Difference between revisions of "20.109(S07): Student presentations, module 2"

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The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You will notice that the papers fall roughly into three categories- measurements made using fluorescent proteins, protein engineering/assay development, and reports describing the biological role of calcium signals.
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The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You will notice that the papers fall roughly into three categories- description/optimization of fluorescent variants,  measurements using fluorescent proteins, and reports describing the biological role of calcium signals.
  
 
You are not limited to the following list of primary research articles. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Search [http://ncbi.nih.gov/PubMed/ pubmed] yourself to find articles of interest to you. Once you have decided on a paper for your presentation, please email it to nkuldell AT mit DOT edu. As you prepare your talk be sure to follow the [[20.109(S07):Guidelines for oral presentations| specific guidelines for oral presentations]] in this class.
 
You are not limited to the following list of primary research articles. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Search [http://ncbi.nih.gov/PubMed/ pubmed] yourself to find articles of interest to you. Once you have decided on a paper for your presentation, please email it to nkuldell AT mit DOT edu. As you prepare your talk be sure to follow the [[20.109(S07):Guidelines for oral presentations| specific guidelines for oral presentations]] in this class.
  
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===Fluorescent reporters===
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===Fluorescent variants===
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Papers (not reviews!) from [[http://tsienlab.ucsd.edu/Publication.htm]]
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#Kogure T, Karasawa S, Araki T, Saito K, Kinjo M, Miyawaki A. A fluorescent variant of a protein from the stony coral Montipora facilitates dual-color single-laser fluorescence cross-correlation spectroscopy. Nat Biotechnol. 2006 May;24(5):577-81. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16648840&query_hl=1&itool=pubmed_DocSum]
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===Protein engineering/assay development===
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# Tramier M, Zahid M, Mevel JC, Masse MJ, Coppey-Moisan M. Sensitivity of CFP/YFP and GFP/mCherry pairs to donor photobleaching on FRET determination by fluorescence lifetime imaging microscopy in living cells. Microsc Res Tech. 2006 Nov;69(11):933-9. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16941642&query_hl=1&itool=pubmed_DocSum]
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===Fluorescent assay development===
 +
#Papers (not reviews!) from [http://tsienlab.ucsd.edu/Publication.htm the Tsien lab]
 +
#Baker BJ, Lee H, Pieribone VA, Cohen LB, Isacoff EY, Knopfel T, Kosmidis EK. Three fluorescent protein voltage sensors exhibit low plasma membrane expression in mammalian cells. J Neurosci Methods. 2006 Nov 24 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17126911&query_hl=1&itool=pubmed_docsum]
 +
#Kawai A, Takano S, Nakamura N, Ohkuma S. Quantitative monitoring of autophagic degradation. Biochem Biophys Res Commun. 2006 Dec 8;351(1):71-7.[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17054905&query_hl=1&itool=pubmed_docsum]
 +
#Pfleger BF, Pitera DJ, Newman JD, Martin VJ, Keasling JD. Microbial sensors for small molecules: Development of a mevalonate biosensor. Metab Eng. 2007 Jan;9(1):30-8.[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17002894&query_hl=1&itool=pubmed_DocSum]
 +
#Xu X, Brzostowski JA, Jin T. Using quantitative fluorescence microscopy and FRET imaging to measure spatiotemporal signaling events in single living cells. Methods Mol Biol. 2006;346:281-96.[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16957297&query_hl=1&itool=pubmed_DocSum]
 +
#Yee DJ, Balsanek V, Bauman DR, Penning TM, Sames D. Fluorogenic metabolic probes for direct activity readout of redox enzymes: Selective measurement of human AKR1C2 in living cells.Proc Natl Acad Sci U S A. 2006 Sep 5;103(36):13304-9. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16938874&query_hl=1&itool=pubmed_DocSum]
 +
#Demarco IA, Periasamy A, Booker CF, Day RN. Monitoring dynamic protein interactions with photoquenching FRET.Nat Methods. 2006 Jul;3(7):519-24. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16791209&query_hl=1&itool=pubmed_DocSum]
 
===Calcium signaling===
 
===Calcium signaling===

Revision as of 16:28, 2 January 2007


20.109: Laboratory Fundamentals of Biological Engineering

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Home        People        Schedule Spring 2007        Lab Basics        OWW Basics       
Genome Engineering        Biophysical Signal Measurement        Expression Engineering        Biomaterial Engineering       

The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You will notice that the papers fall roughly into three categories- description/optimization of fluorescent variants, measurements using fluorescent proteins, and reports describing the biological role of calcium signals.

You are not limited to the following list of primary research articles. 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. Once you have decided on a paper for your presentation, please email it to nkuldell AT mit DOT edu. As you prepare your talk be sure to follow the specific guidelines for oral presentations in this class.

Fluorescent variants

  1. Kogure T, Karasawa S, Araki T, Saito K, Kinjo M, Miyawaki A. A fluorescent variant of a protein from the stony coral Montipora facilitates dual-color single-laser fluorescence cross-correlation spectroscopy. Nat Biotechnol. 2006 May;24(5):577-81. [1]
  2. Tramier M, Zahid M, Mevel JC, Masse MJ, Coppey-Moisan M. Sensitivity of CFP/YFP and GFP/mCherry pairs to donor photobleaching on FRET determination by fluorescence lifetime imaging microscopy in living cells. Microsc Res Tech. 2006 Nov;69(11):933-9. [2]

Fluorescent assay development

  1. Papers (not reviews!) from the Tsien lab
  2. Baker BJ, Lee H, Pieribone VA, Cohen LB, Isacoff EY, Knopfel T, Kosmidis EK. Three fluorescent protein voltage sensors exhibit low plasma membrane expression in mammalian cells. J Neurosci Methods. 2006 Nov 24 [3]
  3. Kawai A, Takano S, Nakamura N, Ohkuma S. Quantitative monitoring of autophagic degradation. Biochem Biophys Res Commun. 2006 Dec 8;351(1):71-7.[4]
  4. Pfleger BF, Pitera DJ, Newman JD, Martin VJ, Keasling JD. Microbial sensors for small molecules: Development of a mevalonate biosensor. Metab Eng. 2007 Jan;9(1):30-8.[5]
  5. Xu X, Brzostowski JA, Jin T. Using quantitative fluorescence microscopy and FRET imaging to measure spatiotemporal signaling events in single living cells. Methods Mol Biol. 2006;346:281-96.[6]
  6. Yee DJ, Balsanek V, Bauman DR, Penning TM, Sames D. Fluorogenic metabolic probes for direct activity readout of redox enzymes: Selective measurement of human AKR1C2 in living cells.Proc Natl Acad Sci U S A. 2006 Sep 5;103(36):13304-9. [7]
  7. Demarco IA, Periasamy A, Booker CF, Day RN. Monitoring dynamic protein interactions with photoquenching FRET.Nat Methods. 2006 Jul;3(7):519-24. [8]

Calcium signaling

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