11:46 AM

STC Biology Department SEA-PHAGES Students and Faculty Publication Contributions

The HHMI supported SEA-PHAGES course completed a very successful year at STC; there are many achievements from the program to look back at. Microbacterium phage DelaGarza, complete genome, is published in the Genebank (Accession number: MT889371.1). The first fourteen authors are also students that worked on the annotation as part of the Spring 2020 Biology 1407 HHMI SEA PHAGES bioinformatics course2.  

The first year of SEA-PHAGES course at STC was very engaging as the faculty were busy not only teaching and guiding students but also publishing scholarly work. SEA-PHAGE faculty across the country collaborated in the annotation and publication of Mycobacterium phage BodEinwohner17, Complete Genome in the Genbank. (Accession number MN945900)1. 

SEA-PHAGES Administration organized a summer workshop and invited SEA -PHAGES faculty to develop online teaching resources for teaching bioinformatics in Fall 2020. The necessity for this workshop was driven by the current COVID-19 pandemic. The teaching resources developed by the faculty team were published in QUBES (Quantitative Undergraduate Biology Education and Synthesis), a resource for education, research, and collaboration in quantitative biology.  

Two SEA-PHAGES faculty from the STC Biology department, Dr. Thomas Ndolo and Dr. Shima Chaudhary, volunteered to collaboratively develop online teaching materials over the summer 2020 session. The completed resources were then made available to all faculty for use in their courses. The SEA-PHAGES team showcased these resources prominently on the program website to facilitate peer-review and promote recognition to those individuals that aided in the development of these materials.  The workshop focused on the following areas of the SEA-PHAGE course: 

1. Develop Teaching Resources  

SEA-PHAGE faculty expressed interest in developing shared teaching resources, particularly for the Phage Genomics/Bioinformatics component. Such shared resources are invaluable given that Phage Genomics was likely to feature prominently during the upcoming academic year.  

2. Discuss Implementation Strategies  

a. to share and discuss strategies that did and did not work well during the 2020 spring semester. 

b. to propose and receive feedback on ideas for the coming semester. 

The outcome of 10-day long virtual scholarly exchanges led to the development of peer-reviewed teaching resources3,4. The reference to the publication is given below.  

1. Anders,K.R., Asai,D.J., Barmoy,M.A., Bates,T.C., Biederman,W.H., Breakwell,D.P., Bullock,S.K., Butela,K.A., Chan,K., Chaudhary,S., Chien,P., Church,J.C., Clifton,K.B., Crane,A.E., Cresawn,S.G., Davila-Aguer,C., Elwess,N.L., Gallagher,C.J., GarciaCostas,A., Garlena,R.A., Gibb,B.P., Gleichsner,A.M., Grasis,J.A., Gusky,S.B., Heller,D.M., Heninger,S.G., Holloway,J.R., Jacobs-Sera,D., Joshi,G.S., Kanther,M.L., Labonte,J.M., Landry,C.A., Lavallee-Adam,M., Lee,L., MacLea,K.S., Mahmoudian-Geller,M., Markov,S.A., Maughan,J.A., Molloy,S.D., Nance,H.A., Ndolo,T.M., Pfeifer,S.P., Phillis,R.W., Pope,W.H., Rivera-Figueroa,F.J., Rocheleau,J.M., Rudner,A.D., Russell,D.A., Sivanathan,V., Starkey,K.D., Sunnen,C.N., Sweet,T.S., Teschke,C.M., Vazquez-Montes,A., Walker,J.R., White,G.J., Williams,D.C., Wisner,E.M. and Hatfull,G.F. (2020). Mycobacterium phage BodEinwohner17, Complete Genome. Genbank. MN945900. 2020. 

2. De La Garza,D., Acevedo,C., Camacho,M., Castro,L., Chavez,L., Dominguez,K., Lopez,T., Martinez,N., Narvaez,S., Nava,M., Rodriguez,H., Thomas,D., Vasquez,A., Winkler,K., Montalvo,D., Ndolo,T., Cervantes,M., Whitefleet-Smith,J.L., Garlena,R.A., Russell,D.A., Pope,W.H., Jacobs-Sera,D. and Hatfull,G.F. (2020). Mycobacterium phage DelaGarza, Complete Genome. Genbank. MT889371. 2020. 

3. Diaz, A., Lee-Soety, J., Chaudhary, S., Pollenz, R. (2020). Writing Genome Announcements Collaboratively. HHMI Science Education Alliance (SEA) Faculty Group, QUBES Educational Resources. doi:10.25334/DFVG-BG93 

4. Rocheleau, J., Mastropaolo, M. D., Sunnen, C. N., Beyer, A. R., Ndolo, T., Williams, D., Saha, S., Dean, N. (2020). Exploring Functions for Common Phage Proteins. HHMI Science Education Alliance (SEA) Faculty Group, QUBES Educational Resources. doi:10.25334/3YA4-H358