Difference between revisions of "20.109(S18):Journal club presentations (Day6 and 7)"

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.

On both journal club presentation days, we will meet in 16-336 and begin at 1:05 pm sharp. Presenters should arrive early and will be able to check their slides on the large screen.

Method of submission

Please submit your completed Journal club slides on the date of your presentation by 1 pm to Stellar, with filename Name_LabSection_Mod2.pptx (for example, NoreenLyell_TR_Mod2.pptx).

The choice of presentation order will be given to students who submitted their slides earliest.

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.

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 Josephine) 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. Belz, J. E. et al. Sustained release talazoparib implants for localized treatment of BRCA1-deficient breast cancer. (2017) Theranostics. PMID:29158830 [DR/TR/Blue] [KEO/WF/Platinum]
2. 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:29340034 [AM/TR/Orange] [CW/WF/Green]
3. Carey, J. P. W. et al. Synthetic lethality of PARP inhibitors in combination with MYC blockade is independent of BRCA status in triple-negative breast cancer. (2017) Cancer Research. PMID:29180466 [DN/WF/Orange] [IDK/TR/Green]
4. Gorthi, A. et al. EWS-FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma. (2018) Nature. PMID:29513652 [SC/TR/Orange]
5. Hou, M-F. et al. The NuRD complex-mediated p21 suppression facilitates chemoresistance in BRCA-proficient breast cancer. (2017) Experimental Cell Research. PMID:28842166 [SC/TR/Purple]
6. Karakashev, S. et al. BET bromodomain inhibition synergizes with PARP inhibitor in epithelial ovarian cancer. (2017) Cell Reports. PMID:29262321 [JM/TR/White] [CN/WF/Green]
7. Kaverina, N. et al. Astrocytes promote progression of breast cancer metastases to the brain via a KISS1-mediated autophagy. (2017) Autophagy. PMID:28981380 [AG/TR/Green] [CR/WF/Purple]
8. Kolluri, K. K. et al. Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells. (2017) eLife. PMID:29345617 [KH/TR/Pink]
9. Kukolj, E. et al. PARP inhibition causes premature loss of cohesion in cancer cells. (2017) Oncotarget. PMID:29262611 [MM/TR/White] [NM/WF/Pink]
10. 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 [MS/TR/Yellow] [YZ/WF/Red]
11. Liu, Q. et al. PARP-1 inhibition with or without ionizing radiation confers reactive oxygen species-mediated cytotoxicity preferentially to cancer cells with mutant TP53. (2018) Oncogene. PMID:29511347
12. Mao, Y. et al. PARP inhibitor olaparib sensitizes cholangiocarcinoma cells to radiation. (2018) Cancer Medicine. PMID:29479816 [AO/TR/Red][JP/WF/Blue]
13. Nieborowska-Skorska, M. et al. Ruxolitinib-induces defects in DNA repair cause sensitivity to PARP inhibitors in myeloproliferative neoplasms. (2017) Blood. PMID:29042365 [NS/TR/GREY][AA/WF/RED]
14. Osoegawa, A. et al. Rapamycin sensitizes cancer cells to growth inhibition by the PARP ihhibitor olaparib. (2017) Oncotarget. PMID:29152062 [BH/TR/Blue][EW/WF/Purple]
15. Porro, A. et al. FAN1 interaction with ubiquitylated PCNA alleviates replication stress and preserves genomic integrity independently of BRCA2. (2017) Nature Communications. PMID:29051491[ZP/TR/Gray] [AA/WF/Platinum]
16. Yamaguchi, H. et al. EZH2 contributes to the response to PARP inhibitors through its PARP-mediated poly-ADP ribosylation in breast cancer. (2017) Oncogene. PMID:28925391

Computational studies

1. Danza, K. et al. MiR-578 and miR-573 as potential players in BRCA-related breast cancer angiogenesis. (2015) PMID:25333258
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. Hugo, W. et al. Genomic and transcriptomic features of response to anti-PD-1 therapy in metastatic melanoma. (2016) Cell. PMID:26997480 [NG/TR/Purple] [NW/WF/Blue]
4. Lin, K-H. et al. RNA-seq transcriptome analysis of breast cancer cell lines under shikonin treatment. (2018) Scientific Reports. PMID:29422643 [GP/WF/Pink] [SS/TR/Yellow]
5. 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
6. Polak, P. et al. A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer. (2017) Nature Genetics. PMID:28825726 [MT/WF/Orange]
7. 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[JF/WF/Platinum]
8. Wang, Y. et al. Computational investigation of homologous recombination DNA repair deficiency in sporadic breast cancer. (2017) Scientific Reports. PMID:29146938 [NX/TR/Red]
9. 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
10. Zhang, X. et al. Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis. (2017) Nature Communications. PMID:28649985 [MA/TR/Pink]

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.

Presentation day reservation

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

Navigation links

Next day: Induce DNA damage and apply drug treatments for cell viability and identification of regulatory motifs in RNA-seq data