User:Emilienne - Revision history

Emilienne: /* Please briefly describe any previous laboratory experience */

Emilienne — Wed, 14 Feb 2007 08:22:28 GMT

Please briefly describe any previous laboratory experience

←Older revision		Revision as of 08:22, 14 February 2007
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	===Please briefly describe any previous laboratory experience===		===Please briefly describe any previous laboratory experience===
-	UROP in Fee Lab in McGovern Institute, BCS. February 06- present. I do brain surgery on songbirds (lesions, tracers, and electrophysiology), perform perfusions, histology, immunochemistry, and microscopy.	+	UROP in Fee Lab in McGovern Institute, BCS. February 06- present. I do brain surgery on songbirds (lesions, tracers, and electrophysiology), and I perform perfusions, histology, immunochemistry, and microscopy.
		+
		+	I am currently exploring the role of the auditory cortex in song development, following up on some interesting previous results from a post-doc in my lab. An interesting side effect of the lesioning surgeries I do (in which the auditory input is removed from the auditory cortex) is that our birds become fearless. This might make another exciting follow-up experiment!

	===Anything else you would like us to know?===		===Anything else you would like us to know?===

Emilienne: /* Please briefly describe any previous laboratory experience */

Emilienne — Wed, 14 Feb 2007 08:19:46 GMT

Please briefly describe any previous laboratory experience

←Older revision		Revision as of 08:19, 14 February 2007
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	===Please briefly describe any previous laboratory experience===		===Please briefly describe any previous laboratory experience===
-	UROP in Fee Lab in McGovern Institute, BCS. February 06- present. I do brain surgery on songbirds (lesions, tracers, and electrophysiology), perform ~~profusions~~, histology, immunochemistry, and microscopy.	+	UROP in Fee Lab in McGovern Institute, BCS. February 06- present. I do brain surgery on songbirds (lesions, tracers, and electrophysiology), perform perfusions, histology, immunochemistry, and microscopy.

	===Anything else you would like us to know?===		===Anything else you would like us to know?===

Emilienne: /* The Family Tree: M13's closest evolutionary relatives */

Emilienne — Wed, 14 Feb 2007 08:00:49 GMT

The Family Tree: M13's closest evolutionary relatives

←Older revision		Revision as of 08:00, 14 February 2007
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	==The Family Tree: M13's closest evolutionary relatives==		==The Family Tree: M13's closest evolutionary relatives==
		+	M13 is a bacteriophage in the family Inoviridae, known for being simple, circular single-stranded-DNA filamentous phage with very similar genetic design. Two of M13's closest relatives are bacteriophage fd and fl. Both of these phage differ from M13 slightly in their coats. M13 has an amide group of asparagine in position 12 whereas fd and fl have a carboxyl group of aspartate. (See http://www.wsu.edu/~hipps/pdf_files/phagep1.pdf ). "As a result of this difference, M13 has one negative charge less per subunit than fd, corresponding to a 25-30% reduction in surface charge density" (Tang et al., “Metal Ion-Induced Lateral Aggregation of Filamentous Viruses fd and M13”. http://www.biophysj.org/cgi/content/full/83/1/566 )
		+
		+	For further information on bacteriophage and a useful comparison of 12 different catergories of phage, see http://www.tulane.edu/~dmsander/WWW/224/Phages.html .

Emilienne: /* Gene Functions and Re-engineering Ideas */

Emilienne — Wed, 14 Feb 2007 06:41:51 GMT

Gene Functions and Re-engineering Ideas

←Older revision		Revision as of 06:41, 14 February 2007
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	\|PXI		\|PXI
	\|Phage Secretion: C-terminals of P1 and P11 interact with N-terminal of P4 to form a complex through which mature phage are secreted.		\|Phage Secretion: C-terminals of P1 and P11 interact with N-terminal of P4 to form a complex through which mature phage are secreted.
		+	\|
	\|}		\|}

Emilienne: /* M13 Design Constraints */

Emilienne — Wed, 14 Feb 2007 06:41:15 GMT

M13 Design Constraints

←Older revision		Revision as of 06:41, 14 February 2007
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	It would be useful to know how the p8 knows how to regulate its production. Since the amount of p8 produced decreases when the genome size is decreased, this leads me to suspect that somehow the amount of p8 is being regulated such that the phage coat will always fit snugly over the phage’s DNA. Therefore, if the size of p8 is doubled, I suspect that only half the amount of protein will be used and the phage will tolerate this change just fine.		It would be useful to know how the p8 knows how to regulate its production. Since the amount of p8 produced decreases when the genome size is decreased, this leads me to suspect that somehow the amount of p8 is being regulated such that the phage coat will always fit snugly over the phage’s DNA. Therefore, if the size of p8 is doubled, I suspect that only half the amount of protein will be used and the phage will tolerate this change just fine.
		+

	Would you expect the phage to tolerate these same modifications to p3?		Would you expect the phage to tolerate these same modifications to p3?
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	3. If the C-terminal is doubled in size, I think that it will still function normally, though it’s possible that it will not be able to pass through the P1-P4-P11 complex through which mature phage are secreted.		3. If the C-terminal is doubled in size, I think that it will still function normally, though it’s possible that it will not be able to pass through the P1-P4-P11 complex through which mature phage are secreted.
		+

	Would you expect the phage to tolerate transcriptional terminators that are		Would you expect the phage to tolerate transcriptional terminators that are

Emilienne: /* M13 Design Constraints */

Emilienne — Wed, 14 Feb 2007 06:40:49 GMT

M13 Design Constraints

←Older revision		Revision as of 06:40, 14 February 2007
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	Would you expect the phage to tolerate p8 modifications that:		Would you expect the phage to tolerate p8 modifications that:
	1. make the protein neutral rather than negatively charged at the C-terminus?		1. make the protein neutral rather than negatively charged at the C-terminus?
-	~~What is the role of the C-terminus?~~ It seems that the C-terminus may need to be charged in order to hold together the p8 proteins that make the phage coat. The charge may also be necessary for intermolecular interaction required to secrete the phage. It seems that a neutral protein will be less likely to have intermolecular interactions than a negatively charged protein, so I think that the phage would struggle to tolerate this modification. (~~Ideas~~ from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12217696&dopt=Abstract )	+
		+	It seems that the C-terminus may need to be charged in order to hold together the P8 proteins that make the phage coat. The charge may also be necessary for intermolecular interaction required to secrete the phage. It seems that a neutral protein will be less likely to have intermolecular interactions than a negatively charged protein, so I think that the phage would struggle to tolerate this modification. (I tried learning about the C-terminus of P8 from the abstract at the following site: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12217696&dopt=Abstract )
		+
	2. encode all the Leucines with the CTA codon instead of the CTG codon?		2. encode all the Leucines with the CTA codon instead of the CTG codon?
		+
	The codon sequence is not important as long as the appropriate amino acid is encoded, so the phage could tolerate this modification.		The codon sequence is not important as long as the appropriate amino acid is encoded, so the phage could tolerate this modification.
		+
	3. double the size of the protein?		3. double the size of the protein?
-	~~To answer this question, it~~ would be ~~helpful~~ to know how the p8 knows how to regulate its production. Since the amount of p8 produced decreases when the genome size is decreased, this leads me to suspect that somehow the amount of p8 is being regulated such that the phage coat will always fit snugly over the phage’s DNA. Therefore, if the size of p8 is doubled, I suspect that only half the amount of protein will be used and the phage will tolerate this change just fine.	+
		+	It would be useful to know how the p8 knows how to regulate its production. Since the amount of p8 produced decreases when the genome size is decreased, this leads me to suspect that somehow the amount of p8 is being regulated such that the phage coat will always fit snugly over the phage’s DNA. Therefore, if the size of p8 is doubled, I suspect that only half the amount of protein will be used and the phage will tolerate this change just fine.

	Would you expect the phage to tolerate these same modifications to p3?		Would you expect the phage to tolerate these same modifications to p3?
		+
	1. C-terminal domain is required for release from the host cell following phage assembly, and contributes to structural stability of phage particle (See abstract http://chem.ps.uci.edu/~gweiss/WeissG-03JMB.pdf ). If we change the charge, it will alter intermolecular interactions, and it may destroy the functionality of p3, thus preventing the release of the phage and/or destabilizing the phage.		1. C-terminal domain is required for release from the host cell following phage assembly, and contributes to structural stability of phage particle (See abstract http://chem.ps.uci.edu/~gweiss/WeissG-03JMB.pdf ). If we change the charge, it will alter intermolecular interactions, and it may destroy the functionality of p3, thus preventing the release of the phage and/or destabilizing the phage.
-	2. ~~encode all the Leucines with the CTA codon instead of the CTG codon?~~	+
-	The codon sequence is not important as long as the appropriate amino acid is encoded, so the phage could tolerate this modification.	+	2. The codon sequence is not important as long as the appropriate amino acid is encoded, so the phage could tolerate this modification.
-	3. if the C-terminal is doubled in size, I think that it will still function normally, though it’s possible that it will not be able to pass through the p1-p4-~~p11~~ complex through which mature phage are secreted.	+
		+	3. If the C-terminal is doubled in size, I think that it will still function normally, though it’s possible that it will not be able to pass through the P1-P4-P11 complex through which mature phage are secreted.

	Would you expect the phage to tolerate transcriptional terminators that are		Would you expect the phage to tolerate transcriptional terminators that are
Line 113:		Line 120:
	2. 100X stronger		2. 100X stronger
	3. 2X weaker		3. 2X weaker
-	4. 100X weaker	+	4. 100X weaker ?
-	Assuming that we want the transcription to be stopped at a transcriptional terminator, it seems that it wouldn’t be a problem if the transcriptional terminator was stronger, unless an excessively strong transcriptional terminator caused the end part of the protein to be cut off.	+
-	If a weak transcriptional terminator causes a protein to have a long tail that could potentially cause problems, should the tail undergo undesired intermolecular interactions of simply take up too much space in the phage. It may also be possible that a weak transcriptional terminator would not successfully stop translation of the protein, which would be a major problem. ~~http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=556655~~	+	Assuming that we want the transcription to be stopped at a transcriptional terminator, it seems that it wouldn’t be a problem if the transcriptional terminator was stronger, unless an excessively strong transcriptional terminator caused the end part of the protein to be cut off. If a weak transcriptional terminator causes a protein to have a long tail that could potentially cause problems, should the tail undergo undesired intermolecular interactions of simply take up too much space in the phage. It may also be possible that a weak transcriptional terminator would not successfully stop translation of the protein, which would be a major problem.

	==The Family Tree: M13's closest evolutionary relatives==		==The Family Tree: M13's closest evolutionary relatives==

Emilienne: /* Gene Functions and Re-engineering Ideas */

Emilienne — Wed, 14 Feb 2007 06:28:20 GMT

Gene Functions and Re-engineering Ideas

←Older revision		Revision as of 06:28, 14 February 2007
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	\|--		\|--
	\|PVI		\|PVI
-	\|	+	\|Rounded Tip: Accessory to P3, buried
-	\|	+	\|Is P6 needed? We could test this by increasing the production of P6 and/or by removing the gene for P6. What if we made P6 responsible for either the entrance or final escape from the host, such the P3 only carried on one of these tasks?
	\|--		\|--
	\|PVII		\|PVII
-	\|	+	\|Blunt End: Companion to p9, buried
-	\|	+	\|Is P7 needed? We could try increasing its expression and/or removing it if we wanted to test this.
	\|--		\|--
	\|PVIII		\|PVIII
-	\|	+	\|Phage Coat: Adjusts to size of genome it packages. ~2700 copies needed to make ~900 nm long coat
-	\|	+	\|If we change the charge of P8, it will affect how the phage interacts with the surroundings. If we want to locate phages, we could also put markers into P8.
	\|--		\|--
	\|PIX		\|PIX
-	\|	+	\|Blunt End
-	\|	+	\|What is the role of the blunt end of the phage? Why not just have P3 on each side of the filament? We could try to test this in order to try to make the filament more versatile by making matching ends
	\|--		\|--
	\|PX		\|PX

Emilienne: /* Gene Functions and Re-engineering Ideas */

Emilienne — Wed, 14 Feb 2007 06:18:02 GMT

Gene Functions and Re-engineering Ideas

←Older revision		Revision as of 06:18, 14 February 2007
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	\|Phage Secretion: C-terminals of P1 and P11 interact with N-terminal of P4 to form a complex through which mature phage are secreted.		\|Phage Secretion: C-terminals of P1 and P11 interact with N-terminal of P4 to form a complex through which mature phage are secreted.
	\|}		\|}
-	~~</div>~~

	==M13 Design Constraints==		==M13 Design Constraints==

Emilienne: /* Gene Functions and Re-engineering Ideas */

Emilienne — Wed, 14 Feb 2007 06:17:32 GMT

Gene Functions and Re-engineering Ideas

←Older revision		Revision as of 06:17, 14 February 2007
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	\|PXI		\|PXI
	\|Phage Secretion: C-terminals of P1 and P11 interact with N-terminal of P4 to form a complex through which mature phage are secreted.		\|Phage Secretion: C-terminals of P1 and P11 interact with N-terminal of P4 to form a complex through which mature phage are secreted.
-	\|	+	\|}
		+	</div>

	==M13 Design Constraints==		==M13 Design Constraints==

Emilienne: /* M13 Design Constraints */

Emilienne — Wed, 14 Feb 2007 06:16:01 GMT

M13 Design Constraints

←Older revision		Revision as of 06:16, 14 February 2007
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	==M13 Design Constraints==		==M13 Design Constraints==
		+	Would you expect the phage to tolerate p8 modifications that:
		+	1. make the protein neutral rather than negatively charged at the C-terminus?
		+	What is the role of the C-terminus? It seems that the C-terminus may need to be charged in order to hold together the p8 proteins that make the phage coat. The charge may also be necessary for intermolecular interaction required to secrete the phage. It seems that a neutral protein will be less likely to have intermolecular interactions than a negatively charged protein, so I think that the phage would struggle to tolerate this modification. (Ideas from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12217696&dopt=Abstract )
		+	2. encode all the Leucines with the CTA codon instead of the CTG codon?
		+	The codon sequence is not important as long as the appropriate amino acid is encoded, so the phage could tolerate this modification.
		+	3. double the size of the protein?
		+	To answer this question, it would be helpful to know how the p8 knows how to regulate its production. Since the amount of p8 produced decreases when the genome size is decreased, this leads me to suspect that somehow the amount of p8 is being regulated such that the phage coat will always fit snugly over the phage’s DNA. Therefore, if the size of p8 is doubled, I suspect that only half the amount of protein will be used and the phage will tolerate this change just fine.
		+
		+	Would you expect the phage to tolerate these same modifications to p3?
		+	1. C-terminal domain is required for release from the host cell following phage assembly, and contributes to structural stability of phage particle (See abstract http://chem.ps.uci.edu/~gweiss/WeissG-03JMB.pdf ). If we change the charge, it will alter intermolecular interactions, and it may destroy the functionality of p3, thus preventing the release of the phage and/or destabilizing the phage.
		+	2. encode all the Leucines with the CTA codon instead of the CTG codon?
		+	The codon sequence is not important as long as the appropriate amino acid is encoded, so the phage could tolerate this modification.
		+	3. if the C-terminal is doubled in size, I think that it will still function normally, though it’s possible that it will not be able to pass through the p1-p4-p11 complex through which mature phage are secreted.
		+
		+	Would you expect the phage to tolerate transcriptional terminators that are
		+	1. 2X stronger
		+	2. 100X stronger
		+	3. 2X weaker
		+	4. 100X weaker
		+	Assuming that we want the transcription to be stopped at a transcriptional terminator, it seems that it wouldn’t be a problem if the transcriptional terminator was stronger, unless an excessively strong transcriptional terminator caused the end part of the protein to be cut off.
		+	If a weak transcriptional terminator causes a protein to have a long tail that could potentially cause problems, should the tail undergo undesired intermolecular interactions of simply take up too much space in the phage. It may also be possible that a weak transcriptional terminator would not successfully stop translation of the protein, which would be a major problem. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=556655
		+
	==The Family Tree: M13's closest evolutionary relatives==		==The Family Tree: M13's closest evolutionary relatives==