Talk:CH391L/S13/Riboswitches - Revision history

Catherine I. Mortensen at 17:05, 4 March 2013

Catherine I. Mortensen — Mon, 04 Mar 2013 17:05:58 GMT

←Older revision		Revision as of 17:05, 4 March 2013
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	*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:45, 25 February 2013 (EST)''': How practical is DNT detecting E. Coli in airports and other public areas considering the time it takes for E. Coli to start producing fluorescent protein?		*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:45, 25 February 2013 (EST)''': How practical is DNT detecting E. Coli in airports and other public areas considering the time it takes for E. Coli to start producing fluorescent protein?
	**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 18:15, 28 February 2013 (EST)''': For that application it's not useful at all, but in a previous paper they used a fluorescently tagged version of the same aptamer to detect TNT ''in vitro'' in a purpose-built instrument [http://link.springer.com/article/10.1007%2Fs00216-008-2150-5 Biosensor-based on-site explosives detection using aptamers as recognition elements]. The aptamer was generated to bind TNT, but DNT was used in the later paper because it's easier to obtain and still binds well. The E.coli system may be more sensitive for detecting small amounts of DNT or TNT in things like groundwater, where they're using it to detect contamination and the speed of the test doesn't matter as much.		**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 18:15, 28 February 2013 (EST)''': For that application it's not useful at all, but in a previous paper they used a fluorescently tagged version of the same aptamer to detect TNT ''in vitro'' in a purpose-built instrument [http://link.springer.com/article/10.1007%2Fs00216-008-2150-5 Biosensor-based on-site explosives detection using aptamers as recognition elements]. The aptamer was generated to bind TNT, but DNT was used in the later paper because it's easier to obtain and still binds well. The E.coli system may be more sensitive for detecting small amounts of DNT or TNT in things like groundwater, where they're using it to detect contamination and the speed of the test doesn't matter as much.
-	~~=IRES=~~	+
	*'''[[User:Kevin Baldridge\|Kevin Baldridge]] 17:08, 25 February 2013 (EST)''':Are there any known examples of a riboswitch with an IRES (Internal Ribosome Entry Site, an alternate way to initiate translation that doesn't use the Shine Dalgarno sequence) expression platform? If not, that might be something we could look into for iGEM, directed evolution or SELEX to design such a system.		*'''[[User:Kevin Baldridge\|Kevin Baldridge]] 17:08, 25 February 2013 (EST)''':Are there any known examples of a riboswitch with an IRES (Internal Ribosome Entry Site, an alternate way to initiate translation that doesn't use the Shine Dalgarno sequence) expression platform? If not, that might be something we could look into for iGEM, directed evolution or SELEX to design such a system.
	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 08:59, 26 February 2013 (EST)''':What would be the advantage of IRES as opposed to a Shine Dalgarno?		**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 08:59, 26 February 2013 (EST)''':What would be the advantage of IRES as opposed to a Shine Dalgarno?

Catherine I. Mortensen at 17:05, 4 March 2013

Catherine I. Mortensen — Mon, 04 Mar 2013 17:05:09 GMT

←Older revision		Revision as of 17:05, 4 March 2013
Line 1:		Line 1:
	*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:45, 25 February 2013 (EST)''': How practical is DNT detecting E. Coli in airports and other public areas considering the time it takes for E. Coli to start producing fluorescent protein?		*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:45, 25 February 2013 (EST)''': How practical is DNT detecting E. Coli in airports and other public areas considering the time it takes for E. Coli to start producing fluorescent protein?
	**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 18:15, 28 February 2013 (EST)''': For that application it's not useful at all, but in a previous paper they used a fluorescently tagged version of the same aptamer to detect TNT ''in vitro'' in a purpose-built instrument [http://link.springer.com/article/10.1007%2Fs00216-008-2150-5 Biosensor-based on-site explosives detection using aptamers as recognition elements]. The aptamer was generated to bind TNT, but DNT was used in the later paper because it's easier to obtain and still binds well. The E.coli system may be more sensitive for detecting small amounts of DNT or TNT in things like groundwater, where they're using it to detect contamination and the speed of the test doesn't matter as much.		**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 18:15, 28 February 2013 (EST)''': For that application it's not useful at all, but in a previous paper they used a fluorescently tagged version of the same aptamer to detect TNT ''in vitro'' in a purpose-built instrument [http://link.springer.com/article/10.1007%2Fs00216-008-2150-5 Biosensor-based on-site explosives detection using aptamers as recognition elements]. The aptamer was generated to bind TNT, but DNT was used in the later paper because it's easier to obtain and still binds well. The E.coli system may be more sensitive for detecting small amounts of DNT or TNT in things like groundwater, where they're using it to detect contamination and the speed of the test doesn't matter as much.
-		+	=IRES=
	*'''[[User:Kevin Baldridge\|Kevin Baldridge]] 17:08, 25 February 2013 (EST)''':Are there any known examples of a riboswitch with an IRES (Internal Ribosome Entry Site, an alternate way to initiate translation that doesn't use the Shine Dalgarno sequence) expression platform? If not, that might be something we could look into for iGEM, directed evolution or SELEX to design such a system.		*'''[[User:Kevin Baldridge\|Kevin Baldridge]] 17:08, 25 February 2013 (EST)''':Are there any known examples of a riboswitch with an IRES (Internal Ribosome Entry Site, an alternate way to initiate translation that doesn't use the Shine Dalgarno sequence) expression platform? If not, that might be something we could look into for iGEM, directed evolution or SELEX to design such a system.
	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 08:59, 26 February 2013 (EST)''':What would be the advantage of IRES as opposed to a Shine Dalgarno?		**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 08:59, 26 February 2013 (EST)''':What would be the advantage of IRES as opposed to a Shine Dalgarno?

Catherine I. Mortensen at 17:04, 4 March 2013

Catherine I. Mortensen — Mon, 04 Mar 2013 17:04:04 GMT

←Older revision		Revision as of 17:04, 4 March 2013
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	*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 19:24, 28 February 2013 (EST)''': Aerobic bacteria are one of the causes of spontaneous combustion of hay stack, manure, and compost piles. What if an eGFP riboswitch was added to these bacteria so that the more they oxidized their surroundings, the more fluorescent protein they would create. Areas of big manure or compost piles would light up in areas vulnerable to catching on fire.This way farmers could better control hay fires and such by noticing the amount of fluorescent protein present. Is this plausible....?		*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 19:24, 28 February 2013 (EST)''': Aerobic bacteria are one of the causes of spontaneous combustion of hay stack, manure, and compost piles. What if an eGFP riboswitch was added to these bacteria so that the more they oxidized their surroundings, the more fluorescent protein they would create. Areas of big manure or compost piles would light up in areas vulnerable to catching on fire.This way farmers could better control hay fires and such by noticing the amount of fluorescent protein present. Is this plausible....?
	*'''[[User:Alvaro E. Rodriguez M.\|Alvaro E. Rodriguez M.]] 22:13, 28 February 2013 (EST)''': You could also briefly mention what the concept of attenuation means...as part of the historical background and google TPP and IGEM as this relevant connection.		*'''[[User:Alvaro E. Rodriguez M.\|Alvaro E. Rodriguez M.]] 22:13, 28 February 2013 (EST)''': You could also briefly mention what the concept of attenuation means...as part of the historical background and google TPP and IGEM as this relevant connection.
		+	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 12:04, 4 March 2013 (EST)''': TPP works at the post transcriptional level as a transcription factor. Can this be considered a ligand in the context of a riboswitch?
	*'''[[User:Thomas Wall\|Thomas Wall]] 23:17, 28 February 2013 (EST)''': E. coli don't have native cobalamin synthesis, people have incorporated the pathway from salmonella into e. coli but it is a completely anaerobic process. Does anyone know if this an enzymatic requirement or a genetically controlled event? I was thinking that we could use the cobalamin riboswitch to monitor an aerobically or anaerobically functioning synthesis pathway. Also, I believe this would be an industrially relevant process as B12 is needed as a cofactor for many processes.		*'''[[User:Thomas Wall\|Thomas Wall]] 23:17, 28 February 2013 (EST)''': E. coli don't have native cobalamin synthesis, people have incorporated the pathway from salmonella into e. coli but it is a completely anaerobic process. Does anyone know if this an enzymatic requirement or a genetically controlled event? I was thinking that we could use the cobalamin riboswitch to monitor an aerobically or anaerobically functioning synthesis pathway. Also, I believe this would be an industrially relevant process as B12 is needed as a cofactor for many processes.
	*'''[[User:Thomas Wall\|Thomas Wall]] 23:30, 28 February 2013 (EST)''': I'm dumb when in comes to riboswitches, is there any reliable computer method for predicting them in the genome? Also it seems like something generalizable to turn an aptamer into a riboswitch needs to be figured out, or maybe it has?		*'''[[User:Thomas Wall\|Thomas Wall]] 23:30, 28 February 2013 (EST)''': I'm dumb when in comes to riboswitches, is there any reliable computer method for predicting them in the genome? Also it seems like something generalizable to turn an aptamer into a riboswitch needs to be figured out, or maybe it has?

Catherine I. Mortensen at 18:58, 1 March 2013

Catherine I. Mortensen — Fri, 01 Mar 2013 18:58:20 GMT

←Older revision		Revision as of 18:58, 1 March 2013
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	***'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:46, 1 March 2013 (EST)''': The presence of a polyuracil region is not dependent on whether or not the hairpin forms. A polymerase will transcribe through a polyuracil region but the speed at which it does this decreases because something about the chemistry of uracil (possibly due to the fact that uracil can only form 2 hydrogen bonds instead of 3 like guanine and cytosine can) slightly destabilizes the polymerase. When the hairpin forms, the polymerase becomes too unstable to hold onto the polyuracil region. It's as if the polymerase runs over a bump and loses control I'd say.		***'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:46, 1 March 2013 (EST)''': The presence of a polyuracil region is not dependent on whether or not the hairpin forms. A polymerase will transcribe through a polyuracil region but the speed at which it does this decreases because something about the chemistry of uracil (possibly due to the fact that uracil can only form 2 hydrogen bonds instead of 3 like guanine and cytosine can) slightly destabilizes the polymerase. When the hairpin forms, the polymerase becomes too unstable to hold onto the polyuracil region. It's as if the polymerase runs over a bump and loses control I'd say.
	*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?		*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?
-	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:57, 1 March 2013 (EST)''':I know there is a lot of research being done with eukaryotes and riboswitches but most of the papers I came across were focused on designing a ligands but I didn't come across any completely synthetically made riboswitches in eukaryotes.	+	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:58, 1 March 2013 (EST)''':I know there is a lot of research being done with eukaryotes and riboswitches but most of the papers I came across were focused on designing a ligands but I didn't come across any completely synthetically made riboswitches in eukaryotes.

	*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?]		*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?]
	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:38, 1 March 2013 (EST)''': A lot of graphs are measured in hours so I assume hours...		**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:38, 1 March 2013 (EST)''': A lot of graphs are measured in hours so I assume hours...

Catherine I. Mortensen at 18:57, 1 March 2013

Catherine I. Mortensen — Fri, 01 Mar 2013 18:57:39 GMT

←Older revision		Revision as of 18:57, 1 March 2013
Line 23:		Line 23:
	***'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:46, 1 March 2013 (EST)''': The presence of a polyuracil region is not dependent on whether or not the hairpin forms. A polymerase will transcribe through a polyuracil region but the speed at which it does this decreases because something about the chemistry of uracil (possibly due to the fact that uracil can only form 2 hydrogen bonds instead of 3 like guanine and cytosine can) slightly destabilizes the polymerase. When the hairpin forms, the polymerase becomes too unstable to hold onto the polyuracil region. It's as if the polymerase runs over a bump and loses control I'd say.		***'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:46, 1 March 2013 (EST)''': The presence of a polyuracil region is not dependent on whether or not the hairpin forms. A polymerase will transcribe through a polyuracil region but the speed at which it does this decreases because something about the chemistry of uracil (possibly due to the fact that uracil can only form 2 hydrogen bonds instead of 3 like guanine and cytosine can) slightly destabilizes the polymerase. When the hairpin forms, the polymerase becomes too unstable to hold onto the polyuracil region. It's as if the polymerase runs over a bump and loses control I'd say.
	*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?		*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?
		+	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:57, 1 March 2013 (EST)''':I know there is a lot of research being done with eukaryotes and riboswitches but most of the papers I came across were focused on designing a ligands but I didn't come across any completely synthetically made riboswitches in eukaryotes.

	*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?]		*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?]
	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:38, 1 March 2013 (EST)''': A lot of graphs are measured in hours so I assume hours...		**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:38, 1 March 2013 (EST)''': A lot of graphs are measured in hours so I assume hours...

Catherine I. Mortensen at 18:46, 1 March 2013

Catherine I. Mortensen — Fri, 01 Mar 2013 18:46:09 GMT

←Older revision		Revision as of 18:46, 1 March 2013
Line 21:		Line 21:
	*'''[[User:Thomas Wall\|Thomas Wall]] 23:30, 28 February 2013 (EST)''': I'm dumb when in comes to riboswitches, is there any reliable computer method for predicting them in the genome? Also it seems like something generalizable to turn an aptamer into a riboswitch needs to be figured out, or maybe it has?		*'''[[User:Thomas Wall\|Thomas Wall]] 23:30, 28 February 2013 (EST)''': I'm dumb when in comes to riboswitches, is there any reliable computer method for predicting them in the genome? Also it seems like something generalizable to turn an aptamer into a riboswitch needs to be figured out, or maybe it has?
	*'''[[User:Yunle Huang\|Yunle Huang]] 00:19, 1 March 2013 (EST)''': Could someone clarify why the polymerase falls off when the hairpin forms? Does the hairpin formation reveal the polyuracil region?		*'''[[User:Yunle Huang\|Yunle Huang]] 00:19, 1 March 2013 (EST)''': Could someone clarify why the polymerase falls off when the hairpin forms? Does the hairpin formation reveal the polyuracil region?
-		+	***'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:46, 1 March 2013 (EST)''': The presence of a polyuracil region is not dependent on whether or not the hairpin forms. A polymerase will transcribe through a polyuracil region but the speed at which it does this decreases because something about the chemistry of uracil (possibly due to the fact that uracil can only form 2 hydrogen bonds instead of 3 like guanine and cytosine can) slightly destabilizes the polymerase. When the hairpin forms, the polymerase becomes too unstable to hold onto the polyuracil region. It's as if the polymerase runs over a bump and loses control I'd say.
	*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?		*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?

	*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?]		*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?]
	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:38, 1 March 2013 (EST)''': A lot of graphs are measured in hours so I assume hours...		**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:38, 1 March 2013 (EST)''': A lot of graphs are measured in hours so I assume hours...

Catherine I. Mortensen at 18:38, 1 March 2013

Catherine I. Mortensen — Fri, 01 Mar 2013 18:38:06 GMT

←Older revision		Revision as of 18:38, 1 March 2013
Line 24:		Line 24:
	*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?		*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?

-	*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?	+	*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?]
		+	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:38, 1 March 2013 (EST)''': A lot of graphs are measured in hours so I assume hours...

Thomas Wall at 06:37, 1 March 2013

Thomas Wall — Fri, 01 Mar 2013 06:37:28 GMT

←Older revision		Revision as of 06:37, 1 March 2013
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	*'''[[User:Alvaro E. Rodriguez M.\|Alvaro E. Rodriguez M.]] 22:13, 28 February 2013 (EST)''': You could also briefly mention what the concept of attenuation means...as part of the historical background and google TPP and IGEM as this relevant connection.		*'''[[User:Alvaro E. Rodriguez M.\|Alvaro E. Rodriguez M.]] 22:13, 28 February 2013 (EST)''': You could also briefly mention what the concept of attenuation means...as part of the historical background and google TPP and IGEM as this relevant connection.
	*'''[[User:Thomas Wall\|Thomas Wall]] 23:17, 28 February 2013 (EST)''': E. coli don't have native cobalamin synthesis, people have incorporated the pathway from salmonella into e. coli but it is a completely anaerobic process. Does anyone know if this an enzymatic requirement or a genetically controlled event? I was thinking that we could use the cobalamin riboswitch to monitor an aerobically or anaerobically functioning synthesis pathway. Also, I believe this would be an industrially relevant process as B12 is needed as a cofactor for many processes.		*'''[[User:Thomas Wall\|Thomas Wall]] 23:17, 28 February 2013 (EST)''': E. coli don't have native cobalamin synthesis, people have incorporated the pathway from salmonella into e. coli but it is a completely anaerobic process. Does anyone know if this an enzymatic requirement or a genetically controlled event? I was thinking that we could use the cobalamin riboswitch to monitor an aerobically or anaerobically functioning synthesis pathway. Also, I believe this would be an industrially relevant process as B12 is needed as a cofactor for many processes.
-	*'''[[User:Thomas Wall\|Thomas Wall]] 23:30, 28 February 2013 (EST)''': I'm dumb when in comes to riboswitches, is ~~their~~ any reliable computer method for predicting them in the genome? Also it seems like something generalizable to turn an aptamer into a riboswitch needs to be figured out, or maybe it has?	+	*'''[[User:Thomas Wall\|Thomas Wall]] 23:30, 28 February 2013 (EST)''': I'm dumb when in comes to riboswitches, is there any reliable computer method for predicting them in the genome? Also it seems like something generalizable to turn an aptamer into a riboswitch needs to be figured out, or maybe it has?
	*'''[[User:Yunle Huang\|Yunle Huang]] 00:19, 1 March 2013 (EST)''': Could someone clarify why the polymerase falls off when the hairpin forms? Does the hairpin formation reveal the polyuracil region?		*'''[[User:Yunle Huang\|Yunle Huang]] 00:19, 1 March 2013 (EST)''': Could someone clarify why the polymerase falls off when the hairpin forms? Does the hairpin formation reveal the polyuracil region?

Marco D Howard at 06:22, 1 March 2013

Marco D Howard — Fri, 01 Mar 2013 06:22:06 GMT

←Older revision		Revision as of 06:22, 1 March 2013
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	*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?		*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?
		+
		+	*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?

Siddharth Das: question

Siddharth Das — Fri, 01 Mar 2013 06:13:38 GMT

question

←Older revision		Revision as of 06:13, 1 March 2013
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	*'''[[User:Thomas Wall\|Thomas Wall]] 23:30, 28 February 2013 (EST)''': I'm dumb when in comes to riboswitches, is their any reliable computer method for predicting them in the genome? Also it seems like something generalizable to turn an aptamer into a riboswitch needs to be figured out, or maybe it has?		*'''[[User:Thomas Wall\|Thomas Wall]] 23:30, 28 February 2013 (EST)''': I'm dumb when in comes to riboswitches, is their any reliable computer method for predicting them in the genome? Also it seems like something generalizable to turn an aptamer into a riboswitch needs to be figured out, or maybe it has?
	*'''[[User:Yunle Huang\|Yunle Huang]] 00:19, 1 March 2013 (EST)''': Could someone clarify why the polymerase falls off when the hairpin forms? Does the hairpin formation reveal the polyuracil region?		*'''[[User:Yunle Huang\|Yunle Huang]] 00:19, 1 March 2013 (EST)''': Could someone clarify why the polymerase falls off when the hairpin forms? Does the hairpin formation reveal the polyuracil region?
		+
		+	*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?

←Older revision		Revision as of 17:05, 4 March 2013
Line 1:		Line 1:
	*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:45, 25 February 2013 (EST)''': How practical is DNT detecting E. Coli in airports and other public areas considering the time it takes for E. Coli to start producing fluorescent protein?		*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:45, 25 February 2013 (EST)''': How practical is DNT detecting E. Coli in airports and other public areas considering the time it takes for E. Coli to start producing fluorescent protein?
	**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 18:15, 28 February 2013 (EST)''': For that application it's not useful at all, but in a previous paper they used a fluorescently tagged version of the same aptamer to detect TNT ''in vitro'' in a purpose-built instrument [http://link.springer.com/article/10.1007%2Fs00216-008-2150-5 Biosensor-based on-site explosives detection using aptamers as recognition elements]. The aptamer was generated to bind TNT, but DNT was used in the later paper because it's easier to obtain and still binds well. The E.coli system may be more sensitive for detecting small amounts of DNT or TNT in things like groundwater, where they're using it to detect contamination and the speed of the test doesn't matter as much.		**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 18:15, 28 February 2013 (EST)''': For that application it's not useful at all, but in a previous paper they used a fluorescently tagged version of the same aptamer to detect TNT ''in vitro'' in a purpose-built instrument [http://link.springer.com/article/10.1007%2Fs00216-008-2150-5 Biosensor-based on-site explosives detection using aptamers as recognition elements]. The aptamer was generated to bind TNT, but DNT was used in the later paper because it's easier to obtain and still binds well. The E.coli system may be more sensitive for detecting small amounts of DNT or TNT in things like groundwater, where they're using it to detect contamination and the speed of the test doesn't matter as much.
-	~~=IRES=~~	+
	*'''[[User:Kevin Baldridge\|Kevin Baldridge]] 17:08, 25 February 2013 (EST)''':Are there any known examples of a riboswitch with an IRES (Internal Ribosome Entry Site, an alternate way to initiate translation that doesn't use the Shine Dalgarno sequence) expression platform? If not, that might be something we could look into for iGEM, directed evolution or SELEX to design such a system.		*'''[[User:Kevin Baldridge\|Kevin Baldridge]] 17:08, 25 February 2013 (EST)''':Are there any known examples of a riboswitch with an IRES (Internal Ribosome Entry Site, an alternate way to initiate translation that doesn't use the Shine Dalgarno sequence) expression platform? If not, that might be something we could look into for iGEM, directed evolution or SELEX to design such a system.
	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 08:59, 26 February 2013 (EST)''':What would be the advantage of IRES as opposed to a Shine Dalgarno?		**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 08:59, 26 February 2013 (EST)''':What would be the advantage of IRES as opposed to a Shine Dalgarno?

←Older revision		Revision as of 17:05, 4 March 2013
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	*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:45, 25 February 2013 (EST)''': How practical is DNT detecting E. Coli in airports and other public areas considering the time it takes for E. Coli to start producing fluorescent protein?		*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:45, 25 February 2013 (EST)''': How practical is DNT detecting E. Coli in airports and other public areas considering the time it takes for E. Coli to start producing fluorescent protein?
	**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 18:15, 28 February 2013 (EST)''': For that application it's not useful at all, but in a previous paper they used a fluorescently tagged version of the same aptamer to detect TNT ''in vitro'' in a purpose-built instrument [http://link.springer.com/article/10.1007%2Fs00216-008-2150-5 Biosensor-based on-site explosives detection using aptamers as recognition elements]. The aptamer was generated to bind TNT, but DNT was used in the later paper because it's easier to obtain and still binds well. The E.coli system may be more sensitive for detecting small amounts of DNT or TNT in things like groundwater, where they're using it to detect contamination and the speed of the test doesn't matter as much.		**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 18:15, 28 February 2013 (EST)''': For that application it's not useful at all, but in a previous paper they used a fluorescently tagged version of the same aptamer to detect TNT ''in vitro'' in a purpose-built instrument [http://link.springer.com/article/10.1007%2Fs00216-008-2150-5 Biosensor-based on-site explosives detection using aptamers as recognition elements]. The aptamer was generated to bind TNT, but DNT was used in the later paper because it's easier to obtain and still binds well. The E.coli system may be more sensitive for detecting small amounts of DNT or TNT in things like groundwater, where they're using it to detect contamination and the speed of the test doesn't matter as much.
-		+	=IRES=
	*'''[[User:Kevin Baldridge\|Kevin Baldridge]] 17:08, 25 February 2013 (EST)''':Are there any known examples of a riboswitch with an IRES (Internal Ribosome Entry Site, an alternate way to initiate translation that doesn't use the Shine Dalgarno sequence) expression platform? If not, that might be something we could look into for iGEM, directed evolution or SELEX to design such a system.		*'''[[User:Kevin Baldridge\|Kevin Baldridge]] 17:08, 25 February 2013 (EST)''':Are there any known examples of a riboswitch with an IRES (Internal Ribosome Entry Site, an alternate way to initiate translation that doesn't use the Shine Dalgarno sequence) expression platform? If not, that might be something we could look into for iGEM, directed evolution or SELEX to design such a system.
	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 08:59, 26 February 2013 (EST)''':What would be the advantage of IRES as opposed to a Shine Dalgarno?		**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 08:59, 26 February 2013 (EST)''':What would be the advantage of IRES as opposed to a Shine Dalgarno?

←Older revision		Revision as of 17:04, 4 March 2013
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	*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 19:24, 28 February 2013 (EST)''': Aerobic bacteria are one of the causes of spontaneous combustion of hay stack, manure, and compost piles. What if an eGFP riboswitch was added to these bacteria so that the more they oxidized their surroundings, the more fluorescent protein they would create. Areas of big manure or compost piles would light up in areas vulnerable to catching on fire.This way farmers could better control hay fires and such by noticing the amount of fluorescent protein present. Is this plausible....?		*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 19:24, 28 February 2013 (EST)''': Aerobic bacteria are one of the causes of spontaneous combustion of hay stack, manure, and compost piles. What if an eGFP riboswitch was added to these bacteria so that the more they oxidized their surroundings, the more fluorescent protein they would create. Areas of big manure or compost piles would light up in areas vulnerable to catching on fire.This way farmers could better control hay fires and such by noticing the amount of fluorescent protein present. Is this plausible....?
	*'''[[User:Alvaro E. Rodriguez M.\|Alvaro E. Rodriguez M.]] 22:13, 28 February 2013 (EST)''': You could also briefly mention what the concept of attenuation means...as part of the historical background and google TPP and IGEM as this relevant connection.		*'''[[User:Alvaro E. Rodriguez M.\|Alvaro E. Rodriguez M.]] 22:13, 28 February 2013 (EST)''': You could also briefly mention what the concept of attenuation means...as part of the historical background and google TPP and IGEM as this relevant connection.
		+	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 12:04, 4 March 2013 (EST)''': TPP works at the post transcriptional level as a transcription factor. Can this be considered a ligand in the context of a riboswitch?
	*'''[[User:Thomas Wall\|Thomas Wall]] 23:17, 28 February 2013 (EST)''': E. coli don't have native cobalamin synthesis, people have incorporated the pathway from salmonella into e. coli but it is a completely anaerobic process. Does anyone know if this an enzymatic requirement or a genetically controlled event? I was thinking that we could use the cobalamin riboswitch to monitor an aerobically or anaerobically functioning synthesis pathway. Also, I believe this would be an industrially relevant process as B12 is needed as a cofactor for many processes.		*'''[[User:Thomas Wall\|Thomas Wall]] 23:17, 28 February 2013 (EST)''': E. coli don't have native cobalamin synthesis, people have incorporated the pathway from salmonella into e. coli but it is a completely anaerobic process. Does anyone know if this an enzymatic requirement or a genetically controlled event? I was thinking that we could use the cobalamin riboswitch to monitor an aerobically or anaerobically functioning synthesis pathway. Also, I believe this would be an industrially relevant process as B12 is needed as a cofactor for many processes.
	*'''[[User:Thomas Wall\|Thomas Wall]] 23:30, 28 February 2013 (EST)''': I'm dumb when in comes to riboswitches, is there any reliable computer method for predicting them in the genome? Also it seems like something generalizable to turn an aptamer into a riboswitch needs to be figured out, or maybe it has?		*'''[[User:Thomas Wall\|Thomas Wall]] 23:30, 28 February 2013 (EST)''': I'm dumb when in comes to riboswitches, is there any reliable computer method for predicting them in the genome? Also it seems like something generalizable to turn an aptamer into a riboswitch needs to be figured out, or maybe it has?

←Older revision		Revision as of 18:58, 1 March 2013
Line 23:		Line 23:
	***'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:46, 1 March 2013 (EST)''': The presence of a polyuracil region is not dependent on whether or not the hairpin forms. A polymerase will transcribe through a polyuracil region but the speed at which it does this decreases because something about the chemistry of uracil (possibly due to the fact that uracil can only form 2 hydrogen bonds instead of 3 like guanine and cytosine can) slightly destabilizes the polymerase. When the hairpin forms, the polymerase becomes too unstable to hold onto the polyuracil region. It's as if the polymerase runs over a bump and loses control I'd say.		***'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:46, 1 March 2013 (EST)''': The presence of a polyuracil region is not dependent on whether or not the hairpin forms. A polymerase will transcribe through a polyuracil region but the speed at which it does this decreases because something about the chemistry of uracil (possibly due to the fact that uracil can only form 2 hydrogen bonds instead of 3 like guanine and cytosine can) slightly destabilizes the polymerase. When the hairpin forms, the polymerase becomes too unstable to hold onto the polyuracil region. It's as if the polymerase runs over a bump and loses control I'd say.
	*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?		*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?
-	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:57, 1 March 2013 (EST)''':I know there is a lot of research being done with eukaryotes and riboswitches but most of the papers I came across were focused on designing a ligands but I didn't come across any completely synthetically made riboswitches in eukaryotes.	+	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:58, 1 March 2013 (EST)''':I know there is a lot of research being done with eukaryotes and riboswitches but most of the papers I came across were focused on designing a ligands but I didn't come across any completely synthetically made riboswitches in eukaryotes.

	*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?]		*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?]
	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:38, 1 March 2013 (EST)''': A lot of graphs are measured in hours so I assume hours...		**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:38, 1 March 2013 (EST)''': A lot of graphs are measured in hours so I assume hours...

←Older revision		Revision as of 18:57, 1 March 2013
Line 23:		Line 23:
	***'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:46, 1 March 2013 (EST)''': The presence of a polyuracil region is not dependent on whether or not the hairpin forms. A polymerase will transcribe through a polyuracil region but the speed at which it does this decreases because something about the chemistry of uracil (possibly due to the fact that uracil can only form 2 hydrogen bonds instead of 3 like guanine and cytosine can) slightly destabilizes the polymerase. When the hairpin forms, the polymerase becomes too unstable to hold onto the polyuracil region. It's as if the polymerase runs over a bump and loses control I'd say.		***'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:46, 1 March 2013 (EST)''': The presence of a polyuracil region is not dependent on whether or not the hairpin forms. A polymerase will transcribe through a polyuracil region but the speed at which it does this decreases because something about the chemistry of uracil (possibly due to the fact that uracil can only form 2 hydrogen bonds instead of 3 like guanine and cytosine can) slightly destabilizes the polymerase. When the hairpin forms, the polymerase becomes too unstable to hold onto the polyuracil region. It's as if the polymerase runs over a bump and loses control I'd say.
	*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?		*'''[[User:Siddharth Das\|Siddharth Das]] 00:58, 1 March 2013 (EST)''': Can riboswitches be synthesized chemically? Correct me if I'm wrong, but I find it interesting that the rational design of riboswitches could provide a means of mediating gene expression in other organisms. What does this "promiscuity" translate to in terms of an evolutionary standpoint?
		+	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:57, 1 March 2013 (EST)''':I know there is a lot of research being done with eukaryotes and riboswitches but most of the papers I came across were focused on designing a ligands but I didn't come across any completely synthetically made riboswitches in eukaryotes.

	*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?]		*'''[[User: Marco Howard\|Marco Howard]] What is the time scale for riboswitche to function. For example, if you use them them as sensors how long does it take to get a positive or negative signal. Also, if you are using them to express a gene, how long does it take for a protein to folded and functional?]
	**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:38, 1 March 2013 (EST)''': A lot of graphs are measured in hours so I assume hours...		**'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 13:38, 1 March 2013 (EST)''': A lot of graphs are measured in hours so I assume hours...