20.109(S20):Journal club presentations (Day4 and 5)

Overview and logistics

You will complete this assignment individually. Please review the 20.109 statement on collaboration and integrity as you proceed.

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.

There are three main parts to this assignment, please review the following information carefully:

Part 1: Though the main goal of this assignment is to critically evaluate published literature and highlight the key findings, there are several important skills that can be learned / developed from the Journal club presentation. For example: presenting in public, creating informative slides, keeping to a time limit, and fielding questions. Unfortunately, it is difficult to entirely recreate this experience in a remote format. Because we still want this assignment to be a useful exercise in verbal communication, everyone will submit a video recording of themselves delivering the Journal club presentation. Please review the options for how to do this below:

*Option 1: Use Zoom

1. Using the Zoom platform you can use the 'Host a Meeting' function to record your presentation.
2. First, select the 'Host a Meeting' dropdown in the top right corner.
3. Then select 'With Video On'.
4. A window will open with the video feed from your computer camera.
5. Click 'Join With Computer Audio'.
6. At the bottom of the window, click 'Share Screen' and select your Journal club presentation slide deck (note: the file needs to be open on your computer), then click 'Share'.
7. To record, scroll over the ID / Stop Share icon at the top of your desktop. A toolbar with options should become visible. Select 'More' and choose 'Record on this Computer. As soon as you select the record tool, the video will start. At the end of your presentation, once again select 'More' and then choose 'Stop Recording'.
8. Note: we want a recording with your face and your slides. If you simply select record without sharing the slides, the video will only have your face.

*Option 2: Use a video recording device

1. For this you can use any device that is capable of recording video (phone, camcorder, etc.).
2. In the video both the presenter and the slides should be visible. If possible, you can show your slides from a television or larger computer monitor...if not, you can simply sit next to your computer and show the slides on the screen.

Using either option, it is helpful when the presenter interacts with the slides. Via Zoom, you can use the cursor or if using a recording device / computer you can use your finger to ensure the audience is directed to important information on the slides.

If neither option is feasible, please contact Noreen as soon as possible so we can brainstorm alternate strategies!

Part 2: In addition to presenting a Journal article, you will also watch presentations completed by your peers. In addition to the skills mentioned above that can be developed by presenting research, there are also skills that can be developed by actively listening to presented research. Therefore, the second part of this assignment is to watch two presentations (Instructors will assign which recordings each student should watch) and formulate two scientifically-based questions for each presenter. Questions can ask for additional information regarding certain procedures / methods, ask for more context regarding the research focus, or ask about the implications of the research...or anything else that you find interesting from the presentation!

Part 3: Lastly, each student will meet one-one-one with Noreen to review and discuss the presentation. During this time you will watch your own recorded presentation and answer the questions written by your peers and those from the Instructors.

Method of submission

Please submit your completed recorded Journal club presentation due by Saturday, April 11th at 10 pm to the class Dropbox folder (link to be shared by Noreen), with filename Name_LabSection_JC (for example, NoreenLyell_JC_MP).

You will submit your completed Journal club slides due by Saturday, April 11th at 10 pm to Stellar, with filename Name_LabSection_JCslides.pptx (for example, NoreenLyell_TR_JCslides.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 for a 10-minute presentation. For longer presentations, the slide count and proposed times may be increased proportionally.

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>[EF/WF/Purple]</b></font color>, which will look like [EF/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.
• The same paper may be presented by a T/R and a W/F student, but may only be presented once per section.

Biological studies

1. Brill, E. et al. “Prexasertib, a cell cycle checkpoint kinases 1 and 2 inhibitor increases in vitro toxicity of PARP inhibition by preventing Rad51 foci formation in BRCA wild type high-grade serous ovarian cancer.” (2017) Oncotarget. PMID:29158830[WZ/WF/Orange][AM/TR/Yellow]
2. Cedemaes, J. et al. “Transcriptional Basis for Rhythmic Control of Hunger and Metabolism within the AgRP Neuron.” (2019). Cell Metabolism. PMID:30827863 [AT/TR/Blue] [AM/WF/Blue]
3. Chen, J. et al. “Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model.” (2019). Scientific Reports. PMID: 30872643[IA/WF/Pink] [IN/TR/Red][LB/TR/Blue]
4. Cheng, Y. et al. “Hydro-Seq enables contamination-free high throughput single-cell RNA-sequencing for circulating tumor cells.” (2019). Nature Communications. PMID: 31092822[KD/WF/Purple]
5. de Lima, D. et al. “Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination. (2019).” PNAS. PMID: 31399544 [CO/WF/Purple] [MW/TR/White]
6. Demircioglu, D. et al. “A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.” (2019). Cell. PMID: 31491388 [MM/TR/Pink]
7. Everaert, C. et al. “Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles (2019).” Scientific Reports. PMID: 31772251 [CA/WF/Green]
8. Gorthi, A. et al. “EWS-FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma.” (2018) Nature. PMID:29513652 [CH/TR/White][LC/WF/Green]
9. Kaverina, N. et al. “Astrocytes promote progression of breast cancer metastases to the brain via a KISS1-mediated autophagy.” (2017) Autophagy. PMID:28981380 [CM/TR/orange] [KG/WF/White]
10. Kolluri, K. K. et al. “Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells.” (2017) eLife. PMID:29345617 [AN/WF/Yellow]
11. Lemacon, D. et al. “MRE11 and EXO1 nucleases degrade reversed forks and elicit MUS81-dependent fork rescue in BRCA2-deficient cells.” (2017) Nature Communications. PMID:29038425 [OL/TR/Yellow]
12. Porro, A. et al. “FAN1 interaction with ubiquitylated PCNA alleviates replication stress and preserves genomic integrity independently of BRCA2.” (2017) Nature Communications. PMID:29051491
13. Shi, L. et al. “Transcriptome profile of rat genes in injured spinal cord at different stages by RNA-sequencing.” (2017). BMC Genomics. PMID: 28201982 [DH/TR/Purple] [EX/WF/Yellow]
14. Subhash, S. et al. “Transcriptome-wide Profiling of Cerebral Cavernous Malformations Patients Reveal Important Long noncoding RNA molecular signatures.” (2019). Scientific Reports. PMID: 31796831 [RB/WF/Orange] [EF/TR/GREY]
15. Wang, C. et al. “PTEN deletion drives aberrations of DNA methylome and transcriptome in different stages of prostate cancer.” (2019). FASEB J. PMID: 31914691 [JP/TR/Pink]
16. Wang, C. “Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae.” (2019). Scientific Reports. PMID: 30842619 [JG/WF/Red]

Computational studies

1. Feng, D. et al. “Single Cell Explorer, collaboration-driven tools to leverage large-scale single cell RNA-seq data.” (2019). BMC Genomics. PMID: 31455220[HH/TR/Green]
2. Forootan, S. S. et al. Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications. (2016) International Journal of Oncology. PMID:26530297
3. Lin, K-H. et al. RNA-seq transcriptome analysis of breast cancer cell lines under shikonin treatment. (2018) Scientific Reports. PMID:29422643 [EH/WF/Silver] [MY/TR/Green]
4. Nieborowska-Skorska, M. et al. Gene expression and mutation-guided synthetic lethality eradicates proliferating and quiescent leukemia cells. (2018) The Journal of Clinical Investigation. PMID:28481221[KL/WF/Red]
5. Polak, P. et al. A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer. (2017) Nature Genetics. PMID:28825726 [KB/WF/Blue]
6. Suchorska, W. M. et al. Comparison of the early response of human embryonic stem cells and human induced pluripotent stem cells to ionizing radiation. (2017) Molecular Medicine Reports. PMID:28259963 [SA/WF/silver] [SG/TR/red]
7. Wang, Y. et al. Computational investigation of homologous recombination DNA repair deficiency in sporadic breast cancer. (2017) Scientific Reports. PMID:29146938 [MJ/TR/Purple]
8. Wei, L. et al. Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts. (2016) Oncotarget. PMID:27823983 [DE/TR/Grey]
9. Zhang, X. et al. Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis. (2017) Nature Communications. PMID:28649985

If the links below do not work, the easiest way to locate each paper is to type the "PMID" (PubMed identifier) in at the PubMed website. If that approach gives you an error for some reason, or in future cases where you might not know the PMID, you can try typing the title of your article into PubMed to find it. If you have trouble accessing your article directly from there, go to http://libraries.mit.edu/vera, which is MIT's collection of journals online. Try selecting "exact title" from the search pulldown menu if the name of your journal is a common word such as Science. For older articles, you need to choose the JSTOR rather than Highwire interface.

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