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.