Literature Read and Summaries - Revision history

Olhoshing: /* Article Summaries */

2010-05-20T16:39:47Z

‎Article Summaries

Olhoshing at 15:36, 20 May 2010

2010-05-20T15:36:29Z

Olhoshing: /* Papers to Read */

2010-03-31T19:55:50Z

‎Papers to Read

Olhoshing: /* Papers to Read */

2010-03-17T04:51:28Z

‎Papers to Read

Olhoshing: /* Papers to Read */

2010-03-17T04:51:05Z

‎Papers to Read

Olhoshing: /* Article Summaries */

2010-03-17T04:38:23Z

‎Article Summaries

Olhoshing: /* Article Summaries */

2010-03-17T04:38:06Z

‎Article Summaries

Olhoshing: /* Article Summaries */

2010-03-17T02:53:22Z

‎Article Summaries

Olhoshing: /* Works Read */

2010-03-16T02:42:12Z

‎Works Read

Olhoshing: /* Works Read */

2010-03-16T02:41:28Z

‎Works Read

← Older revision		Revision as of 16:39, 20 May 2010
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	This looks like a really interesting mutant to use in an elongation project. I don’t have any ideas off the bat what it could be used for. But if there is a random separation of nuclear material, there would be a random separation of plasmid and proteins also. It seems like there’s something there.		This looks like a really interesting mutant to use in an elongation project. I don’t have any ideas off the bat what it could be used for. But if there is a random separation of nuclear material, there would be a random separation of plasmid and proteins also. It seems like there’s something there.
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		+	'''Chen B, Wang Y. (2006). On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinformatics 7: 52.'''
		+
		+	This paper discusses noise attenuation (an analog filter to ensure mean levels of heterogeneity) and noise amplification to drive divergence of cell fate and population heterogeneity. Cellular processes amplify and exploit noise either to enhance population heterogeneity, or using noise to attenuate noise. “In addition to generating heterogeneous populations, cells also use noise to filter noise. Although in most systems, noise degrades a signal, when certain nonlinear effects are present, noise actually enhance a signal; for example stochastic resonance”.
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		+	The focus of this paper is to use mathematical modeling and simulation to formulate a theory for identifying all possible mechanisms of genetic networks to attenuate or amplify noise.

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-== Papers to Read ==
+== Citations of Works Read ==
 * Acar M, Becskei A, van Ourdenaarden A. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Acar_2005.pdf (2005).] Enhancement of cellular memory by reducing stochastic transitions. Nature 435: 228 – 32.
-* Becskei A, Seraphin B, Serrano L. (2001). Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO 20: 2528 – 35.
+* Becskei A, Seraphin B, Serrano L. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Becskei_2001.pdf (2001).] Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO 20: 2528 – 35.
 * Cooper S. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Cooper_1989.pdf (1989).] The constrained hoop: an explanation of the overshoot in cell length during a shift-up of Escherichia coli. J Bacteriol 171: 5239 – 43.
-* Cox CD, Peterson GD, Allen MS, Lancaster JM, McCollum JM, Austin D, Yan L, Sayler GS, Simpson ML. (2003). Analysis of noise in quorum sensing. OMICS 7: 317 – 34.
+* Cox CD, Peterson GD, Allen MS, Lancaster JM, McCollum JM, Austin D, Yan L, Sayler GS, Simpson ML. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Cox_2003.pdf (2003).] Analysis of noise in quorum sensing. OMICS 7: 317 – 34.
 * Danchin A. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Danchin_2009.pdf (2009).] Natural selection and immortality. Biogerontology 10: 503 – 16.
 * Danino T, Mondragon-palomino O, Tsimring L, Hasty J. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Danino_2010.pdf (2010).] A synchronized quorum of genetic clocks. Nature 463: 326 – 30.
 * Engberg B, Hjalmarsson K, Nordstrom K. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Engberg_1975.pdf (1975).] Inhibition of cell division in Escherichia coli K-12 by the R-factor R1 and copy mutants of R1. J Bacteriol 124: 633 – 40.
 * Freed NE, Silander OK, Stecher B, Böhm A, Hardt WD, Ackermann M. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/03/PaperReview02.html (2008).] A simple screen to identify promoters conferring high levels of phenotypic noise. PLoS Genet 4(12): e1000307.
 * Goksor M, Diez A, Enger J, Hanstorp D, Nystrom T. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Goksor_2003.pdf (2003).] Analysis of molecular diffusion in ftsK cell-division mutants using laser surgery.  EMBO Reports 4: 867 – 71.
 * Gustafsson P, Nordstrom K. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Gustafsson_1975.pdf (1975).] Random replication of the stringent plasmid R1 in Escherichia coli K-12. J Bacteriol  123: 443 – 48.
-* Holtz WJ, Keasling JD. (2010). Engineering static and dynamic control of synthetic pathways. Cell 140: 19 – 23.
+* Hasty J, Pradines J, Dolnik M, Collins JJ. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Hasty_2000.pdf (2000).] Noise-based switches and amplifiers for gene expression. PNAS 97: 2075–80.
 * Isaacs FJ, Hasty J, Cantor CR, Collins JJ. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Isaacs_2003.pdf (2003).] Prediction and measurement of an autoregulatory genetic module. PNAS 100: 7714 – 19.
 * Jain V, Kumar M, Chatterji D. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Jain_2006.pdf (2006).] ppGpp: stringent response and survival. J. Microbiol 44: 1 – 10.
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 * Pin C, Rolfe MD, Muñoz-Cuevas M, Hinton JC, Peck MW, Walton NJ, Baranyi J. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Pin_2009.pdf (2009).] Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phase. BMC Syst Biol 16,3: 108.
 * Qi B, Chi YM, Lo HK, Qian L. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Qi_2010_RandomNoGen.pdf (2010).] High-speed quantum random number generation by measuring phase noise of a single-mode laser. Optics Letters 35: 312 – 14.
 * Sohka T, Heins RA, Ostermeier M. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Sohka_2009_JBE.pdf (2009).] Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter. J Biol Eng 8:3:10.
 * Sohka T, Heins RA, Phelan RM, Greisler JM, Townsend CA, Ostermeier M. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Sohka_2009_PNAS.pdf (2009).] An externally tunable bacterial band-pass filter. Proc Natl Acad Sci USA 106: 10135 - 40.
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 * Summers J, Litwin S. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Summers_2006.pdf (2006).] Examining the theory of error catastrophe. J Virol 80: 20 – 26.
 * Vilar JMG, Kueh HY, Barkai N, Leibler S. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Vilar_2002.pdf (2002).] Mechanisms of noise-resistance in genetic oscillators. PNAS 5988 – 92.
-* Wang J, Zhang J, Yuan Z, Zhou T. (2007). Noise-induced switches in network systems of the genetic toggle switch. BMC Sys Biol 1: 50.
+* Wang J, Zhang J, Yuan Z, Zhou T. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Wang_2007.pdf (2007).] Noise-induced switches in network systems of the genetic toggle switch. BMC Sys Biol 1: 50.
-* Zhou T, Chen L, Wang R, Aihara K. (2004). Intercellular communication induced by random fluctuations. Genome Informatics 15: 223 – 33.
+* Zhou T, Chen L, Wang R, Aihara K. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Zhou_2004.pdf (2004).] Intercellular communication induced by random fluctuations. Genome Informatics 15: 223 – 33.
 == Review Summaries ==

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 == Papers to Read ==
 * [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Chen_2006.pdf Chen 2006] On the attenuation and amplification of noise in genetic regulatory networks
 * [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Ghim_2008.pdf Ghim 2008] Genetic noice control via protein oligomerization

@@ Line 8: / Line 8: @@
 * Zhou TS, Chen LN, Aihara K. Molecular communication through stochastic synchronization induced by extracellular fluctuations
 * McMillen D, Kopell N, Hasty J, Collins JJ. Synchronizing genetic relaxation oscillators by intercell signaling.
 == Works Read ==

@@ Line 1: / Line 1: @@
 == Papers to Read ==
 * Isaacs FJ et al. Prediction and measurement of an autoregulatory genetic module
 * Atkinson MR et al. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli
 * Zhou TS, Chen LN, Aihara K. Molecular communication through stochastic synchronization induced by extracellular fluctuations
 * McMillen D, Kopell N, Hasty J, Collins JJ. Synchronizing genetic relaxation oscillators by intercell signaling.
 * Jones T, Gill CO, McMullen LM. Behaviour of log-phase Escherichia coli at temperatures near the minimum for growth.
 == Works Read ==

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-Sohka T, Heins RA, Ostermeier M. (2009). Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter. J Biol Eng 8:3:10.
+'''Sohka T, Heins RA, Ostermeier M. (2009). Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter. J Biol Eng 8:3:10.'''
 This paper is very similar to the first paper (they're maximum a month apart in publishing), describing the band-pass filter system. I think this paper explains the system a bit more easily. When challenged to grow in the presence of beta-lactam antibiotic ampicillin (Amp) and tetracycline (Tet) cells grow and fluoresce only if the cellular beta-lactamase activity regulated through an IPTG-inducible promoter falls within a narrow range. High concentrations of Amp prevent cell growth via inhibition of cell wall synthesis. Cells in regions of low Amp are growth arrested due to the protein synthesis inhibitory effects of Tet. It's only the cells located in regions of intermediate Amp that grow. Increasing the BLA enzyme activity shifts the Amp concentration range required for growth to higher levels, and vice versa. So there is a static regio of enzyme and substrate (Amp) to allow growth. It does not seem like the size of that growth window can be narrowed; the tunability is in reference to controlling the amount of enzyme produced (because it depends on the Amp concentration).
 So this isn't quite the tuning I'm working towards - which is good, that my idea has not previously been done. This paper adds to the previous one that another potential morphogen to take the place of Amp is clavulanic acid (CA), which has different effects on the beta-lactamases. Even there, though there would be an optimal ratio for growth that does not change; it would just be different from the ratio with Amp. So this is an example of creating different windows using slightly different constructs in the device.

← Older revision		Revision as of 04:38, 17 March 2010
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	I found this paper because it is the only one that talks about a bacterial band-pass filter. i think the ideas here will benefit my design for a noise band-pass filter, and perhaps I can apply the use of IPTG as a tuner for some protein - perhaps Tet resistance (TetC) or in order to control some other protein that responds to noise level and starts the feedback loop.		I found this paper because it is the only one that talks about a bacterial band-pass filter. i think the ideas here will benefit my design for a noise band-pass filter, and perhaps I can apply the use of IPTG as a tuner for some protein - perhaps Tet resistance (TetC) or in order to control some other protein that responds to noise level and starts the feedback loop.
		+
		+
		+
		+	Sohka T, Heins RA, Ostermeier M. (2009). Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter. J Biol Eng 8:3:10.
		+
		+	This paper is very similar to the first paper (they're maximum a month apart in publishing), describing the band-pass filter system. I think this paper explains the system a bit more easily. When challenged to grow in the presence of beta-lactam antibiotic ampicillin (Amp) and tetracycline (Tet) cells grow and fluoresce only if the cellular beta-lactamase activity regulated through an IPTG-inducible promoter falls within a narrow range. High concentrations of Amp prevent cell growth via inhibition of cell wall synthesis. Cells in regions of low Amp are growth arrested due to the protein synthesis inhibitory effects of Tet. It's only the cells located in regions of intermediate Amp that grow. Increasing the BLA enzyme activity shifts the Amp concentration range required for growth to higher levels, and vice versa. So there is a static regio of enzyme and substrate (Amp) to allow growth. It does not seem like the size of that growth window can be narrowed; the tunability is in reference to controlling the amount of enzyme produced (because it depends on the Amp concentration).
		+
		+	So this isn't quite the tuning I'm working towards - which is good, that my idea has not previously been done. This paper adds to the previous one that another potential morphogen to take the place of Amp is clavulanic acid (CA), which has different effects on the beta-lactamases. Even there, though there would be an optimal ratio for growth that does not change; it would just be different from the ratio with Amp. So this is an example of creating different windows using slightly different constructs in the device.

← Older revision		Revision as of 02:53, 17 March 2010
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	This looks like a really interesting mutant to use in an elongation project. I don’t have any ideas off the bat what it could be used for. But if there is a random separation of nuclear material, there would be a random separation of plasmid and proteins also. It seems like there’s something there.		This looks like a really interesting mutant to use in an elongation project. I don’t have any ideas off the bat what it could be used for. But if there is a random separation of nuclear material, there would be a random separation of plasmid and proteins also. It seems like there’s something there.
		+
		+
		+
		+	'''Sohka T, Heins RA, Phelan RM, Greisler JM, Townsend CA, Ostermeier M. (2009). An externally tunable bacterial band-pass filter. Proc Natl Acad Sci USA 106: 10135 - 40.'''
		+
		+	The authors here constructed a synthetic circuit, a type 3 feed-forward loop, to make a band-pass filter - a circuit to select for intermediate levels of gene expression. They accomplished this by essentially creating a low-pass and high-pass filter in a series. Figure 1A shows the design of the circuit. The tac promoter is induced by IPTG to express beta-lactamase that hydrolyzes ampicillin, allowing cells to grow in ampicillin if enough BLA is produced. When BLA is low though, it allows Am-pp to build up which induces the ampC promoter. The ampC promoter induced expresses GFP and TetC, so that cells can grow in tetracycline. So BLA levels are controlled so that it is not too low so that cells can survive in Amp and not too high so that cells can survive in Tet. Since BLA expression is controlled by IPTG, the system is tunable by changing the concentration of IPTG. "The position of our band-pass filter for Amp can be externally tuned by adding IPTG to the medium and our band-pass filter for beta-lactamase activity can be externally tuned by adding Amp to the medium." The band-pass filter can be broadened by decreasing the concentration of Tet. (It's unclear to me whether you can narrow the filter, if that is conceptually what changing the concentration of IPTG is doing)
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		+	[[Image:Sohka_2009PNAS_Fig1A.png\|440 px\|center]]
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		+	So the cells require a particular ratio of Amp to IPTG for growth; they emphasized this concept in the paper by forming shapes and letters based on the diffusion of Amp and IPTG from spots on a plate so that the correct Amp:IPTG ratio forms along planned lines. Here Amp and IPTG are seen as "morphogens that are affecting the 'fate' of our bacteria through changes in gene expression and cell physiology." They conclude that this system is a convenient moedl system for studying morphogen gradients that lead to pattern formation.
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		+	I found this paper because it is the only one that talks about a bacterial band-pass filter. i think the ideas here will benefit my design for a noise band-pass filter, and perhaps I can apply the use of IPTG as a tuner for some protein - perhaps Tet resistance (TetC) or in order to control some other protein that responds to noise level and starts the feedback loop.

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 * Qi B, Chi YM, Lo HK, Qian L. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Qi_2010_RandomNoGen.pdf (2010).] High-speed quantum random number generation by measuring phase noise of a single-mode laser. Optics Letters 35: 312 – 14.
 * Sohka T, Heins RA, Ostermeier M. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Sohka_2009_JBE.pdf (2009).] Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter. J Biol Eng 8:3:10.
-* Sohka T, Heins RA, Phelan RM, Greisler JM, Townsend CA, Ostermeier M. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Sohka_2009_PNAS.pdf (2009).] Proc Natl Acad Sci USA 106: 10135 - 40.
+* Sohka T, Heins RA, Phelan RM, Greisler JM, Townsend CA, Ostermeier M. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Sohka_2009_PNAS.pdf (2009).] An externally tunable bacterial band-pass filter. Proc Natl Acad Sci USA 106: 10135 - 40.
 * Srivatsan A, Wang JD. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Srivatsan_2008.pdf (2008).] Control of bacterial transcription, traslation and replication by (p)ppGpp. Curr Opin Microbiol 11: 100 – 05.
 * Stewart EJ, Madden R, Paul G, Taddei F. [http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Stewart_2005.pdf (2005).] Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol 3(2): e45.