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Annual Progress Report

Howard Hughes Medical Institute

Undergraduate Science Education Program

(Covering the period of September 1, 2009-August 31, 2010)


Washington and Jefferson College

Grant # 52006323 (2008)

DRAFT 11-15-10

Program Director:  Alice G. Lee, Ph.D., Professor and Chair of Biology



Student Research

W&J continued to build student/faculty research programs in long-term ecological monitoring (LEM) projects at W&J’s Abernathy Field Station (AFS), utilizing an ArcGIS server for LEM data. Funding provided students with research opportunities in LEM and computational biochemistry for: (1) on-campus LEM and molecular bioinformatics internships; and (2) off-campus internships.  SURE and SURE-AY surveys informed our revisions of the program.  Funding supported development of a website (WebLEM) where W&J and other institutions participating in a new LEM Consortium can post LEM data and curricula for public use.


New, Current, and Future Faculty Development

A postdoctoral fellow was hired for YRS 2 & 3 to teach a limited number of courses in a mentored setting and to assist faculty in applying information technology to LEM projects and related curricula. He has constructed a GIS database, set up our Web Mapping Site through an ArcGIS server, and has created a customized mobile GIS project (ArcPad) for the field data collection. In YR3, he is optimizing methods of input, access, and dissemination, and will train faculty and students on maintenance of the system. 


Support during YR2 enabled current faculty to attend a quantitative biology workshop and to continue their bioinformatics development via the GCAT consortium.


A search conducted during YR2 for a new tenure-track position in molecular biology/bioinformatics failed despite the screening of 97 applications and six on-campus two-day interviews. Members of the Biology Department revised the position description and re-conducted the search over the summer and early fall of 2010. We screened an additional 104 applications during the summer, interviewed three candidates, and an offer was accepted.  We also received approval for an extension from the State of PA for our $150,000 Keystone Initiative Startup Kit (KISK) equipment grant for this position.


Curriculum Development

Funding from HHMI facilitated integration of LEM and bioinformatics/computational biology research opportunities across the NSM/ITL and humanities curriculum, and supported the development of four new courses and the revision of six existing courses. During YR2, HHMI funding supported stipends for course revisions/creations and supplies to support new exercises.  CURE and GCAT surveys and course evaluations informed revisions of these courses.



Outreach programs were cut from our funded 2008 proposal. However, during YR1 a $95,000 grant from the US Department of Education allowed us to continue successful Outreach programs previously supported by our 1996 and 2000 HHMI grants: Young Investigators Awards; Saturday Math and Science; and the summer Active Science Initiative (ASI) for training in-service teachers.  These were implemented in YR2 and will continue in YR3.


Program Administration, Assessment, Dissemination, and Sustainability

Dr. Alice Lee, Professor and Chair of Biology, and Program Director for past HHMI grants, continues to oversee the 2008 HHMI grant assisted by both Internal and External Advisory Boards and a college-wide assessment process for faculty and curriculum. The External Advisory Board performed a site visit and assessment of the programs during YR2. Dr. Lee updated a website for HHMI grant information and activities; during YR3, this site will be linked to the LEM ArcGIS system.  In addition, during YR2, we were successful in acquiring almost $1.2 million in extramural grants and more than $14,000 in W&J grants to enhance HHMI-funded programs.  Though our proposal to the NSF for funding to enhance HHMI-supported laboratory renovations for the planned comprehensive renovation of our Dieter-Porter Life Sciences was not successful, we recently were awarded a $1,000,000 grant from the State of PA budget RCAP to be used toward the renovations.





Objectives: To incorporate student research opportunities, especially in the areas of long-term ecological monitoring (LEM), molecular bioinformatics, and computational biology through on-campus student/faculty research and off-campus Intersession and summer internships. The objective of this activity is to provide undergraduate students with intensive independent research experiences with W&J faculty or off-campus scientists in these emerging areas of the life sciences.  Through this exposure, students will learn detailed information and gain experience that will aid them in determining their future professional and personal goals concerning specific topics in these fields.


Program Maps for Student Research Activities:

  • On-Campus Student Research AY Template i rs/Academic_Departments/Biology/HHMI/ProgamMapforOn-CampusStudentResearchAYTemplate.pdf

  • On-Campus Student Research Summer Template d Files/Academic_Affairs/Academic_Departments/Biology/HHMI/ProgramMapforOn-campusSummerStudentResearchTemplate.pdf

  • On-Campus Student Research Summer 2010: Long-Term Ecological Monitoring

www.washjeff.ed u /uploadedFiles/Academic_Affairs/Academic_Departments/Biology/HHMI/ProgramMapforOn-campusSummerStudentResearch2009-LEM.pdf

  • On-Campus Student Research Summer 2010: Molecular Microbiology s earchSummer2010Planned-Bioinformatics.pdf

  • Off-Campus Student Research Internships i rs/Academic_Departments/Biology/HHMI/ProgramMapforOff-campusInternships.pdf



Total Number of Student Participants Supported


Total Number of Faculty Participants Supported


Total HHMI Expenditures


Matching Funds—Internal (Entrepreneurial Grants, Presidential Discretionary Funds, Faculty Travel)



Matching  Funds—External (Merck, Phi Sigma, WCCF, Cargill)


Awards or Honors


Collaborations with other HHMI-funded programs


Collaborations with other non-HHMI-funded programs


Student/Faculty Manuscripts


Student/Faculty Publications


# Meetings Attended with Students


# Faculty Attending Meetings with Students


# Student Conference Presentations



















Evidence of Progress:

Poster: On-Campus Research: Academic Year 2009-10

Posters: Off-Campus Research: Intersession 2010

Posters: Off-Campus Research: Summer 2010

Posters: On-Campus Research: Summer 2010

Link to the ArcGIS Server:

Abstracts for Meetings:

  • Dr. Faun Doherty and 3 students to the Conference on Undergraduate Research in Mathematics, and the National Joint Mathematics Meeting in San Francisco

www.wash j g y/HHMI/doherty-mathtalkabstract.pdf l oadedFiles/Academic_Affairs/Academic_Departments/Biology/HHMI/doherty-spaghetti model abstract.pdf

  • Dr. Jennifer Logan and 2 students to ACS Meeting

  • Dr. James March, Thomas Contreras and 3 students to ESA Meeting


Publications and Submitted Manuscripts:

Eddens, T., Beaudoin, S., Nolano, S., Steinberger, A., Johnson, K., Little, C.S., and K. Fresa-Dillon. 2011.  Effect of mouse strain, age, and vaccination status on extent and spread of infection by C. pneumoniae . J. Immunology (In preparation).


Doherty, F.C.C., Gentile, P., Magee, J., and C. Miedel. 2011. A vertex ordering result for an application of DNA sequencing using tripartite unit probe interval graphs. Mathematical Modeling of Natural Phenomenon (Submitted ).


Benstead, J.P., Cross, W.F., March, J.G., McDowell, W.H., Ramirez, A, and A.P. Covich. 2010. Biotic and abiotic controls on the ecosystem significance of consume excretion in two contrasting tropical streams. Freshwater Biology 55: 2047-2061. 



Ryan Lehman (ITS ’11), who was supported in YR1 for summer LEM research, and who took the new ITL 310 course in YR1, won third place for his poster, “Developing Semantic Web Technologies for Biological Data Representation” at the Eastern Conference of the Consortium of Computing Sciences in Colleges. His coauthor was Allison Nolan, an undergraduate at Ursinus College. 


Taylor Eddens (BCH ’11), Phi Beta Kappa.


Public Relations:

Taylor Eddens at the World Vaccine Congress:


Internship Application Forms and Information:


Photographs:   http://www.washjeff.ed u /content.aspx?section=15465&menu_id=857&crumb=844&id=18353


  1. On-Campus Student/Faculty Research—Academic Year

Brandon J. Sansom (Biology ’11) completed an independent study (BIO 500) project entitled “Quantifying Community Structure and Ecosystem Function in Streams of the Abernathy Field Station” with Dr. James March, Associate Professor of Biology.  Brandon attended the North American Benthological Society meeting in June 2010 in Santa Fe, NM, and presented a poster of his work. Brandon is currently studying at the University of Aberdeen in Scotland and applying to Ph.D. programs in Zoology to continue research on freshwater ecosystems.  His HHMI-supported research both with Dr. March and with off-campus hosts were key factors in influencing Brandon’s career choice.


Shane M. Polen (Chemistry ’10) completed an independent study (CHM 500) project entitled “High resolution solid-state NMR of polymorphic pharmaceutical compounds” with Dr. Robbie J. Iuliucci, Associate Professor of Chemistry.   HHMI funds were used to purchase chemicals for the project.  Shane presented a poster of his work at the American Chemical Society (ACS) Meeting in 2010. Shane’s natural research ability and Dr. Iuliucci’s mentoring were exemplified when Shane was offered a job with a pharmaceutical company when presenting his poster.   However, Shane learned he does not enjoy scientific research and decided to pursue a career in patent law; he is now enrolled in law school at the University of Pittsburgh.  


Due to our high teaching load, the majority of research during the academic year is being incorporated into courses, specialized research courses, independent studies, and tutorials (e.g. Experimental Biology, BIO 412 had four student/faculty research teams with a total of 21 students in YR2). Thus, during YR2, we had many projects during the academic year, but only two outside the course structure.  Large numbers of students from the sciences, mathematics, and ITL present posters of their work at our W&J course-related research poster sessions each semester (120 students/63 posters in Fall 2009; 156 students; 85 posters in Spring 2010). Other students do research on campus and off campus in the summer, supported by HHMI funding, other REUs and other internal and extramural funding (see above).


  1. On-Campus Student/Faculty Research—Summer 2010

Two student/faculty teams were each supported in YR2 for ten weeks of on-campus research.  HHMI provided the stipends and supplies. W&J provided the housing for the student interns.


1. Long-Term Ecological Monitoring (LEM)

Dr. Thomas Contreras, Assistant Professor of Biology (PI), Dr. Jason Kilgore, Assistant Professor of Biology, Dr. Robert East, Associate Professor and Chair of Environmental Studies, Dr. Byoungjae Lee, HHMI Postdoctoral Fellow, Information Technology Leadership, and Dr. James March, Associate Professor of Biology, worked with three students to continue collecting data as part of W&J’s Long-Term Ecological Monitoring Program (LEM) at W&J’s Abernathy Field Station (AFS).  The students were Charles Irvin (Biology ’11), Brittany Verrico (Biology ’13), and Michelle Wuenstel (Biology ’11).  Because of the proximity of the AFS to W&J’s campus, and our unencumbered access to the property, the field station provides faculty and students with a unique research/teaching opportunity and allows us to continue the long-term monitoring of plant/animal populations and related ecology.


The 2010 LEM summer interns continued the long-term ecological monitoring projects started by on-campus interns during the summer of 2009 and were instrumental in helping to evaluate and refine monitoring protocols instituted in YR1.  This was an important summer for collecting plant abundance and diversity data at our permanent sampling locations due to anthropogenic disturbances on (e.g., construction of a gas line right-of-way) or near the field station (e.g., Marcellus Shale gas drilling) over the past year.  Student interns also learned first-hand about the potential short- term effects of these kinds of disturbances on plant and animal populations and the benefit of long-term monitoring in evaluating the possible effects of these activities on ecosystems and ecological communities. 


Once again, interns were required to design and implement their own research project which they conducted during the summer . (See above links.) We also anticipated that with increased human activity near the station boundaries, and with the recent disturbance at the station related to the gas line construction, there could be an   invasion of AFS by the Emerald Ash Borer beetle ( Agrilus planipennis ).   Our interns decided that starting a formal monitoring program now will allow other students to track the invasion and related effects from the beginning, which is a rare opportunity.


2. Molecular microbiology: Soil bacterial diversity

Dr. Anupama Shanmuganathan, Assistant Professor of Biology (PI), worked with three students for 10 weeks during summer 2010 in assessing soil bacterial diversity in W&J’s Abernathy Field Station. Students were Ian Kohler (Biology ‘13), Peter Leehan (Biology ‘11) and Kyle Yebernetsky (Biology/Business ‘11). The goals of this project were to: a) promote inter-disciplinary thinking in areas such as microbiology, ecology, molecular biology and bioinformatics and apply that to the study of soil bacteria; b) establish a base-line of soil bacterial diversity at the field station so as to make long-term ecological monitoring possible; and c) provide a realistic microbiological research experience.


The students not only mastered basic microbiological techniques and DNA manipulation techniques, but applied more advanced concepts in bioinformatics including deriving phylogeny and plotting phylogenetic trees. Overall, more than 200 bacteria were isolated, identified and catalogued spanning more than 30 families and spread across 6 phyla, including 71 distinct Operational Taxonomic Units (OTUs). Using sophisticated bioinformatics tools, bacterial diversity indices were calculated and phylogeny among the isolates was inferred, thus providing an effective baseline from which future studies can monitor ecological changes in this region by assessing soil bacterial diversity.


After the field or lab portions of their internship, all on-campus summer research students turned in reports, field journals (for the LEM team) and notebooks, all Excel data files and ArcGIS shapefiles/data (for the LEM team), and a poster related to the projects they designed and implemented during the summer.  All students presented their posters during the W&J Summer On-Campus Research Poster Session, October 8-9, 2010.  They will present again at our External Advisory Board Student Research Poster Session on April 8, 2011 and at the Western PA Undergraduate Biology Symposium (Spring 2011). Dr. Shanmuganathan and the three students also presented their results at the Undergraduate Research at the Capitol Conference in Harrisburg, PA October 5, 2010 and will be presenting their results at the National Conference on Undergraduate Research meeting in Ithaca, NY in March 2011; the group will also submit the manuscript, which is currently in preparation for publication in the undergraduate research journal, the Journal of Young Investigators .  Dr. Alice Lee, Program Director, also presented this poster at the HHMI Program Directors’ meeting in October 2010.


  1. Off-Campus Student/Faculty Research
  1. Intersession 2010

HHMI funding supported two students for three weeks of off-campus research during the January Intersession:  Benjamin Daggett (Chemistry ’12); and Katie Steider (Biology ’12).  HHMI support covered living and travel expenses.  Students kept journals and made poster presentations at W&J’s HHMI External Advisory Board meeting on April 9, 2010 and at the 31 st Annual Undergraduate Biology Symposium for Western Pennsylvania on April 17, 2010 at Geneva College. 


  1. Summer 2010

HHMI funding supported three students for ten weeks of off-campus summer research: Taylor Eddens (Biochemistry ’11); Nicholas Tyger (Biology ’12); and Brandon Sansom (Biology ’11).  HHMI funding supported stipend and living expenses.  Students kept journals and made presentations of their work at the W&J Summer Research Poster Session on October 8-9, 2010.  Students will present their work at the April 2011 meeting of W&J’s HHMI External Advisory Board, and at the 32 nd Annual Undergraduate Biology Symposium for Western Pennsylvania.  (See above links.)


Taylor Eddens (Biochemistry ’11) spent the summers of 2009 and 2010 working in the laboratory of Kerin Fresa-Dillon, Ph.D. (W&J Biology ‘79).  Taylor played an integral role in research designed to test the effectiveness of a vaccine against the extra-respiratory spread of Chlamydia pneumonia , a major cause of pneumonia. Taylor and Dr. Fresa-Dillon presented at the World Vaccine Conference in Beijing in March; Taylor was supported by W&J Presidential Discretionary Funds and W&J’s HHMI grant.  Taylor also presented his poster at W&J Summer Research Poster Session on October 8, 2010. (See above links.) He is currently working with Dr. Alice Lee to prepare a manuscript of his work to submit to the Journal of Immunology .  Taylor’s HHMI-supported research has been a major factor in his decision to pursue a career in biomedical research.  At this time, Taylor has been accepted to an MD/PhD program at the University of Pittsburgh, and has other interviews scheduled.


Administration and Assessment of Student Research:

Dr. Candy DeBerry (Director of Off-Campus Research), and Drs. Ronald Bayline and Thomas Contreras (Co-Directors of On-Campus Research) report to the Program Director, Dr. Alice Lee.  An Internal Advisory Board (IAB) helps with funding decisions and annual assessment is provided by an External Advisory Board (EAB).  The HHMI IAB met six times during YR2.  Karen Crenshaw, Executive Director Campaigns and Advancement Operations, replaced retiring Dr. G. Andrew Rembert in YR2.  The HHMI EAB conducted their annual site visit on April 9, 2010. (See below.)



Plans for Revision:

We continue to track numbers of students attending events publicizing internship opportunities and to track numbers of students who apply for and are accepted for summer and Intersession off-campus internships (HHMI-funded and other).  These data are currently also compiled in our annual Biology Assessment Report.  Students receiving funding completed the SURE III. A ffairs/Academic_Depart m ents/Biology/HHMI/WashJeffHHMISUREIIIReport2009.pdf

Student performance is assessed by written evaluation of students by on- and off-campus research supervisors based on the following criteria: attitude/work ethic; attention to detail in lab work; understanding of science and ability to synthesize concepts; ability to interpret data and draw conclusions; ability to design experiments; and general lab skills, and completion of the SURE III.  For longer-term outcomes, we track: student publications; academic honors and awards they receive; and their careers (entrance into graduate programs, etc.).  These data are also currently reported in our Biology Department Assessment Report.  To better publicize internship opportunities, the fall Summer Research Poster Session has been expanded and photographs have been posted.  The list of internship hosts and internship proposal forms located on the Biology and W&J HHMI sites is updated annually.


Other Grants Received During YR2 for Student Research Related to HHMI Activities:


Funding Source

Faculty PI or Recipient


Water Quality Analysis of Wells and Streams

Washington County Comm. Foundation

Dr. James March, Biology



Sand Dune Ecology Research

W&J College 2010

Entrepreneurial Grant

Dr. Jason Kilgore, Biology



Merck Internship Grant: Payout for 2010 Summer Internships

Merck Institute for Science Education

W&J College’s Grant,

Dr. Candy DeBerry, Biology, PI



The Role of AS1C3 in Ischemic Muscle Pain and Fatigue

W&J College 2010

Entrepreneurial Grant

Dr. Heather Cushman, Biology



Long-Term Ecological Monitoring at AFS

Margaret A. Cargill Foundation

W&J College’s Grant, award to

Dr. James March, Biology



Travel Supplement for Int. Vaccine Conference

W&J Presidential Discretionary Funds

Taylor Eddens



Travel to ACS 2010 National Meeting in San Francisco

W&J Presidential Discretionary Funds

Dr. Jennifer Logan, Chemistry



Travel to ACS 2010 National Meeting in San Francisco

Margaret A. Cargill Foundation

W&J College’s Grant, award to

Dr. Jennifer Logan, Chemistry




Objectives: A new faculty appointment in molecular evolution/systematics, a postdoctoral teaching fellowship, and training for currrent faculty to  broaden W&J’s expertise in the emerging disciplines of long-term ecological monitoring through technology and molecular bioinformatics/computational biology and  microarray training for current faculty through GCAT.

Program Maps, Position Descriptions, and CVs for Faculty Development: a dedFiles/Academic_Affairs/Academic_Departments/Biology/HHMI/PositionDescriptionPostdoc.pdf

  • CV: Dr. Byoungjae Lee

  • New Faculty Development:
    • Molecular Evolutionist/Systematist Program Map

www.wash j p loadedFiles/Academic_Affairs/Academic_Departments/Biology/HHMI/ProgramMapforNEWFACDEV-MolecularEvolutionist.pdf

  • Molecular Evolutionist/Systematist Position Description-2009 search

www.washjeff.ed u /uploadedFiles/Academic_Affairs/Academic_Departments/Biology/HHMI/JOBPOSITIONFORMOLECULAREVOLUTIONISTSYSTEMATIST-09-10Search.pdf

  • Molecular Biologist/Bioinformatist Position Description-2010 search

Current Faculty Development:

  • Current Faculty Development Program Map Template p loadedFiles/Academic_Affairs/Academic_Departments/Biology/HHMI/ProgramMapforCurrentFacultyDevelopment.pdf


Total Faculty Supported by HHMI Grant in YR1 (Current and Future Faculty)


Future Faculty Supported by HHMI Grant


Total HHMI Expenditures for Faculty Development


Matching Funds—Internal (Faculty Travel)


Matching Funds—External (Keystone Innovation Starter Kit (KISK) Grant)— EXTENSION



Evidence of Progress:


1. Future Faculty Development:

Dr. Byoungjae (“B.J.”)  Lee began work upon his arrival in summer 2009. His current CV is linked, above.  Dr. Lee’s YR2 research centered around the development of a Web-Based LEM System, including: 1) constructing the GIS database (geodatabase) by using pre-collected LEM data; 2) setting up the Web mapping site ( http://le m ) through the ArcGIS Server; 3) and creating a customized mobile GIS project (ArcPad) for field data collection.


Dr. Lee submitted four manuscripts for publication; two have been published.  In addition, Dr. Lee made oral presentations at three conferences, gave three invited talks, and attended five training sessions/workshops.



Lee, B. 2009. Location-based concierge service with spatially extended topology for moving objects . Journal of GISAK . 17(4).


Lee, B., 2009. Spatial pattern of uncertainties: an accuracy assessment of the TIGER files. Journal of Geography and Geology . 1(2) .


Manuscripts Submitted:

Lee, B. 2010. Capturing person-spatial behavior near boundaries through spatio-temporally extended topology . Submitted to International Journal of Geographical Information Science .


Lee, B. 2010.  U-City: New trends of urban planning in Korea based on pervasive and ubiquitous geotechnology and geoinformation. Submitted to Future Internet (ISSN: 1999-5903) .


Presentations at Meetings:

Lee, B., North, M., and T. Contreras. 2010. WebLEM: Web-Based Long-Term Ecological Monitoring System Development. ESRI International User Conference, San Diego, California.


March J., Contreras, T., Kilgore, J., East, R., North, M., Lee, B., and A. Toomey. 2010. Incorporating Long-term Ecological Monitoring Across Undergraduate Science, Mathematics, and Information Technology Curricula . Annual Meeting of the Ecological Society of America, Pittsburgh, Pennsylvania.


Lee, B. and M. North. 2009.  Web-Based Long-Term Ecological Monitoring System Development . Pennsylvania Geographical Society Annual Meeting, West Chester, Pennsylvania.


Invited Talks:

Capturing Person-Environment Behavior near Boundaries through Spatio-Temporally Extended Topology . Div ision of Environ mental Sci ence & Eco logical Eng ineering, Korea University, August 31, 2010. Seoul, K orea.


Context Awareness for Ubiquitous Geographic Information Service . Department of Geoinformatics , University of Seoul , August 23, 2010. Seoul, K orea.


Knowledge Representation about Person-Environment Behavior near Boundaries for Context Aware Location-Based Service. Korea Research Institute for Human Settlements (KRIHS), August 20, 2010.  Ahnyang, Korea.


Other Meetings and Conferences Attended:

Digital N ation L and Expo , Ilsan , Korea, September 1-2, 2010 .

ESRI International User Conference, San Diego, California , July 12-15, 2010.

ArcPad 8 GPS Correct Training , Ambridge , Pennsylvania , November 19-20, 2009 .

URISA-CAC Workshop , Pittsburgh , Pennsylvania , November 13, 2009 .

Pennsylvania Geographical Society Meeting, West Chester, Pennsylvania , October 26-18, 2009 .


Dr. B.J. Lee’s teaching responsibilities during his first year (YR2 of the grant) included Information Technology & Society (ITL 100), the development of a new course in Geovisualization (ITL 345) for Intersession 2010, the planning of a new course in Ecological Monitoring Information System Management (ITL 244) for Intersession 2011, and preparation for teaching Introduction to GIS (ITL 346) in Spring 2011.  His service to the College during YR2 also included ArcPad 8.0 training for Watershed Management (EVS 330) students, a guest lecture in Applied Statistics for the Life Sciences (BIO/MTH 245), and a WebLEM workshop for the LEM On-campus summer research team.


W&J has been fortunate to have Dr. B. J. Lee with us as his experience with database development and GIS have allowed us to get our long-term ecological monitoring data system in an outstanding working form.  He has constructed a GIS database, set up our Web Mapping Site through an ArcGIC server, and has created a customized mobile GIS project (ArcPad) for the field data collection.  This year, in addition to teaching, Dr. Lee will be training faculty and students on maintenance of the system so that we can continue to expand it when his position is over.  Also, two Biology faculty involved in the LEM research will audit the ITL 244 course in January. 


Dr. Lee has adeptly split his time between developing the web-based data repository to support ongoing ecological research, teaching, and mentoring students and faculty who are developing bioinformatics research projects.   He has received active teaching and research mentoring by members of the ITL and Biology Departments. Dr. Lee’s courses in Information Technology & Society (ITL 100) and Geovisualization (ITL 345) have been extremely well received. He will teach a new course on ecological monitoring information system management and Introduction to GIS (ITL 346) in Spring 2011.  When Dr. Lee leaves W&J, he will have gained more experience working with undergraduates both in and out of the classroom.  In addition, the HHMI grant has supported Dr. Lee’s professional development to attend three conferences: The ESRI International User Conference (2010); the Pennsylvania Geographical Society Annual Meeting (2009); and the 105 th Association of American Geographers Annual Meeting (2009). Dr. Lee also attended other meetings (see above).   This fall, Dr. Alice Lee and ITL faculty have been pleased to have the opportunity to write letters of recommendation for Dr. Lee for tenure-track faculty positions. 


2. New Faculty Development:

A search conducted during YR2 for a new tenure-track position in molecular biology/bioinformatics attracted more than 97 applicants. Five finalists were brought to campus for interviews and two offers were made but the search failed. Members of the Biology Department rewrote the job description and conducted the search during the summer and early fall of 2010. We screened 104 applications over the summer and interviewed 3 candidates. An offer was accepted by Dr. Claire Burns on October 21, 2010; she will begin YR3.


While the basic necessities for teaching courses are already in place, significant new equipment purchases will be required to support new teaching and research programs implemented by the new faculty member.  To that end, we (Dean Czechowski, Dr. Lee, and Dr. DeBerry) were pleased to be funded for a KISK (Equipment for Keystone Innovation Starter Kit) grant from the State of Pennsylvania for $150,000 for the new position.  When the search failed, Dr. Tori Haring-Smith, President of the College, acting on our behalf, applied for and received approval from the State of PA for the KISK start-up equipment grant for this position to be extended until Dec. 31, 2010.  Dr. Burns submitted her equipment list to Dr. Lee on Nov. 15, 2010 so that equipment can be ordered and invoiced, allowing us to use the $150,000 KISK grant funds for Dr. Burn’s start-up equipment for student/faculty research and curriculum development in the area of molecular bioinformatics. 


The HHMI grant will help support the renovation of an office/research space for the new hire.  Planned renovations supported by the HHMI grant include: 1) converting an existing storage room to a molecular bioinformatics laboratory ($55,000); 2) converting a storage room to a research lab for the new molecular bioinformaticist ($18,000); 3) converting a cold storage room to a field ecology suite ($32,000); and 4) converting a storage room into a student data analysis room ($8,000). These renovations were scheduled to commence and be completed during 2010-11 (Year 3 of the grant, $113,000 total).  However, the larger renovations of the Dieter-Porter Life Science Building are delayed until sufficient funds can be acquired, so we will not be using the HHMI funds for renovation until after YR 3.  Fundraising continues; recently, the college was awarded a $1,000,000 grant from the State of Pennsylvania toward the overall renovation project.


Supplies for the initial support of bioinformatics integration will come from the 2008 HHMI grant.  Funding provides B iology , N euroscience, Psychology , and B iochemistry faculty with supplies to integrate bioinformatics projects into existing courses in 2008-2012 for a grand total of $28,400.  Funding also supplies microarrays (gene chips and analysis) for W&J’s participation in GCAT in 2009-12.  Supplies for ongoing work in bioinformatics will come out of the Biology Department budget, which will need to be increased after the grant ends.


Of note: Dr. Burns and a member of the ITL faculty are applying to attend the GCAT Synthetic Biology Workshop June 16-19, 2011.

3. Current Faculty Development:

  1. EOE2010:  Education on the Edge: A Conference on Innovative Undergraduate Education at the Interface of Mathematics and Biology (Drs. Kilgore and Higginbottom)

Dr. Jason Kilgore, Assistant Professor of Biology, and Dr. Ryan Higginbottom, Assistant Professor of Mathematics, attended EOE2010: Education on the Edge: A Conference on Innovative Undergraduate Education at the Interface of Mathematics and Biology from July 9-11, 2010 at the University of Delaware (sponsored by Emory University’s HHMI grant) where they presented a poster entitled, “Cross-Disciplinary Co-Teaching of an Applied Biostatistics Course: Equipping Pre-Health and Biology Students with More Relevant Quantitative Skills.”  Their expenses were largely covered by the HHMI.  Our W&J HHMI grant covered mileage and food.  The focus of the meeting was to explore strategies for incorporating mathematics into the biology programs at the undergraduate level and to use more biological examples in mathematics courses.  One specific result of the workshop is that our newly revived Applied Statistics for the Life Science (BIO/MTH 245) course (covered by HHMI funds during YR1 and co-taught by Drs. Kilgore and Higginbottom in YR2) will be modified for Spring 2011 (YR3).  See Curriculum Development section for the revised Program Map and narrative.


b. The Ecological Society of America Meeting (Dr. March)

Dr. James March, Associate Professor of Biology, was supported to attend the annual meeting of the Ecological Society of America, in Pittsburgh August 1-6, 2010 where he presented a poster entitled, “Integrating Long-term Ecological Research across the Undergraduate Science Curriculum” by J. March, T. Contreras, J. Kilgore, R. East, M. North., B. Lee, and A. Toomey (EVS and Biology ’12). The content of the poster focused on the conceptual idea of our LEM project and superficially covered what we have accomplished to date. Dr. March attended the entire conference in order to network with people at other institutions who are currently doing something similar or are interested in collaborating in the future. Networking at this point is important given that one of the goals of the LEM project is to develop a consortium of other schools that are also doing LEM and to share methods and data. Also, because the meeting was in Pittsburgh this year the cost was low.  Dr. Contreras and the three summer LEM interns joined Dr. March for the scientific portion of the meeting.  The YR2 Summer On-Campus Student Research budget for the LEM team covered the students’ expenses; Dr. Contreras’ expenses were paid by the W&J Faculty Travel Fund.  Dr. Alice Lee, Program Director, presented this LEM poster at the HHMI Program Directors’ meeting in October 2010.


Administration and Assessment of Faculty Development:

Day-to-day oversight of the grant administration of grant programs falls to the Program Director, Dr. Alice Lee, Professor and Chair of Biology, who also served as program director for our 1996 and 2000 HHMI grants.  Dr. Lee is assisted by an Internal Advisory Board, with annual assessment by an External Advisory Board.  The HHMI Internal Advisory Board met six times during YR2.  The HHMI External Advisory Board conducted their formal annual site visit on April 9, 2010. (See below.)

  • Advisory Board Members

  • External Advisory Board Meeting Agenda

  • Report of the HHMI External Advisory Board’s site visit of April 9, 2010


Objectives: To develop curriculum in areas of long-term ecological monitoring (LEM) and molecular bioinformatics/computational biology and related areas.  To integrate LEM research and molecular bioinformatics (in particular, microarray analysis) into the curriculum.  To acquire equipment to support and develop existing facilities for LEM and molecular bioinformatics. 

Program Maps for YR2 Curriculum, Equipment, and Laboratory Development:

Course Program Maps for YR2: add link

  • Curriculum Development Program Map Template
  • BIO 288 Conservation Biology-Revised 2010
  • BIO/MTH 245 Applied Statistics for the Life Sciences-Revised 2010
  • CHM 270 Analytical Chemistry-Revised 2010
  • ITL 310 Systems Analysis-Revised 2010
  • ITL 345 Geovisualization-Intersession 2010
  • BIO 215 Microbiology-Fall 2009
  • Microarrays in Courses (BIO 149/249, BIO 201, BIO 392)-Intersession and Spring 2010
  • PHL 232 Bioethics-for Fall 2010
  • BIO 101/292 Tutorial for implementation in General Biology-Spring 2010 for Fall 2010
  • BIO 215 Microbiology-Fall 2009

Equipment Program Map and Link to the Server:



Total Number of Students Impacted (by YR2 Implementations)


Total Number of Faculty Participants


Total HHMI Expenditures


Courses Developed (10)


No. of Faculty:

Faculty Collaboration

When Taught





BIO 101/292

(new module)

General Biology

(implemented in fall 2010)



Spring 2010

(Fall 2010)


Stipend and supplies

BIO 149/249

(revised course)

Freshman Gene Expression  WS



Intersession 2010


Stipend and supplies

BIO 201

(new module)




Spring 2010


Stipend and supplies

BIO 215

(new module)




Fall 2009


Stipend and supplies


(revised course)

Applied Statistics for the Life Sciences


Mathematics & Biology

Spring 2010


Stipends in YR1

BIO 288

(new course)

Conservation Biology



Spring 2010


Stipend in YR1

BIO 392

(revised course)

Tutorial in Biology



Spring 2010


Stipend and supplies

ITL 244

(new course)

Ecological Monitoring Info. System Mgt.






15 seats


Postdoc: part of teaching load

ITL 345

(new course)




Intersession 2010


Postdoc: part of teaching load

PHL 232

(new course)





Fall 2010




Evidence of Progress:

  Course Syllabi for YR2: add link


Link to the ArcGIS Server:


Summary of Progress in and Plans for Revision:

BIO 101 General Biology (Tutorial in Biology BIO 292)

Dr. Jane Caldwell, Adjunct Instructor of Biology, developed a bioinformatics laboratory exercise for General Biology (BIO 101).  Dr. Caldwell selected six published exercises and supervised a W&J sophomore, Liann Correia (Biology ’12), who carried out each exercise as a tutorial (BIO 292).  She developed a rubric by which to evaluate each exercise.  Two laboratory exercises were selected as challenging for first year biology students.  One exercise teaches students to use and apply bioinformatic tools online; the other requires they apply that knowledge to the results of a simple molecular biology investigation of maize.  These exercises are being implemented in BIO 101 laboratories this fall (127 students).  Assessment will be via student performance on quizzes and comments on course evaluations. Liann presented a poster of her work at the 2010 W&J spring poster session.


BIO/MTH 245 Applied Statistics for the Life Sciences

With HHMI support in YR1, Dr. Jason Kilgore, Assistant Professor of Biology, and Dr. Ryan Higginbottom , Assistant Professor of Mathematics, developed an interdisciplinary course, Applied Statistics for the Life Sciences (BIO/MTH 245).  Students from four different majors (Biology, Environmental Studies, Math, and English) participated in the course in Spring 2010 to learn theory and applications of statistical methods in primary research, with an emphasis on research design.  Students explored probability models, descriptive statistics, and fundamental statistical methods while evaluating methods from primary literature.  They developed original research projects exploring student success data from the Dean’s office, creatine effects on muscle development, survey methods used by ornithologists, and other topics, and presented these posters to faculty across departments.  CURE surveys and post-course evaluations indicated that the course was rigorous, focused on statistical methods from primary literature, relied on both manual and computational (SPSS) approaches, and allowed students to explore a statistical problem through original research.  Students appeared to understand experimental design, participated in discussions, and could digest primary literature. External feedback from our External Advisory Board and EOE2010 conference participants indicated that the approach used in this course was appropriate for modern scientific research. Coteaching was valuable because of the two different perspectives and strengths of the professors as well as instant in-class feedback and adjustment.  The instructors revised the course for Spring 2011 where a 65-min recitation period will be added for software use and quizzes, and the new RISC (Research on the Integrated Science Curriculum) survey will be employed for assessment purposes.


BIO 215 Microbiology

During Fall 2009, Dr. Anupama Shanmuganathan, Assistant Professor of Biology, implemented a soil bacterial diversity research project in the laboratory component of the course, Microbiology (BIO 215). HHMI funding provided the faculty stipend and research supplies. Students working in teams assessed the diversity of soil bacteria at the Abernathy Field Station (AFS), employing techniques in basic microbiology, molecular biology and bioinformatics.  As a result of this project, students identified and catalogued 40 soil bacterial isolates and also obtained valuable experience in presenting their results as a research poster as well as a full-length scientific paper. The effectiveness of integrating the research project in the laboratory curriculum was assessed via CURE surveys. Based on the survey results and personal communication with the students, in Fall 2010 Dr. Shanmuganathan is continuing to implement the same project in the BIO 215 course; however, this time, it is offered with a writing (W) emphasis since the project makes it possible for students to practice and hone their scientific writing skills.


BIO 288 Conservation Biology

Dr. Thomas Contreras, Assistant Professor of Biology, received a stipend to develop a new course, Introduction to Conservation Biology (BIO 288) for Spring 2010.   This course examined: 1) how this scientific discipline has evolved; 2) the basic theory and methodologies used by conservation biologists to assess biodiversity loss over multiple spatial and temporal scales; and 3) current social attitudes and governmental policies concerning the loss of biodiversity in the US and abroad.   The laboratory portion of the course utilized case studies, current methodologies used in the field (including GIS and GPS), and the development of a management plan for W&J’s AFS which incorporated aspects of the LEM research program for adaptive management purposes.   The course was approved for the environmental studies and biology majors.   Student groups researched and developed management plans for important taxa and ecological systems at the station. The group management plans will be compiled and developed into a single comprehensive adaptive management plan for the station. CURE surveys were also used to assess student attitudes towards conservation research and the research required to develop a management plan for the AFS.


CHM 270 Analytical Chemistry

Funding was provided to support Dr. Jennifer Logan, Assistant Professor of Chemistry, Ashley Smith (Chemistry ‘11), and Bridget Piko (Chemistry ‘11) in traveling to the 239 th national meeting of the American Chemical Society in San Francisco, CA (March 21-25, 2010).  The objective of this activity was to present a poster on water analysis results obtained by the 2009 Analytical Chemistry (CHM 270) lab course in YR1-supported curriculum development.  Ashley and Bridget compiled their classmates’ findings and analyzed the levels of hardness, alkalinity, iron, phosphorus, and sulfur in groundwater from the Abernathy Field Station.  The meeting also provided the students with the opportunity to experience a national conference and network with representatives from various graduate schools and industries.  Participating in this conference will help both women stand out in their applications to graduate and professional schools and so an anticipated outcome is acceptance to at least one program, if not more.  In addition, attending the conference helped further several objectives outlined in the program map for CHM 270 water analysis.  These objectives were specifically: 1) s tudents learn about strategies for collaboration when working in pairs; and 2) students learn how to present scientific posters and communicate their findings to a diverse audience.  Based on Ashley and Bridget’s experience at the national conference, Dr. Logan hopes to continue encouraging students to present their research at conferences.  She is also continuing the water analysis project as students seem to have enjoyed the experience (based on CURE and W&J course evaluation comments).


ITL 310 Systems Analysis Course

The Systems Analysis (ITL 310) course, which was revised using HHMI funds in Spring 2009 by Dr. Amanda Holland-Minkley, Associate Professor and Chair of Information Technology Leadership (ITL), was taught again in Fall 2010 with changes prompted by the CURE assessment and W&J course evaluations. These assessments confirmed the positive effect of having students participate in a semester-long team-based research project that forwarded a larger, on-going research initiative. Students reported high engagement with the class and many students continued on with further research related to the course after its end. In Fall 2010, the same structure to the course is being pursued, with all course work centering around a single class research project.


ITL 345 Geovisualization

Dr. Byoungjae Lee, Postdoctoral Fellow, developed a new course in Geovisualization (ITL 345) for Intersession 2010.  Students reviewed cartographic design, production, and visualization in the context of geographic information systems (GIS). The core of this course was a laboratory project where students located data on the Web, processed the data so they could be mapped in ArcGIS (GIS and mapping software), and designed and produced a series of maps based on the data. Students learned how to develop and understand the intellectual and visual hierarchies by collecting appropriate data, constructing the map, and evaluating the map.  Lab work was informed by lectures which focused on the concepts, frameworks, and technical issues of cartographic design, production, and visualization. 


Microarrays in Courses

BIO 149/249 Freshman Gene Expression Workshop  

Using knowledge and skills acquired from attending the GCAT workshop, Dr. Candy DeBerry developed a new version of a freshman laboratory-intensive course based on DNA microarray analysis.  Freshman Gene Expression Workshop (BIO 149/249—with a new theme) was taught for the first time during January 2010 Intersession. GCAT surveys were completed.  Dr. DeBerry concluded that microarrays would be better implemented in more advanced courses over a full semester.


BIO 201 Genetics

Using knowledge and skills acquired from attending the GCAT workshop, Dr. Alice Lee had eight project groups Genetics (BIO 201) laboratories in Spring 2010 investigate gene expression in yeast in the diauxic shift from anaerobic to aerobic metabolism, repeating the experiment of DiRisi et al. 1997. Science 278: 680-686.The projects culminated in eight posters being presented at our spring poster session.  GCAT surveys were completed.  Although the experience was valuable for teaching students how to trouble-shoot research projects, and to gain valuable skills in data assessment, poster preparation, and presentation, it was too labor- and cost-intense for implementation in our typical 200-level course.  Dr. Lee will go back to using less complex projects in Genetics in Spring 2011. 


BIO 392 Tutorials in Biology

Also armed with skills from attending the GCAT workshop, during Spring 2010, Dr. Ronald Bayline used Drosophila microarrays in tutorial (BIO 392) projects with two students from his Fall 2009 Developmental Biology (BIO 202) class.  His goal was to implement microarray work in two different areas—student research and developmental biology courses.  For student research, Dr. Bayline planned to develop research projects investigating different patterns of gene expression during muscle development in the fruit fly, Drosophila melanogaster.   For curriculum development in developmental biology courses, he planned to develop laboratory exercises exploring changes in patterns of gene expression during embryonic development in Drosophila , focusing on early regulatory genes such as Hox genes.  Dr. Bayline determined that although the students benefitted from their experiences with microarrays (one is using the experience to enhance her applications to graduate programs in Genetics; the other’s performance doing related molecular techniques has vastly improved), microarrays did not fit his current research goals.  He also concluded that applying the method to a 200-level class, especially one like Developmental Biology where molecular techniques are not the only techniques that need to be taught, would be time-consuming and difficult. GCAT surveys were not completed—an oversight.


Future Plans for Microarrays in Courses

Dr. DeBerry will implement human microarrays in Spring 2011 in Experimental Biology (BIO 412), a research course where 6-8 students will study gene expression as cells undergo apoptosis.  GCAT surveys will be used.


PHL 232 Bioethics

Dr. Michael P. Wolf, Assistant Professor of Philosophy, received a stipend for the development of Bioethics (PHL232), a philosophy course devoted to debates in applied ethics related to health care and biotechnology.  The course will be a regular offering beginning in Fall of 2010, with regular use of CURE surveys.  The course will include visits from guest speakers; the inaugural offering of this class included a visit from Shannon Brownlee of the New America Foundation.  Rather than the usual poster sessions and research fairs familiar to instructors in the sciences, outstanding students will be encouraged to submit their work to undergraduate philosophy conferences. 


Equipment Purchased : No major equipment was purchased in YR2.


Laboratory Development : None was performed during YR2.


Plans for Revision:

The HHMI grant helps support the renovation of an office/research space for Dr. Burns.  Renovations supported by the HHMI grant will include: (1) converting an existing storage room to a molecular bioinformatics laboratory ($55,000); (2) converting a storage room to a research lab for the new molecular biologist ($18,000); (3) converting a cold storage room to a field ecology suite ($32,000); and (4) converting a storage room into a student data analysis room ($8,000). These renovations were originally scheduled to commence and be completed during 2010-11 (Year 3 of the grant, $113,000 total).  However, comprehensive renovations of the Dieter-Porter Life Science Building are delayed until funds are acquired, so we may not use HHMI renovation funds until after YR 3. The delays continue to negatively impact planned curriculum development and other grant activities.


Administration and Assessment of Curriculum Development:

Day-to-day oversight of the grant administration of grant programs falls to the Program Director, Dr. Alice Lee, Professor and Chair of Biology, who also served as program director for our 1996 and 2000 HHMI grants.  Dr. Lee is assisted by an Internal Advisory Board, with annual assessment by an External Advisory Board.  The HHMI Internal Advisory Board met six times during YR 2. The HHMI External Advisory Board has been sent agendas of meetings and important documents and messages for comments throughout YR1.  They conducted their formal annual site visit on April 9, 2010 (See below.) 

  • Advisory Board Members

  • External Advisory Board Meeting Agenda

  • Report of the HHMI External Advisory Board’s site visit of April 9, 2010

  • Assessment Tools

CURE Surveys for HHMI-Supported Courses:

  • BIO 215-Fall 2009
  • BIO/MTH 245-Spring 2010
  • BIO 288-Spring 2010
  • CHM 270- Spring 2010—Logan
  • CHM 270-Spring 2010—Sunderland
    • Many other courses in Biology and Chemistry not supported by our HHMI grant are now also using the CURE surveys as part of their assessment process. 

GCAT Surveys for HHMI-Supported Courses: t .aspx?section=15465&menu_id=857&crumb=844&id=15618

  • 2010 GCAT Report (Davidson College)
  • GCAT 2010 – Lee Teacher Comments BIO 201
  • GCAT 2010 – DeBerry Teacher Comments BIO 149/249


Course Evaluations are Completed for Every W&J Course

These are on file with the Office of Academic Affairs and with department chairs.

Course Observations by Department Chair and HHMI Program Director

Courses were observed by department chairs and/or Dr. Alice Lee and other tenured faculty.  Annual performance review meetings of faculty with department chairs are ongoing.

Senior Exit Surveys for Biochemistry and Biology Majors 

These are on file with the department chair for Biology and the program director for Biochemistry.  Members of the departments read these. 


Grant Proposal Submitted for Enhancement of HHMI-Supported YR3 Lab Development:

Title of Proposal

Funding Source

Faculty PI



Renovation of Dieter-Porter Life Sciences Building : Enhancing Student-Faculty Research Opportunities

National Science Foundation

Dr. Ronald Bayline , Biology (PI)

Dr. Candy DeBerry, Biology (Co-PI)

Dr. Lynn Wilson, Psychology (Co-PI)

$1,330,110 requested


Not Funded


Renovation of Dieter-Porter Life Science Building

State of PA Budget RCAP

Washington & Jefferson College




Plans for YR3:

YR3 courses include a DNA Microarrays in Experimental Biology (BIO 412), a new Biomedical Ethics course (PHL 232), continued LEM work in Microbiology (BIO 215), and implementation of two new bioinformatics laboratory exercises for General Biology (BIO 101).  Assessment will include CURE, GCAT, and RISC surveys.


Although our 2008 HHMI grant does not support Outreach programs, they were part of the original proposal.   They were cut when the grant was funded at less than the requested amount.   We have been actively seeking extramural support for Outreach, and were successful in 2009.



Total HHMI Expenditures

Not Budgeted in Funded 2008 Grant

External Funds: US Department of Education Outreach Grant

$95,000 acquired YR1;

implemented YR2 & YR3



US Department of Education Outreach Grant FUNDED:

Title of Proposal

Funding Source

Faculty PI


Outreach Grant: Three science-education programs for middle and high school students and teachers.

US Department of Education

Dr. Anne K. McGrain, Biology




In YR1, the college secured a $95,000 grant from the US Department of Education to reestablish and expand outreach programs that were previously funded in our 1996 and 2000 HHMI awards.


Our Active Science Initiative brings in local middle school and high school teachers for two-week summer workshops, each based on a theme.   Our first workshop was “Backyard Biology” in summer 2010. Teachers learned about seasonal changes on physiology of plants and animals.   The teachers received a stipend and funds for a “kit” of supplies to take back to their classrooms.   During the academic year following the workshop, teachers will bring their students to the college for a follow-up activity.   In summer 2011, the topic will be “Kitchen Chemistry.”  


The Young Investigators program brought high school students to the college for independent research projects with faculty beginning in fall 2009.   Students who completed the program during the summer of 2010 received a stipend.   Topics included biodiesel from spent coffee grounds, virtual chemical instruments and buckyballs  


Saturday Science and Math brings high school students to the college for hands-on activities with W&J faculty and students; sessions began October 24, 2009 and have included exercises in mathemagic: puzzles and games, cosmetics chemistry, natural dyes, and HPLC of hot sauce.   The US Department of Education grant supports two years of the three outreach programs.


Public Relations:

An article about the US Dept. of Education Outreach Grant was featured in the October 8, 2009 issue of the W&J Red & Black Article.pdf


Dr. Anne McGrain, Biology Outreach Coordinator, updated our Outreach databases and sent information to teachers in seven local school districts. We have received a great deal of interest in these programs from teachers, all of whom are glad to see our formerly HHMI-supported programs funded again.