20.109(F17):Journal club II (Day 6)

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20.109(F17): Laboratory Fundamentals of Biological Engineering

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       1. Measuring Genomic Instability        2. Manipulating Metabolism        3. Engineering Biomaterials              

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 Oral communication guidelines on the Communication page. In addition, please use the following link to view the full video from Susan McConnell: Designing effective scientific presentations

Selecting an article to present

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 (last name/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 last name and team color: <font color = purple><b>[Lyell/WF/Purple]</b></font color>, which will look like [Lyell/WF/Purple]. Thanks!
  • If you would like to discuss a paper not on the list below, please email it (as .pdf) to your instructor 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.

Method of submission

Please submit your completed slides on Stellar, with filename LastName_LabSection_Mod2JC.doc (for example, Lyell_TR_Mod2JC.pptx).

Your journal club slides are due by 1 pm on the day of your presentation.

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

Length and location 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.

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.

Journal article options

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.

Deciphering the CRISPR system

  1. Alkhnbashi et al. Characterizing leader sequences of CRISPR loci. (2016) Bioinformatics. PMID: 27587677 [Tseng/WF/Orange]
  2. Anderson et al. Systematic analysis of CRISPR-Cas9 mismatch tolerance reveals low levels of off-target activity. (2015) Biotechnol. PMID: 26189696 [Freitas/WF/Red] [Jaicks/TR/Red]
  3. Bondy-Denomy et al. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. (2013) Nature. PMID: 23242138 [Gramatikov/WF/Red] [Frombach/TR/Orange]
  4. Hochstrasser et al. DNA targeting by a minimal CRISPR RNA-guided cascade. (2016) Mol. Cell. PMID: 27588603 [Gomez/WF/Orange][Lampejo/TR/Green]
  5. Ma et al. CRISPR-Cas9 nuclear dynamics and target recognition in living cells. (2016) J. Cell Bio. PMID: 27551060 [Osorio/WF/Blue][Gong/TR/Pink]
  6. Majumdar et al. Target DNA recognition and cleavage by a reconstituted Type I-G CRISPR-Cas immune effector complex. (2016) Extremophiles. PMID: 27582008 [Mulugeta/TR/Green]
  7. Reimann et al. Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs. (2016) Nuc. Acids Res. PMID: 2759984
  8. Sashital et al. Mechanism of foreign DNA selection in a bacterial adaptive immune system. (2012) Mol. Cell. PMID: 22521690 [Noel/TR/Orange] [Tyler/WF/Blue]
  9. Westra et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas9. (2012) PMID: 22521689 [Martinez/TR/Pink]
  10. Zhang et al. Structure and mechanism of the CMR Complex for CRISPR-mediated antiviral immunity. (2012) Mol. Cell"PMID: 22227115 [Nasser/TR/Purple]

Developing and using CRIPSR-based tools

  1. Chew et al. A multifunctional AAV-CRISPR-Cas9 and its host response. (2016) Nat. Meth. PMID: 27595405 [Etwarooah/TR/White]
  2. deSolis et al. The development of a viral mediated CRISPR/Cas9 system with doxycycline dependent gRNA expression for inducible in vitro and in vivo genome editing. (2016) Front. Mol. Neurosci. PMID: 27587996 [Shafquat/TR/Blue]
  3. Jain et al. Development of light-activated CRISPR using guide RNAs with photocleavable protectors. (2016) Angew. Chem. Int. Ed. Engl. PMID: 27554600 [Mamat/TR/White]
  4. Liu et al. Efficient CRISPR/Cas9-mediated versatile, predictable, and donor-free gene knockout in human pluripotent stem cells. (2016) Stem Cell Rep. PMID: 27594587
  1. Liu et al. Directing cellular information flow via CRISPR signal conductors. (2016) Nat. Meth. PMID: 27595406
  2. Narayanan et al. In vivo mutagenesis of miRNA gene families using a scalable multiplexed CRISPR/Cas9 nuclease system. (2016) Sci. Rep. PMID: 27572667
  3. Ou et al. The combination of CRISPR/Cas9 and iPSC technologies in the gene therapy of human β-thalassemia in mice. (2016) Sci. Rep. PMID: 27581487 [Kumar/TR/Blue]
  4. Perli et al. Continuous genetic recording with self-targeting CRISPR-Cas in human cells. (2016) Science. PMID: 27540006
  5. Sasano et al. CRISPR-PCS: a powerful new approach to inducing multiple chromosome splitting in Saccharomyces cerevisiae. (2016) Sci. Rep. PMID: 27530680 [Lutz/TR/Purple] [Yu/WF/Green]
  6. Zhang et al. Efficient production of gene-modified mice using Staphylococcus aureus Cas9. (2016) Sci. Rep. PMID: 27586692[Boyer/TR/yellow]

Presentation day reservation

Please put your name under the day you wish to present. There are up to 6 slots on each day. Slot location does not determine speaker order.

Slot Day 4 (T/R) Day 6 (T/R) Day 4 (W/F) Day 6 (W/F)
1 Rebecca N. Ravenne N. Max F. Iva G.
2 Julia G. Madiha S. Hanna T. Isabella G.
3 Chris J Kristen F. Fei Y. Tyler W.
4 Isaac L. Nolawit M. Daniel O.
5 Shalni Arin L. N/A N/A
6 Steven Truong Riana Hoagland N/A N/A
7 Yun Boyer Zulkayda M. N/A N/A
8 Emma G. Zehreen E. N/A N/A
9 Anna M N/A

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