20.109(S13):Journal club II (Day8): Difference between revisions

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#Ahmed, W., Sawant, S., Huygens, F., Goonetilleke, A. & Gardner, T. Prevalence and occurrence of zoonotic bacterial pathogens in surface waters determined by quantitative PCR. Water research 43, 4918-4928, doi:10.1016/j.watres.2009.03.041 (2009).<b>[ANS/Example Sign-Up/Just an Example]</b>
#Ahmed, W., Sawant, S., Huygens, F., Goonetilleke, A. & Gardner, T. Prevalence and occurrence of zoonotic bacterial pathogens in surface waters determined by quantitative PCR. Water research 43, 4918-4928, doi:10.1016/j.watres.2009.03.041 (2009).<b>[ANS/Example Sign-Up/Just an Example]</b>
#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). <font color = red><b>[AC/TR/red]</b></font color>
#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).<font color = red><b>[ME/WF/red]</b></font color>
#de Boer, R. F., Ott, A., Kesztyus, B. & Kooistra-Smid, A. M. Improved detection of five major gastrointestinal pathogens by use of a molecular screening approach. Journal of clinical microbiology 48, 4140-4146, doi:10.1128/JCM.01124-10 (2010). <font color = blue><b>[EC/WF/Blue]</b></font color>
#de Boer, R. F., Ott, A., Kesztyus, B. & Kooistra-Smid, A. M. Improved detection of five major gastrointestinal pathogens by use of a molecular screening approach. Journal of clinical microbiology 48, 4140-4146, doi:10.1128/JCM.01124-10 (2010). <font color = blue><b>[EC/WF/Blue]</b></font color>
#Etienne, K. A., Kano, R. & Balajee, S. A. Development and validation of a microsphere-based Luminex assay for rapid identification of clinically relevant aspergilli. Journal of clinical microbiology 47, 1096-1100, doi:10.1128/JCM.01899-08 (2009). <font color = purple><b>[JV/WF/Purple]</b></font color>
#Etienne, K. A., Kano, R. & Balajee, S. A. Development and validation of a microsphere-based Luminex assay for rapid identification of clinically relevant aspergilli. Journal of clinical microbiology 47, 1096-1100, doi:10.1128/JCM.01899-08 (2009). <font color = purple><b>[JV/WF/Purple]</b></font color>
Line 37: Line 37:
#Sidhu, J. P., Hodgers, L., Ahmed, W., Chong, M. N. & Toze, S. Prevalence of human pathogens and indicators in stormwater runoff in Brisbane, Australia. Water research 46, 6652-6660, doi:10.1016/j.watres.2012.03.012 (2012). <font color = orange><b>[KG/WF/Orange]</b></font color><font color = pink><b>[MC/TR/pink]</b></font color>
#Sidhu, J. P., Hodgers, L., Ahmed, W., Chong, M. N. & Toze, S. Prevalence of human pathogens and indicators in stormwater runoff in Brisbane, Australia. Water research 46, 6652-6660, doi:10.1016/j.watres.2012.03.012 (2012). <font color = orange><b>[KG/WF/Orange]</b></font color><font color = pink><b>[MC/TR/pink]</b></font color>
#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). <font color = grey><b>[SER/WF/Grey]</b></font color>
#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). <font color = grey><b>[SER/WF/Grey]</b></font color>
#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).
#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). <font color = red><b>[AC/TR/red]</b></font color>
#Metzgar, D. et al. Evaluation and Validation of a Real-Time PCR Assay for Detection and Quantitation of Human Adenovirus 14 from Clinical Samples. PloS one 4, e7081, doi:10.1371/journal.pone.0007081 (2009). <font color = purple><b>[SY/TR/Purple]</b></font color>
#Metzgar, D. et al. Evaluation and Validation of a Real-Time PCR Assay for Detection and Quantitation of Human Adenovirus 14 from Clinical Samples. PloS one 4, e7081, doi:10.1371/journal.pone.0007081 (2009). <font color = purple><b>[SY/TR/Purple]</b></font color>
#Jones, M. S., Hudson, N. R., Gibbins, C. & Fischer, S. L. Evaluation of Type-Specific Real-Time PCR Assays Using the LightCycler and J.B.A.I.D.S. for Detection of Adenoviruses in Species HAdV-C. PloS one 6, e26862, doi:10.1371/journal.pone.0026862 (2011). <font color = blue><b>[SS/WF/Blue]</b></font color>
#Jones, M. S., Hudson, N. R., Gibbins, C. & Fischer, S. L. Evaluation of Type-Specific Real-Time PCR Assays Using the LightCycler and J.B.A.I.D.S. for Detection of Adenoviruses in Species HAdV-C. PloS one 6, e26862, doi:10.1371/journal.pone.0026862 (2011). <font color = blue><b>[SS/WF/Blue]</b></font color>
#van Belkum, A., Renders, N. H. M., Smith, S., Overbeek, S. E. & Verbrugh, H. A. Comparison of conventional and molecular methods for the detection of bacterial pathogens in sputum samples from cystic fibrosis patients1. FEMS Immunology & Medical Microbiology 27, 51-57, doi:10.1111/j.1574-695X.2000.tb01411.x (2000).<font color = red><b>[NF/TR/red]</b></font color>
#van Belkum, A., Renders, N. H. M., Smith, S., Overbeek, S. E. & Verbrugh, H. A. Comparison of conventional and molecular methods for the detection of bacterial pathogens in sputum samples from cystic fibrosis patients1. FEMS Immunology & Medical Microbiology 27, 51-57, doi:10.1111/j.1574-695X.2000.tb01411.x (2000).<font color = red><b>[NF/TR/red]</b></font color><font color = pink><b>[AC/WF/pink]</b></font color>


===Characterizing Microbial Communities===
===Characterizing Microbial Communities===

Latest revision as of 11:23, 18 March 2013


20.109(S13): Laboratory Fundamentals of Biological Engineering

Home        Schedule Spring 2013        Assignments       
DNA Engineering        Protein Engineering        Cell 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 20109.talk AT gmail DOT com 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 email your finished journal club presentation to 20109.submit AT gmail DOT com 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 8 presentations will begin at 1:30 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. Ahmed, W., Sawant, S., Huygens, F., Goonetilleke, A. & Gardner, T. Prevalence and occurrence of zoonotic bacterial pathogens in surface waters determined by quantitative PCR. Water research 43, 4918-4928, doi:10.1016/j.watres.2009.03.041 (2009).[ANS/Example Sign-Up/Just an Example]
  2. 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).[ME/WF/red]
  3. de Boer, R. F., Ott, A., Kesztyus, B. & Kooistra-Smid, A. M. Improved detection of five major gastrointestinal pathogens by use of a molecular screening approach. Journal of clinical microbiology 48, 4140-4146, doi:10.1128/JCM.01124-10 (2010). [EC/WF/Blue]
  4. Etienne, K. A., Kano, R. & Balajee, S. A. Development and validation of a microsphere-based Luminex assay for rapid identification of clinically relevant aspergilli. Journal of clinical microbiology 47, 1096-1100, doi:10.1128/JCM.01899-08 (2009). [JV/WF/Purple]
  5. Kuhn, R. C., Rock, C. M. & Oshima, K. H. Occurrence of Cryptosporidium and Giardia in Wild Ducks along the Rio Grande River Valley in Southern New Mexico. Applied and environmental microbiology 68, 161-165, doi:10.1128/aem.68.1.161-165.2002 (2002). [HH/WF/Pink] [DS/TR/orange]
  6. Lee, S. Y., Lee, S. S., Lyoo, Y. S. & Park, H. M. DNA detection and genotypic identification of potentially human-pathogenic microsporidia from asymptomatic pet parrots in South Korea as a risk factor for zoonotic emergence. Applied and environmental microbiology 77, 8442-8444, doi:10.1128/AEM.05343-11 (2011). [MK/TR/purple][SWC/WF/Green]
  7. 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). [AC/WF/pink]
  8. 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).[NG/TR/blue]
  9. 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).
  10. Pickering, J. W., Larson, M. T., Martins, T. B., Copple, S. S. & Hill, H. R. Elimination of false-positive results in a luminex assay for pneumococcal antibodies. Clinical and vaccine immunology : CVI 17, 185-189, doi:10.1128/CVI.00329-09 (2010). [ZA/WF/purple] [DF/TR/yellow]
  11. 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). [KB/TR/Grey]
  12. Sambol, A. R. et al. Use of rapid influenza diagnostic tests under field conditions as a screening tool during an outbreak of the 2009 novel influenza virus: practical considerations. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 47, 229-233, doi:10.1016/j.jcv.2009.12.015 (2010). [KV/WF/Yellow] [TH/TR/Pink]
  13. 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).
  14. Sidhu, J. P., Hodgers, L., Ahmed, W., Chong, M. N. & Toze, S. Prevalence of human pathogens and indicators in stormwater runoff in Brisbane, Australia. Water research 46, 6652-6660, doi:10.1016/j.watres.2012.03.012 (2012). [KG/WF/Orange][MC/TR/pink]
  15. 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). [SER/WF/Grey]
  16. 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). [AC/TR/red]
  17. Metzgar, D. et al. Evaluation and Validation of a Real-Time PCR Assay for Detection and Quantitation of Human Adenovirus 14 from Clinical Samples. PloS one 4, e7081, doi:10.1371/journal.pone.0007081 (2009). [SY/TR/Purple]
  18. Jones, M. S., Hudson, N. R., Gibbins, C. & Fischer, S. L. Evaluation of Type-Specific Real-Time PCR Assays Using the LightCycler and J.B.A.I.D.S. for Detection of Adenoviruses in Species HAdV-C. PloS one 6, e26862, doi:10.1371/journal.pone.0026862 (2011). [SS/WF/Blue]
  19. van Belkum, A., Renders, N. H. M., Smith, S., Overbeek, S. E. & Verbrugh, H. A. Comparison of conventional and molecular methods for the detection of bacterial pathogens in sputum samples from cystic fibrosis patients1. FEMS Immunology & Medical Microbiology 27, 51-57, doi:10.1111/j.1574-695X.2000.tb01411.x (2000).[NF/TR/red][AC/WF/pink]

Characterizing Microbial Communities

  1. 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 of the United States of America, doi:10.1073/pnas.1212089110 (2013). [ARM/WF/Orange] [ST/TR/Orange]
  2. 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). [JDK/TR/Green]
  3. 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). [JW/WF/Yellow]
  4. 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). [DA/WF/Red]
  5. Bibby, K. & Peccia, J. Identification of Viral Pathogen Diversity in Sewage Sludge by Metagenome Analysis. Environmental Science & Technology, doi:10.1021/es305181x (2013). [EL/TR/Grey]
  6. Brugger, S. D. et al. 16S <italic>rRNA</italic> Terminal Restriction Fragment Length Polymorphism for the Characterization of the Nasopharyngeal Microbiota. PloS one 7, e52241, doi:10.1371/journal.pone.0052241 (2012).[DNN/TR/Green]
  7. Phan, T. G. et al. The Fecal Viral Flora of Wild Rodents. PLoS Pathog 7, e1002218, doi:10.1371/journal.ppat.1002218 (2011).

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).[JZ/TR/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).[KH/WF/Green]

Day Sign-up

Please put your name under the day you wish to present. There are 7 (8??) slots on each day, per lab section. Slot location does not determine speaker order.

Slot Day 6 (T/R) Day 8 (T/R) Day 6 (W/F) Day 8 (W/F)
1 [EFA/TR/Yellow] JDK/TR/Green [KH/WF/Green] SWC/WF/Green
2 [DF/TR/yellow]. [KB/TR/grey] [HH/WF/pink] [DA/WF/red]
3 [NG/TR/blue] [MK/TR/purple] [KG/WF/orange] [EC/WF/blue]
4 [DS/TR/orange] [SY/TR/purple] [SER/WF/Grey] [ME/WF/red]
5 [MC/TR/pink] [TH/TR/pink] [SS/WF/Blue] [AC/WF/pink]
6 EL/TR/Grey DNN/TR/Green [JV/WF/Purple] JW/WF/Yellow
7 [NF/TR/red] [JZ/TR/blue] [EK/WF/Grey] [ZA/WF/purple]
8 [ST/TR/orange] [KV/WF/Yellow]
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