Annual Progress Report

Howard Hughes Medical Institute

Undergraduate Science Education Program

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

Washington and JeffersonCollege

Grant # 52006323 (2008)

DRAFT 11-15-10

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

ANNUAL PROGRESS REPORT SYNOPSIS: YR2

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 23 toteacha limited number of courses in a mentored setting andto 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 anArcGIS 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 YR2for a new tenure-track position in molecular biology/bioinformaticsfailed 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 supportedstipends for course revisions/creations and supplies to support new exercises. CURE and GCAT surveys and course evaluations informed revisions of these courses.

Outreach

Outreach programs were cut from our funded 2008 proposal. However, during YR1 a $95,000 grantfrom 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 grantassisted 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 theLEM ArcGIS system. In addition, during YR2, we were successful in acquiring almost $1.2 million in extramural grants and more than $14,000in 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 grantfrom the State of PA budget RCAP to be used toward the renovations.

  1. STUDENT RESEARCH NARRATIVE:

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
  • On-Campus Student Research Summer Template
  • On-Campus Student Research Summer 2010: Long-Term Ecological Monitoring
  • On-Campus Student Research Summer 2010: Molecular Microbiology
  • Off-Campus Student Research Internships

Progress:

Total Number of Student Participants Supported / 17
Total Number of Faculty Participants Supported / 10
Total HHMI Expenditures / $70,089
Matching Funds—Internal (Entrepreneurial Grants, Presidential Discretionary Funds, Faculty Travel) / $12,975
Matching Funds—External (Merck, Phi Sigma, WCCF, Cargill) / $24,755
Awards or Honors / 1
Collaborations with other HHMI-funded programs / 0
Collaborations with other non-HHMI-funded programs / 0
Student/Faculty Manuscripts / 2
Student/Faculty Publications / 1
# Meetings Attended with Students / 5
# Faculty Attending Meetings with Students / 12
# Student Conference Presentations / 24

Evidence of Progress:

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

  • Shane M. Polen
  • Brandon J. Sansom

Posters: Off-Campus Research: Intersession 2010

  • Benjamin R. Daggett
  • Katie J. Steider

Posters: Off-Campus Research: Summer 2010

  • Taylor J. Eddens
  • Brandon J. Sansom
  • Nicholas J. Tyger

Posters: On-Campus Research: Summer 2010

  • Charles M. Irvin
  • Brittany M. Verrico
  • Michelle C. Wuenstel

Link to the ArcGIS Server:

  • ArcGIS Server on campus or via Virtual Private Network)

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

model abstract.pdf

  • Taylor Eddens (student) to World Vaccine Conference in Beijing
  • Bo Harstine (student) was an author on an abstract at the AAI Meeting
  • Dr. Jennifer Logan and 2 students to ACS Meeting
  • Dr. James March, Thomas Contreras and 3 students to ESA Meeting
  • Brandon Sansom (student) and Dr. James March to NABS Meeting

Publications and SubmittedManuscripts:

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.

Awards:

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:

  • W&J Magazine, pg. 17.
  • Liberal Arts College News

Internship Application Forms and Information:

  • Off-Campus Intersession Research Internship Support Formadd link
  • Off-Campus Summer Research Internship Support Formadd link
  • Biology Department’s Internship Database

Photographs:

  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 ininfluencing 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 pursuea 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 aninvasion 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 masteredbasic 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 portionsof 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 studentspresented 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 threeweeks of off-campus research during the January Intersession: Benjamin Daggett (Chemistry ’12); and Katie Steider (Biology ’12). HHMI support covered living and travelexpenses. Students kept journals and made poster presentations at W&J’s HHMIExternal Advisory Board meeting on April 9, 2010 and at the 31stAnnual Undergraduate Biology Symposium for Western Pennsylvania onApril 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 supportedstipend and living expenses. Students kept journals and made presentations of their work at the W&J Summer Research Poster Session on October8-9, 2010. Students will present their work at the April 2011 meeting of W&J’s HHMI External Advisory Board, and at the 32nd 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 Fundsand 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 metsixtimes 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.)

  • Advisory Board Members
  • External Advisory Board MeetingAgenda
  • Report of the HHMI EAB site visit

Plans for Revision:

We continue to track numbersof students attending events publicizing internship opportunitiesand to tracknumbers 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.

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.