User:Federico Castro M/Undeveloped Ideas - Revision history

Federico Castro M at 17:37, 29 May 2008

2008-05-29T17:37:55Z

←Older revision		Revision as of 17:37, 29 May 2008
Line 1:		Line 1:
	These are ideas that are not completely developed; they might be very basic very crazy or form part of a project that is not currently developed. If you are interested in developing some of these ideas or are already working on them or something related, please contact me, I would be very glad to share information, collaborate and know about the outcome of the project.		These are ideas that are not completely developed; they might be very basic very crazy or form part of a project that is not currently developed. If you are interested in developing some of these ideas or are already working on them or something related, please contact me, I would be very glad to share information, collaborate and know about the outcome of the project.

-	~~#To look for differences in genes associated with the development of the nervous system of chimpanzees and humans.~~	+
-	#Given two identical populations that are independently subjected to identical evolutionary forces, we should expect to find a predictable rate of convergences. The rate of convergences gives us information about the topography of the adaptive map of the populations and how and where can it move.	+	#The problem with antibiotic resistance and VIH drug resistance is an evolutive problem. We could deal with that with an evolutionary approach; we should lead the bacteria or viruses to an isolated peak of adaptation and then submerge that peak.
-	#The problem with antibiotic resistance and VIH drug resistance ~~are~~ evolutive ~~problems~~. We could deal with ~~the problem~~ with an evolutionary approach; we should lead the bacteria or viruses to an isolated peak of adaptation and then submerge that peak.	+
-	#Analyze LUCA (or at least read papers about it). The information about the Last Common Ancestor will provide us with information about the modules it had and this could be very helpful to create an organism from zero.	+
-	#Promoters surely have different rate of change than the ORF they control. Do ORF evolve faster than promoters or viceverza? My guess is that changes in the promoters and not in the ORF account for the major differences betwen organisms… the activity of promoters makes up for the differences between a caterpillar and a butterfly and might also be accounted for differences between humans and chimpanzees.	+
-	#Where did coat proteins of virus come from? How did they evolved? Are they ancient? They seem perfectly fit for protect DNA and their ancestors (or at leas similar analogous genes) might have served the same function eons ago.	+
	#The immune system uses a library of sequences to assemble a great variety of proteins. We could construct and use a similar library of proteins for protein design (The Silver/Phillips method of assembly would be very useful for achieving this goal).		#The immune system uses a library of sequences to assemble a great variety of proteins. We could construct and use a similar library of proteins for protein design (The Silver/Phillips method of assembly would be very useful for achieving this goal).
	#Myxobacteria have the ability to generate complex structures. Could we isolate the genes responsible for that behavior and introduce it in ''Escherichia coli''?		#Myxobacteria have the ability to generate complex structures. Could we isolate the genes responsible for that behavior and introduce it in ''Escherichia coli''?
-	#The homeotic genes have been extensively studied in plants and animals (MADS, Homeobox)... what about fungi and algae? Does regulatory genes have something in common? Could we isolate tose genes and insert them in bacteria?
	#A devise capable of certain function could be achieved, by randomly rewiring a genetic network with invertases and selecting the desired networks.		#A devise capable of certain function could be achieved, by randomly rewiring a genetic network with invertases and selecting the desired networks.
-	#Make a self destructive F plasmid, this would allow some information to be quickly delivered and once it is expressed it would disappear. The plasmid should codify for a restriction endonuclease that would digest the plasmid to tiny bits of DNA, the endonuclease should be very specific and have a very long recognition sequence to ensure that the Bacteria will not be harmed. ~~''Agent Coli, This plasmid will be self destructed in 30 secs''~~	+	#Make a self destructive F plasmid, this would allow some information to be quickly delivered and once it is expressed it would disappear. The plasmid should codify for a restriction endonuclease that would digest the plasmid to tiny bits of DNA, the endonuclease should be very specific and have a very long recognition sequence to ensure that the Bacteria will not be harmed.
	#We could use hormones as means of communication betwen bacteria, while there are some mechanisms implemented for communication, they lack the fast response that is often needed in a multicellular organism to coordinate cells (the molecule used by the luxR/l system as a signal, HSL, takes up to 24 hours to degradate). The system used for producing insulin and detecting the levels of sugars have already been developed by the NYMU 2007 iGEM team. It could be easily modified for communication between cells and the activity of the devise could be easily quantified with cheap medical equipments.		#We could use hormones as means of communication betwen bacteria, while there are some mechanisms implemented for communication, they lack the fast response that is often needed in a multicellular organism to coordinate cells (the molecule used by the luxR/l system as a signal, HSL, takes up to 24 hours to degradate). The system used for producing insulin and detecting the levels of sugars have already been developed by the NYMU 2007 iGEM team. It could be easily modified for communication between cells and the activity of the devise could be easily quantified with cheap medical equipments.
-	#We could also measure POPs by other means than fluorescente shuch as the concentration of a diffusible insuline (insuline levels can be quantified very fast and cheap) or ~~anthibiotic~~ resistance (we could manually count the number of colonies). This could make the ~~measurements of~~ available to laboratories with no funds or equipment and perhaps it would make it all easier.	+	#Use DAP as means to produce a cell communication system, all the parts seemed to work (check the Paris iGEM team of 2007). that also would offer an alternative to the LuxR/LuxL.
		+	#We could also measure POPs by other means than fluorescente shuch as the concentration of a diffusible insuline (insuline levels can be quantified very fast and fairly cheap) or antibiotic resistance (we could manually count the number of colonies). This could make the measurement available to laboratories '''with no funds or equipment''' and perhaps it would make it all easier.
		+	#Also check [[User:Federico_Castro_M/Projects \| My undeveloped projects]]

Ricardo Vidal: FedericoC Undeveloped Ideas moved to User:Federico Castro M/Undeveloped Ideas: Misplaced page outside user namespace.

2008-03-06T03:00:06Z

FedericoC Undeveloped Ideas moved to User:Federico Castro M/Undeveloped Ideas: Misplaced page outside user namespace.

←Older revision

Revision as of 03:00, 6 March 2008

Federico Castro M at 23:06, 26 February 2008

2008-02-26T23:06:00Z

←Older revision		Revision as of 23:06, 26 February 2008
Line 3:		Line 3:
	#To look for differences in genes associated with the development of the nervous system of chimpanzees and humans.		#To look for differences in genes associated with the development of the nervous system of chimpanzees and humans.
	#Given two identical populations that are independently subjected to identical evolutionary forces, we should expect to find a predictable rate of convergences. The rate of convergences gives us information about the topography of the adaptive map of the populations and how and where can it move.		#Given two identical populations that are independently subjected to identical evolutionary forces, we should expect to find a predictable rate of convergences. The rate of convergences gives us information about the topography of the adaptive map of the populations and how and where can it move.
-	#The problem with antibiotic resistance and VIH drug resistance are evolutive problems. We ~~should~~ deal with the problem with an evolutionary approach; we should lead the bacteria or viruses to an isolated peak of adaptation and then submerge that peak.	+	#The problem with antibiotic resistance and VIH drug resistance are evolutive problems. We could deal with the problem with an evolutionary approach; we should lead the bacteria or viruses to an isolated peak of adaptation and then submerge that peak.
	#Analyze LUCA (or at least read papers about it). The information about the Last Common Ancestor will provide us with information about the modules it had and this could be very helpful to create an organism from zero.		#Analyze LUCA (or at least read papers about it). The information about the Last Common Ancestor will provide us with information about the modules it had and this could be very helpful to create an organism from zero.
	#Promoters surely have different rate of change than the ORF they control. Do ORF evolve faster than promoters or viceverza? My guess is that changes in the promoters and not in the ORF account for the major differences betwen organisms… the activity of promoters makes up for the differences between a caterpillar and a butterfly and might also be accounted for differences between humans and chimpanzees.		#Promoters surely have different rate of change than the ORF they control. Do ORF evolve faster than promoters or viceverza? My guess is that changes in the promoters and not in the ORF account for the major differences betwen organisms… the activity of promoters makes up for the differences between a caterpillar and a butterfly and might also be accounted for differences between humans and chimpanzees.

Federico Castro M at 23:05, 26 February 2008

2008-02-26T23:05:00Z

←Older revision		Revision as of 23:05, 26 February 2008
Line 5:		Line 5:
	#The problem with antibiotic resistance and VIH drug resistance are evolutive problems. We should deal with the problem with an evolutionary approach; we should lead the bacteria or viruses to an isolated peak of adaptation and then submerge that peak.		#The problem with antibiotic resistance and VIH drug resistance are evolutive problems. We should deal with the problem with an evolutionary approach; we should lead the bacteria or viruses to an isolated peak of adaptation and then submerge that peak.
	#Analyze LUCA (or at least read papers about it). The information about the Last Common Ancestor will provide us with information about the modules it had and this could be very helpful to create an organism from zero.		#Analyze LUCA (or at least read papers about it). The information about the Last Common Ancestor will provide us with information about the modules it had and this could be very helpful to create an organism from zero.
-	#Promoters surely have different rate of ~~chance~~ than the ORF they control. Do ORF evolve faster than promoters or viceverza? My guess is that changes in the promoters and not in the ORF account for the major differences ~~within~~ organisms… the activity of promoters makes up for the differences between ~~the~~ caterpillar and ~~the~~ butterfly and might also be accounted for differences between humans and chimpanzees.	+	#Promoters surely have different rate of change than the ORF they control. Do ORF evolve faster than promoters or viceverza? My guess is that changes in the promoters and not in the ORF account for the major differences betwen organisms… the activity of promoters makes up for the differences between a caterpillar and a butterfly and might also be accounted for differences between humans and chimpanzees.
-	#Where did coat proteins of virus come from? How did they evolved?	+	#Where did coat proteins of virus come from? How did they evolved? Are they ancient? They seem perfectly fit for protect DNA and their ancestors (or at leas similar analogous genes) might have served the same function eons ago.
-	#The immune system uses a library of sequences to assemble a great variety of proteins. We ~~should~~ construct and use a similar library of proteins for protein design (The Silver/Phillips method of assembly would be very useful for achieving this goal).	+	#The immune system uses a library of sequences to assemble a great variety of proteins. We could construct and use a similar library of proteins for protein design (The Silver/Phillips method of assembly would be very useful for achieving this goal).
-	#Myxobacteria have the ability to generate complex structures. Could we isolate the genes responsible for ~~thet~~ behavior and introduce it in ~~Escherichiacoli~~?	+	#Myxobacteria have the ability to generate complex structures. Could we isolate the genes responsible for that behavior and introduce it in ''Escherichia coli''?
-	#In plants ~~the development is regulated with the~~ MADS, ~~in animals some~~ Homeobox ~~genes…~~ what about fungi and algae? Does regulatory genes have something in common? Could we isolate tose genes and insert them in bacteria?	+	#The homeotic genes have been extensively studied in plants and animals (MADS, Homeobox)... what about fungi and algae? Does regulatory genes have something in common? Could we isolate tose genes and insert them in bacteria?
-	#A devise ~~could be~~ capable of ~~achieving a~~ function could be achieved, by randomly rewiring a genetic network with invertases and selecting the desired networks	+	#A devise capable of certain function could be achieved, by randomly rewiring a genetic network with invertases and selecting the desired networks.
-	#Make a self destructive F plasmid, this would allow some information to be quickly ~~transmitted~~ and once it is expressed it would disappear. The plasmid should codify for a restriction endonuclease that would digest the plasmid to tiny bits of DNA, the endonuclease should be very specific and have a very long recognition sequence to ensure that the Bacteria will not be harmed.	+	#Make a self destructive F plasmid, this would allow some information to be quickly delivered and once it is expressed it would disappear. The plasmid should codify for a restriction endonuclease that would digest the plasmid to tiny bits of DNA, the endonuclease should be very specific and have a very long recognition sequence to ensure that the Bacteria will not be harmed. ''Agent Coli, This plasmid will be self destructed in 30 secs''
-	#We could use hormones as means of communication ~~in small organisms~~, while there are some mechanisms implemented for communication, they lack the fast response that is often needed in a multicellular organism to coordinate cells (the molecule used by the luxR/l system as a signal, HSL, takes up to 24 hours to degradate). The system used for producing insulin and detecting the levels of sugars have already been developed by the NYMU 2007 iGEM team. It could be easily modified for communication between cells and the activity of the devise could be easily quantified with cheap medical equipments.	+	#We could use hormones as means of communication betwen bacteria, while there are some mechanisms implemented for communication, they lack the fast response that is often needed in a multicellular organism to coordinate cells (the molecule used by the luxR/l system as a signal, HSL, takes up to 24 hours to degradate). The system used for producing insulin and detecting the levels of sugars have already been developed by the NYMU 2007 iGEM team. It could be easily modified for communication between cells and the activity of the devise could be easily quantified with cheap medical equipments.
	#We could also measure POPs by other means than fluorescente shuch as the concentration of a diffusible insuline (insuline levels can be quantified very fast and cheap) or anthibiotic resistance (we could manually count the number of colonies). This could make the measurements of available to laboratories with no funds or equipment and perhaps it would make it all easier.		#We could also measure POPs by other means than fluorescente shuch as the concentration of a diffusible insuline (insuline levels can be quantified very fast and cheap) or anthibiotic resistance (we could manually count the number of colonies). This could make the measurements of available to laboratories with no funds or equipment and perhaps it would make it all easier.

Federico Castro M at 22:52, 26 February 2008

2008-02-26T22:52:50Z

←Older revision		Revision as of 22:52, 26 February 2008
Line 1:		Line 1:
	These are ideas that are not completely developed; they might be very basic very crazy or form part of a project that is not currently developed. If you are interested in developing some of these ideas or are already working on them or something related, please contact me, I would be very glad to share information, collaborate and know about the outcome of the project.		These are ideas that are not completely developed; they might be very basic very crazy or form part of a project that is not currently developed. If you are interested in developing some of these ideas or are already working on them or something related, please contact me, I would be very glad to share information, collaborate and know about the outcome of the project.

-	# To look for differences in genes associated with the development of the nervous system of chimpanzees and humans.	+	#To look for differences in genes associated with the development of the nervous system of chimpanzees and humans.
-		+	#Given two identical populations that are independently subjected to identical evolutionary forces, we should expect to find a predictable rate of convergences. The rate of convergences gives us information about the topography of the adaptive map of the populations and how and where can it move.
-	# Given two identical populations that are independently subjected to identical evolutionary forces, we should expect to find a predictable rate of convergences. The rate of convergences gives us information about the topography of the adaptive map of the populations and how and where can it move.	+	#The problem with antibiotic resistance and VIH drug resistance are evolutive problems. We should deal with the problem with an evolutionary approach; we should lead the bacteria or viruses to an isolated peak of adaptation and then submerge that peak.
-		+	#Analyze LUCA (or at least read papers about it). The information about the Last Common Ancestor will provide us with information about the modules it had and this could be very helpful to create an organism from zero.
-	# The problem with antibiotic resistance and VIH drug resistance are evolutive problems. We should deal with the problem with an evolutionary approach; we should lead the bacteria or viruses to an isolated peak of adaptation and then submerge that peak.	+	#Promoters surely have different rate of chance than the ORF they control. Do ORF evolve faster than promoters or viceverza? My guess is that changes in the promoters and not in the ORF account for the major differences within organisms… the activity of promoters makes up for the differences between the caterpillar and the butterfly and might also be accounted for differences between humans and chimpanzees.
-		+	#Where did coat proteins of virus come from? How did they evolved?
-	# Analyze LUCA (or at least read papers about it). The information about the Last Common Ancestor will provide us with information about the modules it had and this could be very helpful to create an organism from zero.	+	#The immune system uses a library of sequences to assemble a great variety of proteins. We should construct and use a similar library of proteins for protein design (The Silver/Phillips method of assembly would be very useful for achieving this goal).
-		+	#Myxobacteria have the ability to generate complex structures. Could we isolate the genes responsible for thet behavior and introduce it in Escherichiacoli?
-	# Promoters surely have different rate of chance than the ORF they control. Do ORF evolve faster than promoters or viceverza? My guess is that changes in the promoters and not in the ORF account for the major differences within organisms… the activity of promoters makes up for the differences between the caterpillar and the butterfly and might also be accounted for differences between humans and chimpanzees.	+	#In plants the development is regulated with the MADS, in animals some Homeobox genes… what about fungi and algae? Does regulatory genes have something in common? Could we isolate tose genes and insert them in bacteria?
-		+	#A devise could be capable of achieving a function could be achieved, by randomly rewiring a genetic network with invertases and selecting the desired networks
-	# Where did coat proteins of virus come from? How did they evolved?	+	#Make a self destructive F plasmid, this would allow some information to be quickly transmitted and once it is expressed it would disappear. The plasmid should codify for a restriction endonuclease that would digest the plasmid to tiny bits of DNA, the endonuclease should be very specific and have a very long recognition sequence to ensure that the Bacteria will not be harmed.
-		+	#We could use hormones as means of communication in small organisms, while there are some mechanisms implemented for communication, they lack the fast response that is often needed in a multicellular organism to coordinate cells (the molecule used by the luxR/l system as a signal, HSL, takes up to 24 hours to degradate). The system used for producing insulin and detecting the levels of sugars have already been developed by the NYMU 2007 iGEM team. It could be easily modified for communication between cells and the activity of the devise could be easily quantified with cheap medical equipments.
-	# The immune system uses a library of sequences to assemble a great variety of proteins. We should construct and use a similar library of proteins for protein design (The Silver/Phillips method of assembly would be very useful for achieving this goal).	+	#We could also measure POPs by other means than fluorescente shuch as the concentration of a diffusible insuline (insuline levels can be quantified very fast and cheap) or anthibiotic resistance (we could manually count the number of colonies). This could make the measurements of available to laboratories with no funds or equipment and perhaps it would make it all easier.
-		+
-	# Myxobacteria have the ability to generate complex structures. Could we isolate the genes responsible for thet behavior and introduce it in Escherichiacoli?	+
-		+
-	# In plants the development is regulated with the MADS, in animals some Homeobox genes… what about fungi and algae? Does regulatory genes have something in common? Could we isolate tose genes and insert them in bacteria?	+
-		+
-	# A devise could be capable of achieving a function could be achieved, by randomly rewiring a genetic network with invertases and selecting the desired networks	+
-		+
-	# Make a self destructive F plasmid, this would allow some information to be quickly transmitted and once it is expressed it would disappear. The plasmid should codify for a restriction endonuclease that would digest the plasmid to tiny bits of DNA, the endonuclease should be very specific and have a very long recognition sequence to ensure that the Bacteria will not be harmed.	+
-		+
-	# We could use hormones as means of communication in small organisms, while there are some mechanisms implemented for communication, they lack the fast response that is often needed in a multicellular organism to coordinate cells (the molecule used by the luxR/l system as a signal, HSL, takes up to 24 hours to degradate). The system used for producing insulin and detecting the levels of sugars have already been developed by the NYMU 2007 iGEM team. It could be easily modified for communication between cells and the activity of the devise could be easily quantified with cheap medical equipments.	+
-		+
-	# We could also measure POPs by other means than fluorescente shuch as the concentration of a diffusible insuline (insuline levels can be quantified very fast and cheap) or anthibiotic resistance (we could manually count the number of colonies). This could make the measurements of available to laboratories with no funds or equipment and perhaps it would make it all easier.	+

Federico Castro M: New page: These are ideas that are not completely developed; they might be very basic very crazy or form part of a project that is not currently developed. If you are interested in developing some o...

2008-02-26T22:52:00Z

New page: These are ideas that are not completely developed; they might be very basic very crazy or form part of a project that is not currently developed. If you are interested in developing some o...

New page

These are ideas that are not completely developed; they might be very basic very crazy or form part of a project that is not currently developed. If you are interested in developing some of these ideas or are already working on them or something related, please contact me, I would be very glad to share information, collaborate and know about the outcome of the project.

# To look for differences in genes associated with the development of the nervous system of chimpanzees and humans.

# Given two identical populations that are independently subjected to identical evolutionary forces, we should expect to find a predictable rate of convergences. The rate of convergences gives us information about the topography of the adaptive map of the populations and how and where can it move.

# The problem with antibiotic resistance and VIH drug resistance are evolutive problems. We should deal with the problem with an evolutionary approach; we should lead the bacteria or viruses to an isolated peak of adaptation and then submerge that peak.

# Analyze LUCA (or at least read papers about it). The information about the Last Common Ancestor will provide us with information about the modules it had and this could be very helpful to create an organism from zero.

# Promoters surely have different rate of chance than the ORF they control. Do ORF evolve faster than promoters or viceverza? My guess is that changes in the promoters and not in the ORF account for the major differences within organisms… the activity of promoters makes up for the differences between the caterpillar and the butterfly and might also be accounted for differences between humans and chimpanzees.

# Where did coat proteins of virus come from? How did they evolved?

# The immune system uses a library of sequences to assemble a great variety of proteins. We should construct and use a similar library of proteins for protein design (The Silver/Phillips method of assembly would be very useful for achieving this goal).

# Myxobacteria have the ability to generate complex structures. Could we isolate the genes responsible for thet behavior and introduce it in Escherichiacoli?

# In plants the development is regulated with the MADS, in animals some Homeobox genes… what about fungi and algae? Does regulatory genes have something in common? Could we isolate tose genes and insert them in bacteria?

# A devise could be capable of achieving a function could be achieved, by randomly rewiring a genetic network with invertases and selecting the desired networks

# Make a self destructive F plasmid, this would allow some information to be quickly transmitted and once it is expressed it would disappear. The plasmid should codify for a restriction endonuclease that would digest the plasmid to tiny bits of DNA, the endonuclease should be very specific and have a very long recognition sequence to ensure that the Bacteria will not be harmed.

# We could use hormones as means of communication in small organisms, while there are some mechanisms implemented for communication, they lack the fast response that is often needed in a multicellular organism to coordinate cells (the molecule used by the luxR/l system as a signal, HSL, takes up to 24 hours to degradate). The system used for producing insulin and detecting the levels of sugars have already been developed by the NYMU 2007 iGEM team. It could be easily modified for communication between cells and the activity of the devise could be easily quantified with cheap medical equipments.

# We could also measure POPs by other means than fluorescente shuch as the concentration of a diffusible insuline (insuline levels can be quantified very fast and cheap) or anthibiotic resistance (we could manually count the number of colonies). This could make the measurements of available to laboratories with no funds or equipment and perhaps it would make it all easier.