Point of View: Teaching troubleshooting skills to graduate students

  1. Gina Partipilo
  2. Yang Gao
  3. Alexis J Holwerda
  4. Yassir Lekbach
  5. Ismar E Miniel Mahfoud
  6. Trevor R Simmons
  7. Bailey M Tibbett
  8. Rebecca E Wilen
  9. Marcus S Benyamin
  10. Benjamin K Keitz  Is a corresponding author
  1. McKetta Department of Chemical Engineering, University of Texas at Austin, United States
  2. Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, United States
2 figures, 1 table and 1 additional file

Figures

How Pipettes and Problem Solving works.

The leader presents a scenario in which a hypothetical experiment has produced unexpected results. Graduate students ask questions about the experimental setup and the results. The students then discuss the scenario and potential experiments that might help to isolate the problem that has caused the unexpected results. Once they have reached a consensus on a suitable experiment, the leader reveals the results of their proposed experiment. Based on these results, the students try to figure out the source of the problem that is leading to the unexpected results. If they are correct, the exercise is over. If they are wrong, the cycle can be repeated. Elements of luck or chance can be introduced by rolling dice to determine, for example, any time or budget constraints on the proposed experiments. The Pipettes and Problem Solving logo (top right) was designed by students.

Asking the right questions.

The aim of Pipettes and Problem Solving is to teach graduate students how to troubleshoot experiments that are giving unexpected results. To achieve this goal students are encouraged to ask questions that will help them to design experiments that will help them to identify the source of the problem (first column). They are not allowed to guess the problem, or to suggest ways of working around the problem (second column).

Tables

Table 1
Resources for the eight scenarios listed in this table are provided in Supplementary file 1.

The following is provided for each scenario: background information; a description of the scenario; the protocol for the experiment that produced the unexpected result; the results of the experiment; information on the source of the error; background information that can be used to answer questions; references; and example slides that can be used in real meetings.

ScenarioKey words1/2/mundane
MTT assayMammalian cell biology; cytotoxicity; analytical chemistry1
Membrane surface chargeSynthetic biology; bioelectronics; imaging electrochemical devices2
Streptavidin-conjugation assayAntibody; molecular biology; biochemistry; immunology1
Golden gate cloningCloning; Golden Gate assembly; PCR; primers; synthetic biology2
Recombinant quorum sensing expression and activity verificationquorum sensing; synthetic biology; plasmid cloning structural biology2
Gibson cloning troublesSynthetic biology; Gibson assembly; genetic engineeringMundane
T cell cytokine release ELISAMammalian cell biology; T cell activation; cytokine release1
Metabolite tracking by aqueous FTIR spectroscopyFourier transform infrared (FTIR) spectroscopy; analytical chemistry; synthetic biology1

Additional files

Supplementary file 1

Resources for the eight scenarios listed in Table 1 (zip file).

For each scenario there is a Word file that contains the following: background information; a description of the scenario; the protocol for the experiment that produced the unexpected result; the results of the experiment; information on the source of the error; background information that can be used to answer questions; and references. There is also a PowerPoint file for each scenario that contains example slides that can be used in real meetings. There are also templates for the Word and PowerPoint files.

https://cdn.elifesciences.org/articles/100761/elife-100761-supp1-v1.zip

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  1. Gina Partipilo
  2. Yang Gao
  3. Alexis J Holwerda
  4. Yassir Lekbach
  5. Ismar E Miniel Mahfoud
  6. Trevor R Simmons
  7. Bailey M Tibbett
  8. Rebecca E Wilen
  9. Marcus S Benyamin
  10. Benjamin K Keitz
(2024)
Point of View: Teaching troubleshooting skills to graduate students
eLife 13:e100761.
https://doi.org/10.7554/eLife.100761