IGEM:Caltech/2008 - Revision history

Josh K. Michener at 18:40, 20 October 2008

2008-10-20T18:40:42Z

←Older revision		Revision as of 18:40, 20 October 2008
Line 47:		Line 47:
	To do so, two new devices have been created: a randomly activated off-to-on switch and a population variation generator. Initially, a cell is in a default state (S0), the switch is off, and the fate of the cell is undetermined. However, each time a cell replicates the plasmid that contains the switch, there is a chance that the switch turns on. Once the switch is on, it activates the population variation generator, which in turn determines the fate of the cell by setting it to one of three states - S1, S2, or S0 (the original default). That cell and all of its descents then stay in the determined state.		To do so, two new devices have been created: a randomly activated off-to-on switch and a population variation generator. Initially, a cell is in a default state (S0), the switch is off, and the fate of the cell is undetermined. However, each time a cell replicates the plasmid that contains the switch, there is a chance that the switch turns on. Once the switch is on, it activates the population variation generator, which in turn determines the fate of the cell by setting it to one of three states - S1, S2, or S0 (the original default). That cell and all of its descents then stay in the determined state.

-		+	<biblio>
		+	#hooper pmid=12055347
		+	#mazmanian pmid=16009137
		+	#donskey pmid=15307031
		+	#krammer pmid=16902895
		+	#westendorf pmid=15708311
		+	#rao pmid=16040799
		+	#duan pmid=18433007
		+	#suttie pmid=8527227
		+	</biblio>
	\|}		\|}

Allen Lin at 12:26, 1 August 2008

2008-08-01T12:26:27Z

←Older revision		Revision as of 12:26, 1 August 2008
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	{{clear}}		{{clear}}

-	==[[/Project/~~Population Variation~~\|~~Population Variation~~]]==	+	==[[/Project/Asynchronous Random State Generator\|Asynchronous Random State Generator]]==

	Given that we have created four different states for a cell to be in, we need to in some manner combine them into one system. However, we need to ensure that any particular cell is in only one of these states, and not more than one, or else the load on the cell may be too big. In other words, we want to make these states mutually exclusive.		Given that we have created four different states for a cell to be in, we need to in some manner combine them into one system. However, we need to ensure that any particular cell is in only one of these states, and not more than one, or else the load on the cell may be too big. In other words, we want to make these states mutually exclusive.

Fei Chen: /* Phage Pathogen Defense */

2008-07-30T07:35:31Z

Phage Pathogen Defense

←Older revision		Revision as of 07:35, 30 July 2008
Line 38:		Line 38:
	Bacteriophage λ is a temperate phage with an E. Coli. host, λ infects E. Coli through the lamB receptor, and absence of this receptor prevents λ infection. We will takes advantage of this aspect of bacteriophage λ to create E. Coli which are resistant to the phage, but release the phage to destroy susceptible pathogenic E. Coli.		Bacteriophage λ is a temperate phage with an E. Coli. host, λ infects E. Coli through the lamB receptor, and absence of this receptor prevents λ infection. We will takes advantage of this aspect of bacteriophage λ to create E. Coli which are resistant to the phage, but release the phage to destroy susceptible pathogenic E. Coli.

-	The second approach is more versatile, and can target more strains of pathogenic bacteria. It is ~~being modeled with the temperate bacteriophage SP02, and its host B. Subtilis. We wish~~ to create a phasmid ~~with~~ the ~~SP02 lysogen by combining the lysogen with an~~ E. Coli plasmid ~~origin~~ of ~~replication~~. This allows the ~~phage genome~~ to pass on as a plasmid within ~~our engineered~~ E. Coli, ~~but~~ when ~~the plasmid is conjugated~~ to ~~B. Subtilis~~, the ~~virus~~ is induced ~~and destroys the pathogens~~.	+	The second approach is more versatile, and can target more strains of pathogenic bacteria. The goal is to create a phasmid out of the genome of a temperate bacteriophage. A phasmid combines a E. Coli plasmid Origin of Replication with a linear phage genome, circularizing it. This allows the phasmid to pass on as a plasmid within E. Coli, however when transferred to its native host, the phage phage is induced.
-		+
	{{clear}}		{{clear}}

Fei Chen: /* Phage Pathogen Defense */

2008-07-30T07:31:44Z

Phage Pathogen Defense

←Older revision		Revision as of 07:31, 30 July 2008
Line 35:		Line 35:
	[[Image:Phage.jpg\|thumb\|left\|Phage attached to bacteria, electron micrograph]]		[[Image:Phage.jpg\|thumb\|left\|Phage attached to bacteria, electron micrograph]]
	Another aspect of bacterial pathogen defense for our probiotic is to produce bacteriophages, which would rapidly infect and wipe out all of the pathogens. There are basically methods to approach phage production, differentiated by the type of phage used. The first uses the bacteriophage λ, which targets E. Coli. The other is exploring the use of a temperate bacteriophage from B. Subtilis, however this method, if successful, can be adapted to temperate bacteriophages of any bacterial strain.		Another aspect of bacterial pathogen defense for our probiotic is to produce bacteriophages, which would rapidly infect and wipe out all of the pathogens. There are basically methods to approach phage production, differentiated by the type of phage used. The first uses the bacteriophage λ, which targets E. Coli. The other is exploring the use of a temperate bacteriophage from B. Subtilis, however this method, if successful, can be adapted to temperate bacteriophages of any bacterial strain.
		+
		+	Bacteriophage λ is a temperate phage with an E. Coli. host, λ infects E. Coli through the lamB receptor, and absence of this receptor prevents λ infection. We will takes advantage of this aspect of bacteriophage λ to create E. Coli which are resistant to the phage, but release the phage to destroy susceptible pathogenic E. Coli.
		+
		+	The second approach is more versatile, and can target more strains of pathogenic bacteria. It is being modeled with the temperate bacteriophage SP02, and its host B. Subtilis. We wish to create a phasmid with the SP02 lysogen by combining the lysogen with an E. Coli plasmid origin of replication. This allows the phage genome to pass on as a plasmid within our engineered E. Coli, but when the plasmid is conjugated to B. Subtilis, the virus is induced and destroys the pathogens.

	{{clear}}		{{clear}}

Fei Chen at 07:30, 30 July 2008

2008-07-30T07:30:17Z

←Older revision		Revision as of 07:30, 30 July 2008
Line 33:		Line 33:

	==[[/Project/Phage Pathogen Defense\|Phage Pathogen Defense]]==		==[[/Project/Phage Pathogen Defense\|Phage Pathogen Defense]]==
-		+	[[Image:Phage.jpg\|thumb\|left\|Phage attached to bacteria, electron micrograph]]
	Another aspect of bacterial pathogen defense for our probiotic is to produce bacteriophages, which would rapidly infect and wipe out all of the pathogens. There are basically methods to approach phage production, differentiated by the type of phage used. The first uses the bacteriophage λ, which targets E. Coli. The other is exploring the use of a temperate bacteriophage from B. Subtilis, however this method, if successful, can be adapted to temperate bacteriophages of any bacterial strain.		Another aspect of bacterial pathogen defense for our probiotic is to produce bacteriophages, which would rapidly infect and wipe out all of the pathogens. There are basically methods to approach phage production, differentiated by the type of phage used. The first uses the bacteriophage λ, which targets E. Coli. The other is exploring the use of a temperate bacteriophage from B. Subtilis, however this method, if successful, can be adapted to temperate bacteriophages of any bacterial strain.

Fei Chen at 07:22, 30 July 2008

2008-07-30T07:22:13Z

←Older revision		Revision as of 07:22, 30 July 2008
Line 30:		Line 30:
	[[Image:neutrophil-shigella.jpg\|thumb\|left\|A neutrophil trapping Shigella]]		[[Image:neutrophil-shigella.jpg\|thumb\|left\|A neutrophil trapping Shigella]]
	Several types of bacteria can cause illness in humans by infecting the gut. ''Salmonella'' and ''E. coli'' are probably the two people most frequently associate with food poisoning. There are other pathogenic bacteria that can infect our gut as well. ''Shigella'' and ''Campylobacter'' can cause cramping, diarrhea and dysentery. ''Vibrio cholerae'', which also infects the gut, is the cause of cholera. The body normally relies on white blood cells (neutrophils) to clear bacteria from the body. Once a bacterium is engulfed, the neutrophil releases a sudden and toxic amount of reactive oxygen species, comprised of a mixture of superoxide, hydrogen peroxide, and hypochlorous acid. This is event is termed the oxidative burst. However, white blood cells do not patrol the gut lumen and so there is no active clearance of pathogens. The goal of this project is to engineer a beneficial gut microbe capable of detecting a harmful bacterium and, in turn, generate an oxidative burst sufficient to kill the pathogen.		Several types of bacteria can cause illness in humans by infecting the gut. ''Salmonella'' and ''E. coli'' are probably the two people most frequently associate with food poisoning. There are other pathogenic bacteria that can infect our gut as well. ''Shigella'' and ''Campylobacter'' can cause cramping, diarrhea and dysentery. ''Vibrio cholerae'', which also infects the gut, is the cause of cholera. The body normally relies on white blood cells (neutrophils) to clear bacteria from the body. Once a bacterium is engulfed, the neutrophil releases a sudden and toxic amount of reactive oxygen species, comprised of a mixture of superoxide, hydrogen peroxide, and hypochlorous acid. This is event is termed the oxidative burst. However, white blood cells do not patrol the gut lumen and so there is no active clearance of pathogens. The goal of this project is to engineer a beneficial gut microbe capable of detecting a harmful bacterium and, in turn, generate an oxidative burst sufficient to kill the pathogen.
		+	{{clear}}
		+
		+	==[[/Project/Phage Pathogen Defense\|Phage Pathogen Defense]]==
		+
		+	Another aspect of bacterial pathogen defense for our probiotic is to produce bacteriophages, which would rapidly infect and wipe out all of the pathogens. There are basically methods to approach phage production, differentiated by the type of phage used. The first uses the bacteriophage λ, which targets E. Coli. The other is exploring the use of a temperate bacteriophage from B. Subtilis, however this method, if successful, can be adapted to temperate bacteriophages of any bacterial strain.
		+
	{{clear}}		{{clear}}

Line 37:		Line 43:

	To do so, two new devices have been created: a randomly activated off-to-on switch and a population variation generator. Initially, a cell is in a default state (S0), the switch is off, and the fate of the cell is undetermined. However, each time a cell replicates the plasmid that contains the switch, there is a chance that the switch turns on. Once the switch is on, it activates the population variation generator, which in turn determines the fate of the cell by setting it to one of three states - S1, S2, or S0 (the original default). That cell and all of its descents then stay in the determined state.		To do so, two new devices have been created: a randomly activated off-to-on switch and a population variation generator. Initially, a cell is in a default state (S0), the switch is off, and the fate of the cell is undetermined. However, each time a cell replicates the plasmid that contains the switch, there is a chance that the switch turns on. Once the switch is on, it activates the population variation generator, which in turn determines the fate of the cell by setting it to one of three states - S1, S2, or S0 (the original default). That cell and all of its descents then stay in the determined state.
		+

	\|}		\|}

Josh K. Michener at 00:24, 23 July 2008

2008-07-23T00:24:02Z

←Older revision		Revision as of 00:24, 23 July 2008
Line 28:		Line 28:

	==[[/Project/Oxidative Burst\|Oxidative Burst]]==		==[[/Project/Oxidative Burst\|Oxidative Burst]]==
-	[[Image:neutrophil-shigella.jpg\|thumb\|left\|A neutrophil trapping Shigella]	+	[[Image:neutrophil-shigella.jpg\|thumb\|left\|A neutrophil trapping Shigella]]
	Several types of bacteria can cause illness in humans by infecting the gut. ''Salmonella'' and ''E. coli'' are probably the two people most frequently associate with food poisoning. There are other pathogenic bacteria that can infect our gut as well. ''Shigella'' and ''Campylobacter'' can cause cramping, diarrhea and dysentery. ''Vibrio cholerae'', which also infects the gut, is the cause of cholera. The body normally relies on white blood cells (neutrophils) to clear bacteria from the body. Once a bacterium is engulfed, the neutrophil releases a sudden and toxic amount of reactive oxygen species, comprised of a mixture of superoxide, hydrogen peroxide, and hypochlorous acid. This is event is termed the oxidative burst. However, white blood cells do not patrol the gut lumen and so there is no active clearance of pathogens. The goal of this project is to engineer a beneficial gut microbe capable of detecting a harmful bacterium and, in turn, generate an oxidative burst sufficient to kill the pathogen.		Several types of bacteria can cause illness in humans by infecting the gut. ''Salmonella'' and ''E. coli'' are probably the two people most frequently associate with food poisoning. There are other pathogenic bacteria that can infect our gut as well. ''Shigella'' and ''Campylobacter'' can cause cramping, diarrhea and dysentery. ''Vibrio cholerae'', which also infects the gut, is the cause of cholera. The body normally relies on white blood cells (neutrophils) to clear bacteria from the body. Once a bacterium is engulfed, the neutrophil releases a sudden and toxic amount of reactive oxygen species, comprised of a mixture of superoxide, hydrogen peroxide, and hypochlorous acid. This is event is termed the oxidative burst. However, white blood cells do not patrol the gut lumen and so there is no active clearance of pathogens. The goal of this project is to engineer a beneficial gut microbe capable of detecting a harmful bacterium and, in turn, generate an oxidative burst sufficient to kill the pathogen.
	{{clear}}		{{clear}}

Josh K. Michener at 00:23, 23 July 2008

2008-07-23T00:23:44Z

←Older revision		Revision as of 00:23, 23 July 2008
Line 28:		Line 28:

	==[[/Project/Oxidative Burst\|Oxidative Burst]]==		==[[/Project/Oxidative Burst\|Oxidative Burst]]==
-	[[Image:neutrophil-shigella.jpg\|thumb\|left\|A neutrophil trapping Shigella ~~(Picture courtesy of http://medicineworld.org/news/news-archives/infectious-disease-news/May-17-2007.html]~~]	+	[[Image:neutrophil-shigella.jpg\|thumb\|left\|A neutrophil trapping Shigella]
	Several types of bacteria can cause illness in humans by infecting the gut. ''Salmonella'' and ''E. coli'' are probably the two people most frequently associate with food poisoning. There are other pathogenic bacteria that can infect our gut as well. ''Shigella'' and ''Campylobacter'' can cause cramping, diarrhea and dysentery. ''Vibrio cholerae'', which also infects the gut, is the cause of cholera. The body normally relies on white blood cells (neutrophils) to clear bacteria from the body. Once a bacterium is engulfed, the neutrophil releases a sudden and toxic amount of reactive oxygen species, comprised of a mixture of superoxide, hydrogen peroxide, and hypochlorous acid. This is event is termed the oxidative burst. However, white blood cells do not patrol the gut lumen and so there is no active clearance of pathogens. The goal of this project is to engineer a beneficial gut microbe capable of detecting a harmful bacterium and, in turn, generate an oxidative burst sufficient to kill the pathogen.		Several types of bacteria can cause illness in humans by infecting the gut. ''Salmonella'' and ''E. coli'' are probably the two people most frequently associate with food poisoning. There are other pathogenic bacteria that can infect our gut as well. ''Shigella'' and ''Campylobacter'' can cause cramping, diarrhea and dysentery. ''Vibrio cholerae'', which also infects the gut, is the cause of cholera. The body normally relies on white blood cells (neutrophils) to clear bacteria from the body. Once a bacterium is engulfed, the neutrophil releases a sudden and toxic amount of reactive oxygen species, comprised of a mixture of superoxide, hydrogen peroxide, and hypochlorous acid. This is event is termed the oxidative burst. However, white blood cells do not patrol the gut lumen and so there is no active clearance of pathogens. The goal of this project is to engineer a beneficial gut microbe capable of detecting a harmful bacterium and, in turn, generate an oxidative burst sufficient to kill the pathogen.
	{{clear}}		{{clear}}

Josh K. Michener at 00:23, 23 July 2008

2008-07-23T00:23:01Z

←Older revision		Revision as of 00:23, 23 July 2008
Line 19:		Line 19:
	Folate is the generic term for the various forms of Vitamin B9, which include dihydrofolate (DHF), tetrahydrofolate (THF), and folic acid. An essential vitamin for cell survival, folate is involved in amino synthesis (and thus DNA synthesis) as well as single-carbon-transfer reactions. Though humans don't produce folate, folate deficiency can cause serious birth defects and anemia. As a result, most cereals and breads are supplemented with folate. Folate has also been shown to have good bioavailability in the large intestine, and so is more easily absorbed by the host than other vitamins.		Folate is the generic term for the various forms of Vitamin B9, which include dihydrofolate (DHF), tetrahydrofolate (THF), and folic acid. An essential vitamin for cell survival, folate is involved in amino synthesis (and thus DNA synthesis) as well as single-carbon-transfer reactions. Though humans don't produce folate, folate deficiency can cause serious birth defects and anemia. As a result, most cereals and breads are supplemented with folate. Folate has also been shown to have good bioavailability in the large intestine, and so is more easily absorbed by the host than other vitamins.

-	Our aim is to engineer a strain of ''E. coli'' that will overexpress folate such that a person without access to green, leafy vegetables or folate-supplemented foods can still obtain the necessary daily amount by having this strain residing in their gut.~~<br><br><br><br><br><br><br>~~	+	Our aim is to engineer a strain of ''E. coli'' that will overexpress folate such that a person without access to green, leafy vegetables or folate-supplemented foods can still obtain the necessary daily amount by having this strain residing in their gut.
		+	{{clear}}

	==[[/Project/Lactose intolerance\|Lactose intolerance]]==		==[[/Project/Lactose intolerance\|Lactose intolerance]]==
Line 29:		Line 30:
	[[Image:neutrophil-shigella.jpg\|thumb\|left\|A neutrophil trapping Shigella (Picture courtesy of http://medicineworld.org/news/news-archives/infectious-disease-news/May-17-2007.html]]		[[Image:neutrophil-shigella.jpg\|thumb\|left\|A neutrophil trapping Shigella (Picture courtesy of http://medicineworld.org/news/news-archives/infectious-disease-news/May-17-2007.html]]
	Several types of bacteria can cause illness in humans by infecting the gut. ''Salmonella'' and ''E. coli'' are probably the two people most frequently associate with food poisoning. There are other pathogenic bacteria that can infect our gut as well. ''Shigella'' and ''Campylobacter'' can cause cramping, diarrhea and dysentery. ''Vibrio cholerae'', which also infects the gut, is the cause of cholera. The body normally relies on white blood cells (neutrophils) to clear bacteria from the body. Once a bacterium is engulfed, the neutrophil releases a sudden and toxic amount of reactive oxygen species, comprised of a mixture of superoxide, hydrogen peroxide, and hypochlorous acid. This is event is termed the oxidative burst. However, white blood cells do not patrol the gut lumen and so there is no active clearance of pathogens. The goal of this project is to engineer a beneficial gut microbe capable of detecting a harmful bacterium and, in turn, generate an oxidative burst sufficient to kill the pathogen.		Several types of bacteria can cause illness in humans by infecting the gut. ''Salmonella'' and ''E. coli'' are probably the two people most frequently associate with food poisoning. There are other pathogenic bacteria that can infect our gut as well. ''Shigella'' and ''Campylobacter'' can cause cramping, diarrhea and dysentery. ''Vibrio cholerae'', which also infects the gut, is the cause of cholera. The body normally relies on white blood cells (neutrophils) to clear bacteria from the body. Once a bacterium is engulfed, the neutrophil releases a sudden and toxic amount of reactive oxygen species, comprised of a mixture of superoxide, hydrogen peroxide, and hypochlorous acid. This is event is termed the oxidative burst. However, white blood cells do not patrol the gut lumen and so there is no active clearance of pathogens. The goal of this project is to engineer a beneficial gut microbe capable of detecting a harmful bacterium and, in turn, generate an oxidative burst sufficient to kill the pathogen.
-	~~<br><br><br><br><br><br><br><br><br>~~	+	{{clear}}

	==[[/Project/Population Variation\|Population Variation]]==		==[[/Project/Population Variation\|Population Variation]]==

Allen Lin: /* Oxidative Burst */

2008-06-30T06:44:37Z

Oxidative Burst

←Older revision		Revision as of 06:44, 30 June 2008
Line 29:		Line 29:
	[[Image:neutrophil-shigella.jpg\|thumb\|left\|A neutrophil trapping Shigella (Picture courtesy of http://medicineworld.org/news/news-archives/infectious-disease-news/May-17-2007.html]]		[[Image:neutrophil-shigella.jpg\|thumb\|left\|A neutrophil trapping Shigella (Picture courtesy of http://medicineworld.org/news/news-archives/infectious-disease-news/May-17-2007.html]]
	Several types of bacteria can cause illness in humans by infecting the gut. ''Salmonella'' and ''E. coli'' are probably the two people most frequently associate with food poisoning. There are other pathogenic bacteria that can infect our gut as well. ''Shigella'' and ''Campylobacter'' can cause cramping, diarrhea and dysentery. ''Vibrio cholerae'', which also infects the gut, is the cause of cholera. The body normally relies on white blood cells (neutrophils) to clear bacteria from the body. Once a bacterium is engulfed, the neutrophil releases a sudden and toxic amount of reactive oxygen species, comprised of a mixture of superoxide, hydrogen peroxide, and hypochlorous acid. This is event is termed the oxidative burst. However, white blood cells do not patrol the gut lumen and so there is no active clearance of pathogens. The goal of this project is to engineer a beneficial gut microbe capable of detecting a harmful bacterium and, in turn, generate an oxidative burst sufficient to kill the pathogen.		Several types of bacteria can cause illness in humans by infecting the gut. ''Salmonella'' and ''E. coli'' are probably the two people most frequently associate with food poisoning. There are other pathogenic bacteria that can infect our gut as well. ''Shigella'' and ''Campylobacter'' can cause cramping, diarrhea and dysentery. ''Vibrio cholerae'', which also infects the gut, is the cause of cholera. The body normally relies on white blood cells (neutrophils) to clear bacteria from the body. Once a bacterium is engulfed, the neutrophil releases a sudden and toxic amount of reactive oxygen species, comprised of a mixture of superoxide, hydrogen peroxide, and hypochlorous acid. This is event is termed the oxidative burst. However, white blood cells do not patrol the gut lumen and so there is no active clearance of pathogens. The goal of this project is to engineer a beneficial gut microbe capable of detecting a harmful bacterium and, in turn, generate an oxidative burst sufficient to kill the pathogen.
-	<br><br><br><br><br><br><br><br>	+	<br><br><br><br><br><br><br><br><br>

	==[[/Project/Population Variation\|Population Variation]]==		==[[/Project/Population Variation\|Population Variation]]==