20.109(S15):Journal club II (Day9)

From OpenWetWare
Jump to navigationJump to search

20.109(S15): Laboratory Fundamentals of Biological Engineering

Dilution curves F13.jpg

Home        People        Schedule Spring 2015        Assignments        Lab Basics        OWW Basics       
DNA Engineering        System Engineering        Biomaterials Engineering              

Logistics of Paper Sign-Up and Presentation

  • Once you have decided on a paper for your presentation, please "reserve" it by putting your (initials/lab section/team color) next to the listing here. 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 for approval.
  • For visibility, please use the following format to sign up if possible, substituting in your own initials and team color: [ANS/WF/Purple]. Thanks!
  • The same paper may be presented by a T/R and a W/F student, but may only be presented once per section.

As you prepare your talk be sure to follow the specific guidelines for oral presentations in this class.

  • Please post your finished journal club presentation to Stellar no later than 1 pm on the day of your presentation.
  • The order in which your presentations are received will be the order of speakers.
  • Both Day 6 and Day 9 presentations will begin at 1:15 pm sharp in room 16-336.

Paper Options

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. Search PubMed yourself to find articles of interest to you.

The easiest way to locate each paper is to type the "doi" (digital object identifier) in at the DOI website. If that approach gives you an error for some reason, or in future cases where you might not know the doi, 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.

Microbe/Disease Detection

  1. Choudhary, M. L. et al. Development of a multiplex one step RT-PCR that detects eighteen respiratory viruses in clinical specimens and comparison with real time RT-PCR. Journal of virological methods 189, 15-19, doi:10.1016/j.jviromet.2012.12.017 (2013). [CDD/WF/Green]
  2. Liu, J. et al. A Laboratory-Developed TaqMan Array Card for Simultaneous Detection of 19 Enteropathogens. Journal of clinical microbiology 51, 472-480, doi:10.1128/JCM.02658-12 (2013). [JH/TR/Green]
  3. Lu, X., Trujillo-Lopez, E., Lott, L. & Erdman, D. D. Quantitative Real-time PCR Assay Panel for Detection and Type-Specific Identification of the Epidemic Respiratory Human Adenoviruses. Journal of clinical microbiology, doi:10.1128/JCM.03297-12 (2013).[ACO/TR/ORANGE]
  4. O'Leary, J., Corcoran, D. & Lucey, B. Comparison of the EntericBio multiplex PCR system with routine culture for detection of bacterial enteric pathogens. Journal of clinical microbiology 47, 3449-3453, doi:10.1128/JCM.01026-09 (2009).
  5. Rota, J. S. et al. Comparison of the Sensitivity of Laboratory Diagnostic Methods from a Well-Characterized Outbreak of Mumps in New York City, 2009. Clinical and vaccine immunology : CVI, doi:10.1128/CVI.00660-12 (2013). [TAL/WF/RED][LA/TR/Yellow]
  6. Schnee, C. et al. A novel rapid DNA microarray assay enables identification of 37 Mycoplasma species and highlights multiple Mycoplasma infections. PloS one 7, e33237, doi:10.1371/journal.pone.0033237 (2012). [VTV/WF/ORANGE]
  7. Zangger, H. et al. Detection of leishmania RNA virus in leishmania parasites. PLoS neglected tropical diseases 7, e2006, doi:10.1371/journal.pntd.0002006 (2013). [LMA/WF/Green]
  8. Fagan, P. K., Hornitzky, M. A., Bettelheim, K. A. & Djordjevic, S. P. Detection of Shiga-Like Toxin (stx1 andstx2 ), Intimin (eaeA), and Enterohemorrhagic Escherichia coli (EHEC) Hemolysin (EHEC hlyA) Genes in Animal Feces by Multiplex PCR. Applied and environmental microbiology 65, 868-872 (1999). [KAW/WF/ORANGE]
  9. Bittar, F. et al. Molecular Detection of Multiple Emerging Pathogens in Sputa from Cystic Fibrosis Patients. PloS one 3, e2908, doi:10.1371/journal.pone.0002908 (2008). [KYL/WF/RED] [JB/TR/Green]
  10. Brodie, E. L. et al. Urban aerosols harbor diverse and dynamic bacterial populations. Proceedings of the National Academy of Sciences 104, 299-304, doi:10.1073/pnas.0608255104 (2007). [AB/WF/BLUE]


Characterizing Microbial Communities

  1. Afshinnekoo, E. et al., Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. CELS 1–16, doi:http://dx.doi.org/10.1016/j.cels.2015.01.001 (2015). [HMZ/WF/Yellow]
  2. Goodrich, J.K., et al., Human Genetics Shape the Gut Microbiome. Cell 159:789-799, doi: http://dx.doi.org/10.1016/j.cell.2014.09.053 (2014). [WMY/TR/ORANGE] [SMS/WF/PINK]
  3. Tunney, M. M. et al. Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. American journal of respiratory and critical care medicine 177, 995-1001, doi:10.1164/rccm.200708-1151OC (2008). [DP/TR/BLUE] [JSH/WF/YELLOW]
  4. DeLeon-Rodriguez, N. et al. Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications. Proceedings of the National Academy of Sciences, doi:10.1073/pnas.1212089110 (2013).
  5. Smith, D. et al. Free Tropospheric Transport of Microorganisms from Asia to North America. Microb Ecol 64, 973-985, doi:10.1007/s00248-012-0088-9 (2012).
  6. Bibby, K. & Peccia, J. Identification of Viral Pathogen Diversity in Sewage Sludge by Metagenome Analysis. Environmental Science & Technology, doi:10.1021/es305181x (2013). [KSK/WF/Platinum]
  7. Brugger, S. D. et al. 16S rRNA Terminal Restriction Fragment Length Polymorphism for the Characterization of the Nasopharyngeal Microbiota. PloS one 7, e52241, doi:10.1371/journal.pone.0052241 (2012).
  8. Phan, T. G. et al. The Fecal Viral Flora of Wild Rodents. PLoS Pathog 7, e1002218, doi:10.1371/journal.ppat.1002218 (2011).
  9. Morowitz, M. J. et al. Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proceedings of the National Academy of Sciences 108, 1128-1133, doi:10.1073/pnas.1010992108 (2011).
  10. Smillie, C. S. et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480, 241-244, doi:http://www.nature.com/nature/journal/v480/n7376/abs/nature10571.html - supplementary-information (2011). [LNB/WF/PINK]
  11. Theriot, C. M. et al. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat Commun 5, doi:10.1038/ncomms4114 (2014). [AZL/WF/Purple]
  12. Xenoulis, P. G. et al. Molecular characterization of the cloacal microbiota of wild and captive parrots. Veterinary Microbiology 146, 320-325, doi:http://dx.doi.org/10.1016/j.vetmic.2010.05.024 (2010).
  13. Kuss, S. K. et al. Intestinal Microbiota Promote Enteric Virus Replication and Systemic Pathogenesis. Science 334, 249-252, doi:10.1126/science.1211057 (2011). [JL/WF/Platinum]
  14. Ferreira, R. B. R. et al. The Intestinal Microbiota Plays a Role in <italic>Salmonella</italic>-Induced Colitis Independent of Pathogen Colonization. PLoS ONE 6, e20338, doi:10.1371/journal.pone.0020338 (2011).[WW/WF/Platinum]
  15. Kane, M. et al. Successful Transmission of a Retrovirus Depends on the Commensal Microbiota. Science 334, 245-249, doi:10.1126/science.1210718 (2011). [IHA/TR/Purple]
  16. Willing, B. P., Vacharaksa, A., Croxen, M., Thanachayanont, T. & Finlay, B. B. Altering Host Resistance to Infections through Microbial Transplantation. PLoS ONE 6, e26988, doi:10.1371/journal.pone.0026988 (2011). [MKG/WF/Purple] [CR/TR/Yellow]
  17. Lee, S. M. et al. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature 501, 426-429, doi:10.1038/nature12447, http://www.nature.com/nature/journal/v501/n7467/abs/nature12447.html - supplementary-information (2013).< [JH/TR/GREEN]


Related Topics

  1. Compton, A. A. & Emerman, M. Convergence and Divergence in the Evolution of the APOBEC3G-Vif Interaction Reveal Ancient Origins of Simian Immunodeficiency Viruses. PLoS Pathog 9, e1003135, doi:10.1371/journal.ppat.1003135 (2013). [RRK/WF/BLUE]
  2. Zanetti, F., Berinstein, A. & Carrillo, E. Effect of host selective pressure on Newcastle disease virus virulence. Microbial pathogenesis 44, 135-140, doi:10.1016/j.micpath.2007.08.012 (2008).[EEE/TR/BLUE]

Day Sign-up

Please put your name under the day you wish to present. There are up to 8 slots on each day. Slot location does not determine speaker order.

Slot Day 6 (T/R) Day 9 (T/R) Day 6 (W/F) Day 9 (W/F)
1 Juan Hurtado Imraan Alas Lauren Adelaar Joseph Han
2 Lyla Atta Will Yashar Cortni Dick Hannah Zlotnick
3 Jessie Blumenfeld Arinze Okeke NA Sonia Scaria
4 Deborah Plana Will White Lauren Bush
5 Christian Richardson Vipul Vachharajani Kristina Kim
6 NA NA Katherine Whang Marissa Griffin
7 NA NA Krystal Lai Alex Lim
8 NA NA Tara Lee Jennifer Li
9 NA NA Anastassia Bobokalonova Rachel Katz


For M2D1

  1. Prepare for the first day of Module 1 by reading the module overview and day one introduction.

Due M2D3

  1. The Primer Design Memo assignment is due by 5 pm.

Navigation Links

Previous Day: Diagnostic primer analysis

Next Day: Introduction to cell strains and plating