20.109(S21):Journal club presentation

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20.109(S21): Laboratory Fundamentals of Biological Engineering

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Spring 2021 schedule        FYI        Assignments        Homework        Communication |        Accessibility

       M1: Antibody engineering        M2: Drug discovery        M3: Protein engineering       

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 mini-presentation 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, 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 Instructors (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. Afroz, et. al. "Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathogenic aggregation." (2017) Nat. Commun. 8:45. doi:10.1038/s41467-017-00062-0. [VM/TR/Yellow]
  2. Archbold, et. al. "TDP43 nuclear export and neurodegeneration in models of amyotrophic lateral sclerosis and frontotemporal dementia." (2018) Sci. Rep. 8:4604. doi:10.1038/s41598-018-22858-w.[RB/TR/Blue]
  3. Ash, et. al. "Dioxins and related environmental contaminants increase TDP-43 levels." (2017) Mol. Neurodegen. 12:35. doi:10.1186/s13024-017-0177-9. [OL/TTh/Red]
  4. Ash, et. al. "Heavy metal neurotoxins induce ALS-linked TDP-43 pathology." (2019) Tox. Sci. 167:105-115. doi:10.1093/toxsci/kfy267. [CL/TR/Yellow][VD/WF/Purple]
  5. Becker et. al. "Therapeutic reduction of ataxin-2 extends lifespan and reduces pathology in TDP-43 mice." (2017) Nature. 544:367-371. doi:10.1038/nature22038. [LSH/TR/Orange]
  6. Chen, et. al. "RRM adjacent TARDBP mutations disrupt RNA binding and enhance TDP-43 proteinopathy." (2019) Brain. 142:3753-3770. doi:10.1093/brain/awz313.[LP/WF/Pink]
  7. Chen, et. al. "Aggregation of the nucleic acid-binding protein TDP-43 occurs via distinct routes that are coordinated with stress granule formation." (2019) J. Biol. Chem. 294:3696-3706. doi:10.1074/jbc.RA118.006351. [AW/TR/Teal]
  8. Davis, et. al. "TDP-43 interacts with mitochondrial proteins critical for mitophagy and mitochondrial dynamics." (2018) Neurosci. Lett. 678:8-15. doi:10.1016/j.neulet.2018.04.053. [MW/TTh/Red]
  9. Flores, et. al. "An intramolecular salt bridge linking TDP43 RNA binding, protein stability, and TDP43-dependent neurodegeneration." (2019) Cell Rep. 27:1133-1150. doi:10.1016/j.celrep.2019.03.093. [BM/WF/Red] [CC/TR/Blue]
  10. French, et. al. "Detection of TAR DNA-binding protein 43 (TDP-43) oligomers as initial intermediate species during aggregate formation." (2019) J. Biol. Chem. 294:6696-6709. doi:10.1074/jbc.RA118.005889. [SC/WF/Teal]
  11. Gao, et. al. "TDP-43 inhibitory peptide alleviates neurodegeneration and memory loss in an APP transgenic mouse model for Alzheimer's disease." (2020) Mol. Basis Dis. 1866:165580. doi:10.1016/j.bbadis.2019.165580. [JW/TR/Orange] [VW/WF/Teal]
  12. Hawley, et. al. "Evidence of a negative feedback network between TDP-43 and miRNAs dependent on TDP-43 nuclear localization." (2020) J. Mol. Biol. 432:166695. doi:10.1016/j.jmb.2020.10.029. [ML/WF/Orange]
  13. Herzog, et. al. "TDP-43 dysfunction restricts dendritic complexity by inhibiting CREB activation and altering gene expression." (2020) Proc. Natl. Acad. Sci. 117:11760-11769. doi:10.1073/pnas.1917038117.[MH/TR/Green] [SB/WF/Blue]
  14. Konopka, et. al. "Impaired NHEJ repair in amyotrophic lateral sclerosis is associated with TDP-43 mutations." (2020) Mol. Neurodegen. 15:51. doi:10.1186/s13024-020-00386-4.[LC/TR/Pink] [VH/WF/Green]
  15. Morera, et. al. "TDP-43 regulates transcription at protein-coding genes and Alu retrotransposons." (2019) Gene Reg. Mech. 1862:194434. doi:10.1016/j.bbagrm.2019.194434.[SK/WF/RED] [AP/TR/Purple]
  16. Neelagandan, et. al. "TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease." (2018) Nuc. Acids Res. 47:341-361. doi:10.1093/nar/gky972. [CT/TR/Red]
  17. Ormeno, et. al. "Chaperone mediated autophagy degrades TDP-43 protein and is affected by TDP-43 aggregation." (2020) Front. Mol. Neurosci. 13:19. doi:10.3389/fnmol.2020.00019. [DF/WF/Yellow]
  18. Paez-Colasante, et. al. "Cytoplasmic TDP43 binds microRNAs: new disease targets in amyotrophic lateral sclerosis." (2020) Front. Cell. Neurosci. 14:117. doi:10.3389/fncel.2020.00117. [IS/TR/Green]
  19. Pozzi, et. al. "Virus-mediated delivery of antibody targeting TAR DNA-binding protein-43 mitigates associated neuropathology." (2019) J. Clin. Invest. 129:1581-1595. doi:10.1172/JCI123931. [SS/TR/Teal] [MLA/WF/Yellow]
  20. Pozzi, et. al. "Monoclonal full-length antibody against TAR DNA binding protein 43 reduces related proteinopathy in neurons." (2020) JCI Insight. 5:e140420. doi:10.1172/jci.insight.140420. [AW/WF/Pink]
  21. Sanna, et. al. "HDAC1 inhibition ameliorates TDP-43-induced cell death in vitro and in vivo." (2020) Cell Death Dis. 11:369. doi:10.1038/s41419-020-2580-3. [EL/TR/Pink].
  22. Shih, et. al. "TDP-43 interacts with amyloid-β, inhibits fibrillization, and worsens pathology in a model of Alzheimer's disease." (2020) Nat. Commun. 11:5950. doi:10.1038/s41467-020-19786-7. [LL/TR/Purple] [SH/WF/Purple].
  23. Velebit, et. al. "Astrocytes with TDP-43 inclusions exhibit reduced noradrenergic cAMP and Ca2+ signaling and dysregulated cell metabolism." (2020) Sci. Rep. 10:6003. doi:10.1038/s41598-020-62864-5.
  24. Vogt, et. al. "TDP-43 induces p53-mediated cell death of cortical progenitors and immature neurons." (2018) Sci. Rep. 8:8097. doi:10.1038/s41598-018-26397-2. [HF/TTh/Purple] [AV/WF/Blue]
  25. Wang, et. al. "TDP-43 induces mitochondrial damage and activates the mitochondrial unfolded protein response." (2019) PLOS Gen. 15:e1007947. doi:10.1371/journal.pgen.1007947. [KE/WF/Orange]
  26. Wood, et. al. "TDP-43 dysfunction results in R-loop accumulation and DNA replication defects." (2020) J. Cell Sci. 133:jcs244129. doi:10.1242/jcs.244129. [AD/WF/Green]

Presentation day reservation

Please put your name under the day you wish to present. The order here does not determine speaker order.

Slot Tuesday, April 6 (T/R section) Wednesday, April 7 (W/F section) Thursday, April 8 (T/R section) Friday, April 9 (W/F section)
1 Alex Poret Seung Hyun Kim Louise Lima Selam Bulti
2 Melissa Hummel Kanoe Evile Laura Schmidt-Hong Daphne Faber
3 Emily Larson Marcos Labrado Jennifer Wen Luci Padilla
4 Charles Coffey Marissa Abbott Carly Long Vladlena Hornet
5 Amber Williams Veronica Will Mary Woo Alexandra Wolff
6 Isabella Salinas Victor Damptey Rami Bikdash Abby VanLonkhuyzen
7 Vainavi Mukkamala Seung Hyeon Shim Christina Ta Sophia Chen
8 Haley Fernandez Bhuvna Murthy Olivia Lucchese Anna Dawson
9 Lauren Castle Shruthi Shekar