20.109(F15):Journal Club II (Day8)

From OpenWetWare
Jump to navigationJump to search

20.109(F15): Laboratory Fundamentals of Biological Engineering

20109 F15 TestImage.png

Home        People        Schedule Fall 2015        Assignments        Homework        Lab Basics        Wiki Basics       
DNA Engineering        Protein Engineering        Biomaterials Engineering              

Overview and logistics

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 follow the specific guidelines for oral presentations in this class.

You will complete this assignment individually.

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 (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>[ANS/WF/Purple]</b></font color>, which will look like [ANS/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 Name_LabSection_Mod2JC.doc (for example, NoreenLyell_TR_Mod2JC.doc).

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

  • The order in which your presentations are received will be the order of speakers.

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 1:15 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.

Developing and examining calcium sensors

  1. Robin, J. et al. Differential nanosecond protein dynamics in homologous calcium sensors. (2015) ACS Chem Biol epub ahead of print. PMID:26204433
  2. Cai, B. et al. A cell-based functional assay using a green fluorescent protein-based calcium indicator dCys-GCaMP. (2014) Assay Drug Dev Tech 12:342-351. PMID:25105973
  3. Wu, J. et al. Red fluorescent genetically encoded Ca2+ indicators for use in mitochondria and endoplasmic reticulum. (2014) Biochem J 464:13-22. PMID:25164254
  4. Chen, T. et al. Ultrasensitive fluorescent proteins for imaging neuronal activity. (2013) Nature 499:295-302. PMID:23868258
  5. Tian, L. et al. Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. (2009) Nature Meth 6:875-884. PMID:19898485
  6. Ackerboom, J. et al. Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics. (2013) Front Mol Neurosci 6:eCollection. PMID:23459413
  7. Muto, A. et al. Genetic visualization with an improved GCaMP calcium indicator reveals spatiotemporal activation of the spinal motor neurons in zebrafish. (2011) PNAS 108:5425-5430. PMID:21383146
  8. Gee, J. et al. Imaging activity in astrocytes and neurons with genetically encoded calcium indicators following in utero electroporation. (2015) Front Mol Neurosci 15:eCollection. PMID:25926768
  9. Fosque, B. et al. Labeling of active neural circuits in vivo with designed calcium integrators. (2015) Science 13:755-760. PMID:25678659
  10. Inoue, M. et al. Rational design of a high-affinity, fast, red calcium indicator R-CaMP2. (2015) Nature Meth 12:64-70. PMID:25419959
  11. Cui, G. et al. Deep brain optical measurements of cell type-specific neural activity in behaving mice. (2014) Nat Protoc 9:1213-1228. PMID:24784819
  12. Miyamoto, A. et al. Optimal microscopic systems for long-term imaging of intracellular calcium using a ratiometric genetically-encoded calcium indicator. (2013) Biochem Biophys Res Commun 434:252-257. PMID:23535376

Using calcium sensors in biological systems

  1. Muto, A. et al. Real-time visualization of neuronal activity during perception. (2013) Curr Biol 23:307-311. PMID:23375894
  2. Luongo, F. et al. Putative microcircuit-level substrates for attention are disrupted in mouse models of autism. (2015) Biol Psych epub ahead of print. PMID:26022075
  3. Tang, W. et al. Stimulation-evoked Ca2+ signals in astrocytic processes at hippocampal CA3-CA1 synapses of adult mice are modulated by glutamate at ATP. (2015) J Neurosci 35:3016-3021. PMID:25698739
  4. Esterberg, R. et al. Disruption of intracellular calcium regulation is integral to aminoglycoside-induced hair cell death. (2013) J Neurosci 33:7513-7525. PMID:23616556
  5. Vanni, M. P. et al. Mesoscale transcranial spontaneous activity mapping in GCaMP3 transgenic mice reveals extensive reciprocal connections between areas of somatomotor cortex. (2014) J Neurosci 34:15931-15946. PMID:25429135
  6. Rothermel, M. et al. Functional imaging of cortical feedback projections to the olfactory bulb. (2014) Front Neur Cir 8:eCollecion. PMID:25071454
  7. Weitz, A. C. et al. Imaging the response of the retina to electrical stimulation with genetically encoded calcium indicators. (2013) J Neurophysiol 109:1979-1988. PMID:23343890
  8. Tang, P. et al. In vivo two-photon imaging of axonal dieback, blood flow, and calcium influx with methylprednisolone therapy after spinal cord injury. (2015) Sci Rep epub ahead of print. PMID:25989524
  9. Cui, G et al. Concurrent activation of striatal direct and indirect pathways during action initiation. (2013) Nature 494:238-242. PMID:23354054
  10. Boesmans, W. et al. Imaging neuron-glia interactions in the enteric nervous system. (2013) Front Cell Neurosci 7:eCollection. PMID:24155689
  11. Addis, R. et al. Optimization of direct fibroblast reprogramming to cardiomyocytes using calcium activity as a functional measure of success. (2013) J Mol Cell Cardiol 60:97-106. PMID:23591016
  12. Kirchmaier, B. et al. The Popeye domain containing 2 (popdc2) gene in zebrafish is required for heart and skeletal muscle development. (2012) Dev Biol 363:438-450. PMID:22290329
  13. Schwarz, J. et al. Reduced muscle contraction and a relaxed posture during sleep-like Lethargus. (2012) Worm 1:12-14. PMID:24058817

Presentation day reservation

Please put your name under the day you wish to present. There are up to 9 slots on each day. Slot location does not determine speaker order.

Slot Day 5 (T/R) Day 8 (T/R) Day 5 (W/F) Day 8 (W/F)

Navigation links

Next day: Module 3 starts: Growth of phage materials

Previous day: Assess protein function