BRINGING CHLAMYDIA AND CONFLICT TO THE CLASSROOM AN INTERACTIVE DISCUSSION ACTIVITY TO ASSESS STUDENTS' ABILITY TO READ PRIMARY LITERATURE

Bekah Le, Charles Yi, Vaishali Jayashankar, Seong Kim, and Rabi Murad University of California, Irvine Dept. of Developmental and Cell Biology GAANN Fellows

© 2015, UCI GAANN

How to read a science paper…?

• Rationale for this workshop: •  The ability to read and analyze primary literature is a necessary

skill for students pursuing health science and research careers.

•  Students don’t often get to practice this skill, especially in large classrooms.

•  Students should learn about the “realities” of research and the process of discovery.

3/4/2014 Piled Higher and Deeper

http://www.phdcomics.com/comics/archive_print.php?comicid=974 1/1

Piled  Higher  and  Deeper  by  Jorge  Cham www.phdcomics.com

title:  "We're  all  doomed"  -­  originally  published  2/6/2008

3/4/2014 Piled Higher and Deeper

http://www.phdcomics.com/comics/archive_print.php?comicid=974 1/1

Piled  Higher  and  Deeper  by  Jorge  Cham www.phdcomics.com

title:  "We're  all  doomed"  -­  originally  published  2/6/2008

© 2015, UCI GAANN

D140: “How to read a science paper” •  This workshop presents a module that stemmed from an

upper division elective course developed by three Ph.D. candidates.

• Small class size – 15 students per discussion.

• Modules consisting of: •  Research seminar given by current graduate student. •  “Journal Club” style discussion.

•  Presentations, figure facts worksheet (Round, 2013) and pre- and post-module online quizzes.

• Class sessions devoted to Dev Bio techniques.

© 2015, UCI GAANN

Students self-reported increase in confidence

0

5

10

15

5 4 3 2 1

Generally, I feel confident about

working in a biological research laboratory*

5 4 3 2 1

I am sure I could conduct independent biological research*

5 4 3 2 1

I can handle reading and interpreting primary

scientific literature*

0

5

10

15

5 4 3 2 1

I generally feel confident explaining biological

research to non-scientists*

5 4 3 2 1 5 4 3 2 1

I generally feel confident explaining biological research to my PI*

I generally feel confident explaining biological

research to my peers in small groups*

Num

ber

of S

tude

nts

Num

ber

of S

tude

nts

Pre-Test Post-Test

Pre-Test Post-Test

Strongly

Agree Agr

eeNeu

tral

Disagree

Strongly

Disagree Stro

ngly

Agree Agr

eeNeu

tral

Disagree

Strongly

Disagree Stro

ngly

Agree Agr

eeNeu

tral

Disagree

Strongly

Disagree

Strongly

Agree Agr

eeNeu

tral

Disagree

Strongly

Disagree Stro

ngly

Agree Agr

eeNeu

tral

Disagree

Strongly

Disagree Stro

ngly

Agree Agr

eeNeu

tral

Disagree

Strongly

Disagree

* P-value ≤ 0.05 (Wilcoxon signed-rank test) © 2015, UCI GAANN

Structure of today’s workshop • Present a module that can be incorporated into an

existing course: •  Introduction to the topic and basic techniques

•  Individual reading of one of two papers (shortened for workshop)

•  Discussion of same paper in small groups

•  Discussion of both papers in combined groups

•  Whole class discussion of both papers

• Closing discussion on module and modifications.

© 2015, UCI GAANN

• Most commonly reported notifiable disease in the U.S. (regular, frequent information about individual cases is necessary for prevention and control of disease)

Chlamydia trachomatis causes significant disease

Number of reported notifiable disease cases in the U.S. in 2012

Chlamydia trachomatis genital infections

Gonorrhea

Salmonellosis

Syphilis

Chicken Pox

AIDS

Other CDC, 2014

© 2015, UCI GAANN

The number of reported Chlamydia genital infections are increasing annually in the U.S.

CDC, 2009

© 2015, UCI GAANN

C. trachomatis relies on a host cell for survival

• Obligate intracellular bacterium

• Modulation of host cell pathways promotes bacterial growth •  Avoidance of fusion with

lysosomal pathway •  Acquisition of host lipids

and nutrients

• Host cell complements minimal chlamydial genome

J. Lee, UC Irvine

© 2015, UCI GAANN

Chlamydia induces specific host-pathogen interactions

Golgi reorganization Resistance to apoptosis Heuer et al., Nature, 2009 Fischer et al., J Exp Med, 2004

Intermediate filament re-organization

Kumar and Valdivia, Cell Host Microbe, 2008

Enhance lipid acquisition Preserve host cell and ensure bacterial

replication

Support the chlamydial inclusion

© 2015, UCI GAANN

How does Chlamydia induce host-pathogen interactions? • Secreted effectors

• Chlamydial proteins that can be translocated into the host cell cytoplasm

• Modulate normal cellular proteins and processes

• Others?

© 2015, UCI GAANN

Immunofluorescence Review

1.  Begin with fixed cells or tissue sections

2.  Block non-specific protein binding 3.  Add primary antibody against

protein of interest 4.  Add tagged secondary antibody

against primary antibody 5.  Add color substrate for enzyme

tags or visualize fluorescent tags

Chen et al., PLoS Pathog, 2012

Chlamydial MOMP Golgi ManII DNA

Proteintech Group © 2015, UCI GAANN

Western Blot Review Lyse Cells

Lysate containing proteins

C-Nap1

γ-Tubulin Non-specific band

Cleavage product

Loading control

1.  Collect lysate from cells 2.  Denature proteins 3.  SDS-PAGE 4.  Transfer to membrane 5.  Blot with specific primary

antibodies to protein of interest 6.  Blot with secondary antibodies

to visualize proteins 7.  How do you control for loading

errors?

J. Lee, UC Irvine © 2015, UCI GAANN

Please read your assigned paper individually

Heuer et al

Chen et al

© 2015, UCI GAANN

Please form groups based on paper and color

Heuer et al Heuer et al

Chen et al Chen et al

Please discuss your responses to the questions with your

group members

© 2015, UCI GAANN

Please merge with a group that has the other paper

Please exchange the following information by comparing

the following information: hypothesis, key results and conclusions

Heuer et al Chen et al

Heuer et al Chen et al

+

+

© 2015, UCI GAANN

Questions addressing both papers • Please spend 10 minutes to answer the following

questions: • State the hypothesis being tested by the authors (one

sentence, do not copy from the authors’ text) • Based on the data presented, what conclusion can be

drawn from each individual paper? •  From reading both of these papers, what conclusion did

you draw about the role of golgin-84 cleavage play in chlamydia infection?

• Can you think of an interpretation that will explain both sets of data?

© 2015, UCI GAANN

Whole group discussion • Can you think of an interpretation that will explain both

sets of data? • What are the significance of these papers? How do these

differing results impact the field? • What can you do to resolve different research findings in

literature?

A potential “end of activity” assignment for students: Write a paragraph on what you learned about critically reading

scientific literature.

© 2015, UCI GAANN

How could this module be implemented in lecture and lab courses?

© 2015, UCI GAANN

Suggestions for implementing this module

Choosing papers •  Interesting biological or pathological problem

•  Classic paper or current papers that are controversial/relevant • Paper could cover topics and techniques from lecture and

lab courses • Articles with straightforward techniques and clear

questions would be ideal

Other Modifications (please see our lesson plan) • Students can read the paper before coming to class • Assignment based on the paper could be assigned • When the questions are handed out can be varied

© 2015, UCI GAANN

Thank you for attending and please fill out the provided evaluation form!

© 2015, UCI GAANN