20.109(S22):Journal club presentation

From Course Wiki
Jump to: navigation, search
20.109(S22): Laboratory Fundamentals of Biological Engineering

Sp17 20.109 M1D7 chemical structure features.png

Spring 2022 schedule        FYI        Assignments        Homework        Class data        Communication        Accessibility

       M1: Drug discovery        M2: Metabolic engineering        M3: Project design       

Overview and logistics

You will complete this assignment individually.

Please review the 20.109 statement on collaboration and integrity as you proceed.

In Module 1, you delivered a Research talk that was focused on your research project. For this assignment, you will present work completed by other scientists that has been peer-reviewed and published. Reading, understanding, and explaining research related to your project are all important skills that will be important as you flex your scientist muscles.

As you prepare your talk be sure to review the resources provided on the Communication tab. In addition, please use the following link to view the full video from Susan McConnell: Designing effective scientific presentations. Lastly, review the Journal club presentation Evaluation rubric (linked here)!

Method of submission

Please submit your completed Journal club slides 1 hr prior to your scheduled laboratory session time to Stellar, with filename Name_LabSection_JC.pptx (for example, ImaStudent_TR_JC.pptx).

Length and format of presentations

You will have 10 minutes to discuss the journal article you select. It may be very difficult, or impossible, to discuss all of the figures within the article adequately in only 10 minutes. Therefore, this assignment is not only to present the work, but also to identify the data that is most important to the conclusions. It is also critical to consider how your presentation 'flows' from one experiment to the next. As when you write your own research, you want to deliver a coherent story during your journal presentation.

Format considerations

The timing provided here is a guideline for a 10-minute presentation. Your presentation may vary depending on the content.

Section Minutes Number of slides DO DON'T
Introduction ~2 2-3
  • Introduce the key concepts that the audience will need to follow your presentation.
  • Briefly state the overall scope and significance of the study -- what is the central question and why is it interesting?
  • Try to summarize background material with a model slide rather than lines of text. If text is needed, bring in the details as you speak using PowerPoint animation.
  • Don't assume you are addressing an expert audience.
  • Don't give more information than is absolutely needed to understand the rest of your talk.
  • Don't put too much information on each slide.
Data ~7 4-6
  • Present the data in a logical sequence, letting each slide build upon the previous ones.
  • Include a title for each slide. The title should be the conclusion and should be unique to the information on the slide.
  • Make every element of your slide visible to the entire room. This means 20-point font or greater.
  • Interpret each slide thoroughly and carefully.
  • Point out strengths and weaknesses of the data along the way.
  • Don't read your talk. Similarly, do not read lists from slides.
  • Don't put much information on each slide. Each slide should make only one point.
  • Never say, "I know you can't read this, but...". Everything on each slide should be legible.
  • Don't be afraid to remind the audience how the data fits into the overall question
Summary ~1 1
  • Review each of your main messages.
  • Clearly state what the study contributed to the field.
  • Don't repeat experimental details.
Question & Answer ? 0
  • Answer the question being asked. If you are unclear about the question, ask for clarification.
  • Respect every question and questioner.
  • Don't take too long with one question. If the discussion is involved, suggest meeting after the talk to discuss it more.

Helpful hints

  • A 10-minute talk is NOT a 30-minute talk given while racing through slides and speaking very quickly.
  • Consider ways to transition from one slide to the next to ensure the information is tied together.
  • Practice your presentation in front of people rather than in a room by yourself and practice several times!
  • Familiarize yourself with using a laser pointer and/or slide changer if you will use one during the actual presentation.
  • If you do choose to use a pointer, use it to direct attention to specific elements on the screen, rather than constantly gesturing in the general vicinity of your slide; otherwise, the audience will not know what's important. When you later make your own slides and figures, the apparent need for a pointer may actually mean you need to make a clearer slide.

Article selection

You may choose to select a journal article from those provided by the teaching faculty or you can select an article that is related to your Module 2 research from any peer-reviewed journal.

  • If you choose an article from below, please "reserve" it by putting your (initials/lab section/team color) next to the listing here.
    • For visibility, please use the following format to sign up if possible, substituting in your own initials and team color: <font color = purple><b>[IS/WF/Purple]</b></font color>, which will look like [IS/WF/Purple]. Thanks!
  • If you would like to discuss a paper not on the list below, please email it (as .pdf) to the teaching faculty (Noreen, Leslie, and Becky) with a brief description of the work.
    • The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You are not limited to the primary research articles on this list. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Feel free to search PubMed yourself to find articles of interest to you.

Please review the articles before making your final selection to ensure it is a paper that you find interesting and that you are comfortable presenting!

  1. Birkholz et. al. The autoregulator Aca2 mediated anti-CRISPR repression. (2019) Nucleic Acids Research. PMID: 31428783
  2. Degrief et. al. Preloading budding yeast with all-in-one CRIPSR/Cas9 vectors for easy and high-efficient genome editing. (2018) Journal of Biological Methods. PMID: 31453248
  3. Dong et. al. Systematic immunotherapy target discovery using genome-scale in vivo CRISPR screens in CD8 T cells. (2019) Cell. PMID: 31442407 [ET/TR/Blue]
  4. English et. al. Programmable CRISPR-responsive smart materials. (2019) Biomaterials. PMID: 31439791 [AZ/TR/Red] [SA/WF/Pink]
  1. Grunewald et. al. CRISPR DNA base editors with reduced RNA off-target and self-editing activities. (2019) Nature Biotechnology. PMID: 31477922 [IG/TR/Yellow] [RK/WF/Purple]
  2. Guoling et. al. A Cas9-transcription factor fusion protein enhances homology-directed repair efficiency. (2021) Journal of Biological Chemistry. PMID: 33689695 [LB/TR/Green] [VY/WF/White]
  3. Hanewich-Hollatz et. al. Conditional guide RNAs: a programmable conditional regulation of CRISPR/Cas function in bacterial and mammalian cells via dynamic RNA nanotechnology. (2019) ACS Central Science. PMID: 31403072 [MG/TR/Purple][HD/WF/Red]
  4. Hochrein et. al. High-performance allosteric conditional guide RNAs for mammalian cell-selective regulation of CRISPR/Cas. (2021) American Chemical Society Synthetic Biology. PMID: 33930275
  5. Hu et. al. Label-free CRISPR/Cas9 assay for site-specific nucleic acid detection. (2019) Analytical Chemistry. PMID: 31340642
  6. Jain et. al. Precise regulation of Cas9-mediated genome engineering by anti-CRISPR-based inducible CRISPR controllers. (2021) American Chemical Society Synthetic Biology. PMID: 34006094[KS/WF/Green]
  7. Kang et. al. Regulation of gene expression by altered promoter methylation using a CRISPR/Cas9-mediated epigenetic editing system. (2019) Nature Research. PMID: 31427598 [ZP/TR/Red]
  8. Kim et. al. Efficient CRISPR-Cas9-based knockdown of RUNX2 to induce chondrogenic differentiation of stem cells. (2022) Biomaterials Science. PMID: 34904600 [LZ/WF/Blue]
  9. Liang et. al. A CRISPR-Cas12a-derived biosensing platform for the highly sensitive detection of diverse small molecules. (2019) Nature Communications. PMID: 31413315 [SD/TR/Teal] [FO/WF/Blue]
  10. Liu et. al. Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria. (2019) Nature Communications. PMID: 31451697
  11. Matsuda et. al. Optimized CRISPR/Cas9-mediated in vivo genome engineering applicable to monitoring dynamics of endogenous proteins in the mouse neural tissues. (2019) Nature Research. PMID: 31383899 [YC/TR/Blue] [EL/WF/Orange]
  12. Nandy et. al. Heat-shock-inducible CRISPR/Cas9 system generates heritable mutations in rice. (2019) Plant Direct.[KK/TR/White]PMID: 31404128
  13. Nihongaki et. al. A split CRISPR-Cpf1 platform for inducible genome editing and gene activation. (2019) Nature Chemical Biology. PMID: 31406371 [SK/WF/Pink]
  14. Ratner et. al. Catalytically active Cas9 mediates transcriptional interference to facilitate bacterial virulence. (2019) Molecular Cell. PMID: 31439791 [SR/TR/Gray]
  15. Soto-Perez et. al. CRISPR-Cas system of a prevalent human gut bacterium reveals hyper-targeting against phages in a human virome catalog. (2019) Cell Host & Microbe. PMID: 31492655 [AM/WF/Yellow][SP/TR/Gray]
  16. Stanley et. al. Anti-CRISPR-associated proteins are crucial repressors of anti-CRISPR transcription. (2019) Cell. PMID: 31474367 [MS/TR/Purple] [SL/WF/Purple]
  17. Tuladhar et. al. CRISPR-Cas9-based mutagenesis freqently provokes on-target mRNA misregulation. (2019) Nature Communications. PMID: 31492834
  18. Wang et. al. Cas12aVDet: a CRISPR/Cas12a-based platform for rapid and visual nucleic acid detection. (2019) Analytical Chemistry. PMID: 31460749 [BMW/TR/White] [MR/WF/Red]
  19. Wang et. al. CRISPR-mediated live imaging of genome editing and transcription. (2019) Science. PMID: 31488703 [GS/TR/Green] [DW/WF/White]
  20. Xiong et. al. Supramolecular CRISPR-OFF switches with host-guest chemistry. (2022) Nucleic Acids Research. PMID: 35100423 [AA/TR/Yellow]
  21. Yan et. al. Highly efficient temperature inducible CRISPR-Cas9 gene targeting in Drosophila suzukii. (2021) International Journal of Molecular Science. PMID: 34201604 [MH/TR/Orange] [ZG/WF/Green]
  22. Young et. al. A CRISPR platform for targeted in vivo screens identifies Toxoplasms gondii virulence factors in mice. (2019) Nature Communications. PMID: 31481656
  23. Zhang et. al. Increasing yield potential through manipulating of an ARE1 ortholog related to nitrogen use efficiency in wheat by CRISPR/Cas9. (2021) Journal of Integrative Plant Biology. PMID: 34270164 [AP/TR/Purple] [VB/WF/Yellow]
  24. Zhou et. al. Cas9 deactivation with photocleavable guide RNAs. (2021) Molecular Cell. PMID: 33662274 [JL/TR/Orange] [SK/WF/Orange]