May 30 – June 2, 2023
Tuesday, May 30
3-5pm Arrival in Atlanta – take ground transportation to hotel near Emory University
Dinner on your own
8pm Welcome and Dessert Reception – meet in lobby at hotel and walk to 1510 Clifton Rd. O. Wayne Rollins Building, Room 2052
Homework: Read Berasategui et al. 2021 (especially Fig 1 and 2) and one other paper from the suggested readings.
Wednesday, May 31
8:30-9:00am Breakfast – Room 2052, O. Wayne Rollins Building
9:00 – 9:15am Workshop Expectations and Implementation Process – Room 109, 1462 Clifton Rd. Building [presentation]
9:15-10:30am Discussion on CUREs in laboratory classes – Room 109, 1462 Clifton Rd. Building [presentation]
Each workshop will start with a session on inquiry-based learning, defining CUREs in laboratory classes, and the value of CUREs. We will discuss the different approaches to inquiry-based learning, ranging from guided-inquiry to open-ended inquiry to CUREs. In addition, we will discuss definitions of CUREs based on participants’ responses compared to other prior definitions, and how research in laboratory courses affects student outcomes.
10:30-10:45am Break—Room 2052, O. Wayne Rollins Building
10:45-11:15am Importance of microbiomes and insect microbiomes — Room 109, 1462 Clifton Rd Building [presentation]
11:15am-noon Bean Beetles as a model system – Rooms 109 and 119, 1462 Clifton Rd. Building [presentation]
In this session, we will introduce participants to bean beetles as a model system for teaching and research. Participants also will be introduced to our website resources (www.beanbeetles.org). These resources include a handbook on the use of bean beetles, links to websites of researchers who study this species, extensive bibliographies of research articles on the genus Callosobruchus and other bruchid beetles in different sub-disciplines of biology, more than thirty-five class-tested inquiry-based laboratory activities using Bean Beetles complete with student handouts, instructor’s notes, and sample student data, and links to resources on inquiry-based learning. Participants will develop expertise in handling Bean Beetles, sexing adults, identifying eggs on beans, and culturing beetles.
Noon-1pm Lunch—Room 2052
1-3pm Bean Beetle microbiome protocols 1 – Room 119, 1462 Clifton Rd. Building
During this session, we will begin by simulating the process of eliciting student-generated research questions based on background reading, followed by student-generated experimental design. Then, participants will make bean beetle microbiome preparations and plate these preparations on different media to identify and tabulate the bacterial communities during a session on the next day. Participants will score the phenotypes of the bacterial colonies on the plates staged prior to the workshop.
3-3:15pm Break—Room 2052
3:15-6:30pm Bean Beetle microbiome protocols 2 – Room 119, 1462 Clifton Rd. Building
Participants will pick bacterial colonies for Sanger sequencing of a portion of the 16s rRNA gene. Participants will amplify a portion of 16s rRNA gene of cultured microbes using PCR. We also will confirm that each participant has an account for DNA Subway.
6:30pm Dinner – Room 2052, O. Wayne Rollins Building
Homework: Begin working through the DNA Subway tutorial until at least the DADA2 step. We will return to this on Thursday afternoon. [presentation]
Thursday, June 1
8:30-9:00am Breakfast – Room 2052, O. Wayne Rollins Building
9:00-12:00pm Bean Beetle microbiome protocols 3 – Room 119, 1462 Clifton Rd. Building
Participants perform electrophoresis of the PCR products to verify successful amplification. In addition, participants will examine the bacteria cultured the previous day. At the end of the session, we will begin microbiome data analyses.
11:00-11:15am Break – Room 113, 1462 Clifton Rd. Building
Noon-1pm Lunch—Room 2052, O. Wayne Rollins Building
1-1:30pm Identifying bacterial taxa based on Sanger sequence data – Room 109
In this session, participants will use sample Sanger sequence data to identify bacterial taxa using BLASTn. [sample .ab1 file][TEAL][sample fasta data][BLAST]
1:30 – 3pm Microbial community ecology analyses 1 – Room 109
Colony phenotype and colony-based 16s rRNA sequence results can be used to describe microbial communities. In this session, we will guide participants in a discussion on the community-level ecological analyses that can be calculated (such as species richness, species diversity and other methods) and how they may be interpreted. Participants will work in teams and have access to appropriate datasets from previous experiments. [sample class colony phenotype dataset] [sample class Sanger sequence dataset] [presentation]
3-3:15pm Break – Room 2052 in O. Wayne Rollins Science Research Building
3:15-4:45pm Bioinformatics of next gen sequence data – Room 109
Working in teams, participants will continue to work through a tutorial designed for teaching undergraduate students how to carry out processing of microbial community sequencing data using the DNA Subway computer application.
4:45-6:15pm Microbial community ecology analyses – Room 109
Working in teams, participants will work through a tutorial designed for teaching undergraduate students how to carry out community ecology analyses on taxonomy data generated from the bioinformatics pipeline. We will be using an online app (the BeanBeetleMicrobiome app) for this purpose. If you were unable to complete the DNA Subway analysis, you can download the files that you will need here. [level-5][level-5-transposed][metadata]
7pm Dinner – meet outside hotel (to walk to 7:30pm dinner) – Double Zero in Emory Village
Friday, June 2
8:30-9:00am Breakfast – Room 2052, O. Wayne Rollins Building
9:00-11:30am Implementing the Bean Beetle microbiome CURE and overcoming barriers – Room 109, O. Wayne Rollins Building
This session will dedicate time for each faculty team to discuss implementation plans. Use Google Slide on Implementation.
Following this discussion, each faculty pair will prepare and present their ideas on implementation of the CURE and overcoming barriers. In addition, we will facilitate a discussion with the workshop participants on overcoming barriers to implementing CUREs in the participants’ laboratory courses.
10:00-10:15am Break — Room 2052
11:30am – Noon Wrap-up, next steps, and workshop assessment – Room 109
Noon-1:00pm Lunch Room 2052