Intermediate Immunology

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Intermediate Immunology

Hewitt Hall  conference room (3022)
Tuesday/Thursday, 2 - 2:30PM

Course Coordinators

Eric Pearlman
Matt Inlay
Roberto Tinoco
Francesco Marangoni


This is the second part of a two-quarters course covering basic and advanced concepts in immunology. Participation to 215A is a prerequisite for participation to this course (215B). The course will also cover in-depth analyses of selected topics within the broader field of immunology, including relevant research techniques, while improving critical thinking skills. There will be a combination of didactic lectures with discussions of primary literature.

Time and Place:

Tuesday/Thursday, 2-3:20 pm Hewitt Hall, room 3022. Classes will be conducted live, but recordings will be made available to the students. If you cannot attend the live classes, please contact the coordinator(s).

Text (Recommended)

Janeway’s Immunobiology, Garland Science, 9th Edition. Copies are available at the UCI bookstore. This book is also available as an e-book through Vital Source, including the option of renting the book or purchasing individual chapters:

Please note that while we will only cover selected chapters of the textbook, the text would be a goodresource during graduate school. If you want to borrow a copy, talk to the course organizers as somecopies may be available. Additional reading material will be posted on the course website, in pdf format.


Attendance is mandatory for all classes and journal clubs, one excused absence allowed.


Grading in the class will be based on 2 measures:

1) participation in the class and the paper discussions, 2) an original research proposal, written.

100 points total:
40% participation in class and paper discussions
30% oral presentation
30% for written proposal

Paper discussions

After a lecture covering a topic is given, a journal article on that topic will be discussed the following class. All students are expected to read the paper and participate in the discussion via the following format:

  • Half the students will be assigned the paper, and will organize amongst themselves how to present it to the other half of the class. All students are expected to have read the entire paper, but will only present their section. One or two students will present a background on the subject of the paper, and each figure will be presented by one or two students. The students do not need to evaluate the paper, but explain each figure so that the class can understand what the researchers did and why. One or two students will also present the main conclusions of the paper, as the authors describe it.
  • The other half of the students are expected to evaluate and critique the paper. They will ask questions of the presenters, and offer their opinions as to the veracity of the paper’s findings. These students will also self-organize by figure, with one or two students assigned to each figure, and one or two to the conclusions.
  • The two groups are not adversarial, and both can agree on the strengths or weaknesses of the paper.

Oral presentation of research proposal

Towards the end of the quarter, each student will present their idea for an original research proposal to the class, based on one of the papers covered in the class. The proposal should describe 1 or more experiments they would conduct, and can either be a follow-up to what was covered in the paper, or could springboard in a completely new direction. It should be connected in some way to the paper, but can diverge from the topic quite substantially. Examples include:

  • Experiments that you thought the original authors should have performed, or what you think they would perform on their next paper.
  • Using a technique or method the authors didn’t use to study their question or model system.
  • Taking the methods the authors used and applying it to a completely new question.

For the actual presentation, each student will get 10 minutes to present their proposal to the class. As the papers their proposals are based on will have already been covered, it is expected that any background given will be short (1 slide or 1 minute). Experimental details will need to be presented, including strategy, design, and appropriate controls. Predicted results will need to be presented, with interpretation.
Students will get some say in which paper they will base their proposal on, but the instructors will spread out the selections to avoid clustering on one or a few papers.

Written proposal

In line with the oral presentation, each student will write a short 2-3 page proposal to accompany their presentation. The written proposal will be identical to the oral presentation. A draft of the written proposal will be presented to the instructors prior to the oral presentation, who will provide feedback to help shape the proposal. The final proposal will be submitted at the end of the class after the oral presentation.

Evaluation of instructors:

The students’ feedback on the quality of lessons and teachers is a key tool for the continuous improvement of the course. It is compulsory for all students to evaluate their instructors. The evaluation process will be explained by instructors to the students during lesson time.


Please note that the schedule here is not set in stone and may be adjusted depending on circumstances.

1/4/22 Immunometabolism Nicholas
1/6/22Paper discussion 1Nicholas
1/11/22Immune agingWagar
1/13/22Paper discussion 2Wagar
1/18/22New Frontiers of AnalysisKessenbrock
1/20/22Bioengineered Tools for Immunotherapeutic DiscoveryZhao
1/25/22Autoimmunity and autoinflammationVillalta
1/27/22Paper discussion 3 Villalta
2/3/22Paper discussion 4Blurton-Jones
2/8/22Bacterial and fungal immunologyPearlman
2/10/22Paper discussion 5Pearlman
2/15/22Parasite ImmunologyLodoen
2/17/22Paper Discussion 6 Lodoen
2/22/22Viral immunology Tinoco
2/24/22Cancer ImmunologyMarangoni
3/1/22Paper Discussion 7Marangoni
3/3/22Presentation on exam prepInlay
3/8/22Students’ presentations 
3/10/22Students’ presentations 
Finals WeekRemaining presentations, if any.

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