Howard Hughes Medical Institute

Student Genomics Researcher Abigail Rosenberger '15
Photo by Gordon Dimmig '17

The Genomics Leadership Initiative at Juniata College has been funded by the Howard Hughes Medical Institute (HHMI) and the National Science Foundation. The Initiative seeks to achieve its goal by developing a genomics certificate program, a leadership module, and student summer research experiences.

Genomics Certificate Program

Comprised of seven courses, the genomics certificate addresses both the science and the broader ethical, legal and social implications (ELSI) surrounding progress and discoveries in the field of genomics. The ethical, legal and social issues surrounding advances in genomics provides a strong focus for practicing a breadth of knowledge and skills; the understanding of the scientific foundation of genomics provides the focus for developing an interdisciplinary base and cross disciplinary understanding of the life sciences in an era of “big data”. To help support this part of the program the grant has also funded an ELSI faculty development workshop, a seminar series, stipends for faculty developing new or revised classes, and stipends for faculty to formally assess the learning gains of students as a result of programmatic activities.

Certificate Courses and Requirements: Follow this link the read more about the Genomics Certificate including program requirements, core courses, course descriptions and a suggested curricular progression.

Faculty may apply for course development funds related to the certificate and leadership program below by following this link.

Students interested in pursuing a genomics certificate should do they following:

  • Notify us. Let us know you are interested by visiting the Genomics Certificate Notice of Interest link and sending your name to the program director. This does not obligate you to joining the program but it does put you on our radar so that we can assist you if you choose to go through the certificate process.
  • Take the pre-test. We need you to take a few pre-tests to establish your baseline knowledge of genomics and ELSI. Please click through to the Genomics Certificate Pre-Assessment to learn more about the pre-tests for the program.

Student Summer Research Experience

Student research is a high-impact educational practice that helps students develop expertise, confidence, and effective communication skills.  Research projects are a platform for undergraduates to apply knowledge and engage in the full scholarly process. The ability to work within an interdisciplinary team and develop strong organizational and interpersonal skills is essential for successful completion of the project, and the ability to communicate findings to peers and the lay public is an essential skill for future scientists and leaders.   

The grant provides support for summer undergraduate research projects using cutting edge Next-Generation sequencing approaches for 40 students. Supporting elements include faculty summer mentoring stipends, a powerful compute cluster, commercial software for data analysis, a Bioinformatics postdoc shared between Juniata and Penn State who will teach at Juniata while doing research at Penn State, and a summer faculty development workshop run by the GCAT-SEEK consortium.

Leadership Program

This initiative develops leadership through two discrete methods:

  • Study of theory in coursework and case-study experiences and
  • The practice of and exposure to leadership in a research environment

Two existing Juniata courses explore skills and styles of leadership: “Behavior Analysis of Organizations” in business and “Judgment and Decision Making” in psychology. Another class, “Leadership,” is being developed to provide additional focus on challenges of providing leadership in the information age within global and cultural contexts. Additionally, a series of executive residencies, integrated with a number of courses, are being developed in a work group led by Provost Lakso. Juniata has an established program facilitating short-term residencies with executives from diverse organizations, including medicine. The residencies explore leadership traits and characteristics, including creating a vision, relationship and team development to get “work done through others,” and how to recognize and organize tasks for optimal productivity.

Common Acronyms Defined

GCAT-SEEK: Genome consortium for active teaching using next-generation sequencing
NSF: National science foundation
RCN/UBE: Research coordination networks for undergraduate biology education
GLI: Genomics leadership initiative
HHMI: Howard Hughes Medical Institute
ELSI: Ethical, legal, and societal implications
IS: Integrative science
CURE (aka CRE): Course-based undergraduate research experience
HIP: High impact [teaching] practices (see http://leap.aacu.org/toolkit/high-impact-practices)
SoTL: Scholarship of teaching and learning
PBL: Problem-based learning

HHMI Supported Publications

Published manuscripts or books supported by Juniata's HHMI grant.  Undergraduate authors*

1. Bagchi S, Lamendella R, Strutt S*, Van Loosdrecht MCM, and Saikaly PE (2016). Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor. Sci. Rep. 6, 28327. doi:10.1038/srep28327.

2. Bagchi S, Tellez BG, Rao HA, Lamendella R, and Saikaly PE (2015). Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time. Appl. Microbiol. Biotechnol. 99, 2361–2370. doi:10.1007/s00253-014-6134-4.

3. Bergeron N*, Williams PT, Lamendella R, Faghihnia N, Grube A*, Li X (2016). Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk. Br. J. Nutr. 116, 2020–2029. doi:DOI: 10.1017/S0007114516004165.

4. Buonaccorsi VP, Hamlin D*, Fowler B*, Wisyanski C*, Sickler A* (2017). An introduction to Eukaryotic Genome Analysis in non-model species for undergrads: A tutorial from the Genome Consortium for Active Teaching.  CourseSource. Vol 4.

5. Buonaccorsi VP, Malloy J*, Peterson M, Brubaker K, Grant CJ (2017). Population genomic analysis of brook trout Salvelinus fontinalis in Pennsylvania's Appalachian region.  Trans. Am. Fish. Soc. 146(3), pp.485-494.

6. Buonaccorsi V, Peterson MP, Aguilar A, Grove D, Hunt A, Lamendella R, Newman J, Praul, C, Tobin T, Trun N, Roberts W, Roney J (2014). Vision and Change through the Genome Consortium for Active Teaching Using Next-Generation Sequencing (GCAT-SEEK).  CBE-Life Sci. Ed. 13,1-2.

7. Fowler BL*, Buonaccorsi VP (2016). Genomic characterization of sex identification markers in Sebastes carnatus and S. chrysomelas rockfishes.  Mol. Ecol. 25, 2165–2175.

8. Grant CJ, Weimer AB*, Marks NK*, Perow ES*, Oster JM*, Brubaker KM, Trexler RV*, Solomon CM*, Lamendella R (2015). Marcellus and mercury: Assessing potential impacts of unconventional natural gas extraction on aquatic ecosystems in northwestern Pennsylvania. J. Environ. Sci. Heal. Part A 50, 482–500. doi:10.1080/10934529.2015.992670.

9. Jansson J, Halfvarson J, Lamendella R, Brislawn C*, Vazquez-Baeza Y, Walters W, Bramer L, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure E*, Dunklebarger M*, and Knight R (2017). Dynamics of the human gut microbiome in Inflammatory Bowel Disease, Nature Microbiology. 2:17004.

10. Lamendella R, Bagchi S, Tellez BG, Rao HA, Lamendella R, and Saikaly PE (2013). r-RNA subtracted m-RNA metatranscriptomics of granular anammox process. in Published Proceedings of Microbial Ecology and Water Engineering doi:Reference No. IWA-12895.

11. Lamendella R, Li KC, Oerther D, and Santo Domingo JW (2013). Molecular Diversity of Bacteroidales in Fecal and Environmental Samples and Swine-Associated Subpopulations. Appl. Environ. Microbiol. 79, 816–824. doi:10.1128/AEM.02535-12.

12. Lamendella R, Strutt S*, Borglin S, Chakraborty R, Tas N, Mason OU (2014). Assessment of the deepwater horizon oil spill impact on gulf coast microbial communities. Front. Microbiol. 5. doi:10.3389/fmicb.2014.00130.

13. Lutz AK*, Grant CJ (2015). Impacts of hydraulic fracturing development on macroinvertebrate biodiversity and gill morphology of net-spinning caddisfly (Hydropsychidae diplectrona) in Northwestern Pennsylvania, USA. Journal of Freshwater Ecology.31:211-217  DOI:10.1080/02705060.2015.1082157  http://www.tandfonline.com/eprint/bzKh8Q8SYtf96WzD9iHE/full#.Ve2tqvnF-So7)  

14. Peterson MP, Malloy JT*, Buonaccorsi VP, & Marden JH (2015). Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching. CourseSource. Vol 2.

15. Podany AB, Wright J*, Lamendella R, Soybel DI, and Kelleher SL (2016). ZnT2-Mediated Zinc Import Into Paneth Cell Granules Is Necessary for Coordinated Secretion and Paneth Cell Function in Mice. Cell. Mol. Gastroenterol. Hepatol. 2, 369–383. doi:http://dx.doi.org/10.1016/j.jcmgh.2015.12.006.

16. Prestat E, David MM, Hultman J, Ta N, Lamendella, R, Dvornik J (2014). FOAM (Functional Ontology Assignments for Metagenomes): A Hidden Markov Model (HMM) database with environmental focus. Nucleic Acids Res. 42. doi:10.1093/nar/gku702.

17. Sangster W, Hegarty JP, Schieffer KM, Wright JR*, Hackman J*, Toole DR* (2016). Bacterial and fungal microbiota changes distinguish C. difficile infection from other forms of diarrhea: Results of a prospective inpatient study. Front. Microbiol. 7. doi:10.3389/fmicb.2016.00789.

18. Sowell D (2015).  Medicine on the Periphery: Public Health in Yucatán, Mexico, 1870-1960 (New York: Lexington Books)

19. Trexler R*, Solomon C*, McClure EE*, Brislawn CJ*, Grube AM*, Wright JR* (2014). Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in northwestern Pennsylvania. Front. Microbiol. 5. doi:10.3389/fmicb.2014.00522.

20. Tuten BS. (2014). Lactation and Breast Diseases in Antiquity: Medical Authorities on Breast Health and Treatment, in special issue Women and Womanhood in the Middle Ages, ed. Piotr Górecki, Quaestiones Medii Aevi Novae 19: 103-138.

21. Ulrich N*, Rosenberger A*, Brislawn C*, Wright J*, Kessler C*, Toole D* (2016). Restructuring of the aquatic bacterial community by hydric dynamics associated with Superstorm Sandy. Appl. Environ. Microbiol. 82, 3525–3536. doi:10.1128/AEM.00520-16.

In Review

22. Chan JP, Brown J*, Hark B*, Nolan A*, Servello D*, and Staab TA (2015) The Influence of Sphingolipids on Life History and Health Span Traits in Caenorhabditis elegans. In review at PlosOne.

23. Dries DR, Zhu Y, Brooks MM, Forero DA, Adachi M, Cenik B, West JM, Arbella J*, Han Y, Yu C, Nordin A, Adolfsson R, Del-Favero J, Lu QR, Callaerts P, Birnbaum SG, Yu G. Hypomyelination and compulsive grooming and hyperactivity in mutant mice defective in γ-secretase activity in oligodendrocytes. In review at J Biological Chemistry.

24. Toole DR*, Cannon GH*, Brislawn CJ*, Graves JM*, Lamendella R, Muth TR, Muth NZ.

Differences in soil fungal assemblages associated with native and nonnative tree species of varying weediness. In review at Biological Invasions

In Prep

25. Buonaccorsi V, Sickler A*, Peterson M, Fowler BS*. Whole genome analysis of divergent natural selection between depth-partitioned sibling species in the Sebastes marine species flock. In preparation for submission to Molecular Ecology.

26. Lamendella R, Hackman J*, Ulrich N*, Wright J*, Toole DR*, Brislawn C*, Sabey K*, Solomon C*, McClure, EE*. Teaching Metagenomics at Undergraduate Institutions: A tutorial from the Genome Consortium for Active Teaching. In preparation for submission to CourseSource

27. Scales J*, Melber A*, Hoffman C*, Keeney JB. Ty transposition in yeast: stress regulation by the host gene RTT105. In preparation for resubmission to Mobile DNA.

28. Wright J*, Bernard W*, Kirchner V*, Ulrich N*, McLimans C*, Hazen TC, Macbeth T, Marabello D, McDermott J, Mackelprang R, Lamendella R. Bacterial Community Dynamics in Dichloromethane-contaminated Groundwater Undergoing Natural Attenuation. In preparation for submission to Frontiers in Microbiology.

Funded Programs for Research in Biology at Juniata

The National Science Foundation has awarded Juniata College a $445,039 grant to fund a series of faculty development workshops to be held at Juniata College and other college and university campuses on genomics education over the next five years. 

The HHMI (Howard Hughes Medical Institute) has awarded $1 million in support of Juniata’s Genomics Leadership Initiative (GLI), to prepare leaders in science, medicine and society.

GCAT-SEEK is a group of educators who seek to incorporate new, massively-parallel sequencing technologies into the undergraduate curriculum to provide students with a hands-on opportunity to apply these revolutionary cutting-edge tools to investigate biological questions.

NSF S-STEM scholarship program: The National Science Foundation (NSF) has awarded Juniata College a "Scholarships in Science, Technology, Engineering and Math" (S-STEM) grant to provide community/two year college transfer students with scholarships of up to $10,000 per year for the two years needed to complete a B. S. degree.