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KP Ramirez Week 4

2010-02-09T19:09:42Z

Assignment:

←Older revision		Revision as of 19:09, 9 February 2010
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	• Which subject of the study was that HIV sequence from? Which section of		• Which subject of the study was that HIV sequence from? Which section of
	the record contains information about who the HIV was collected from?		the record contains information about who the HIV was collected from?
		+	*S3V5-10 Subject 3, Visit 5, 10th clone. Found under features and source
		+	• Download several (4 to 6) sequences in FASTA format to your local hard drive
		+	by selecting several at the same time in the summary view so they are saved
		+	into a single text file. Be careful to remember where you put the file and what
		+	you name it so that you can find it later.
		+	*Completed
		+	• Open the file that you saved with a word processor to confirm that you have
		+	the sequences and that they are in the FASTA format. In the FASTA format each
		+	sequence is preceeded by a label which begins with the greater than sign (>).
		+	*Completed
		+
		+
		+
		+
		+
		+
		+
		+

	{{Kevin A Paiz-Ramirez}}		{{Kevin A Paiz-Ramirez}}

Salomon Garcia: Week 4

2010-02-09T19:09:12Z

Activity 1 Part 2: pic added and answered questions.

←Older revision		Revision as of 19:09, 9 February 2010
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	# What was the accession number of the sequence you chose?		# What was the accession number of the sequence you chose?
	# Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from?		# Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from?
		+	[[Image:Picture 3.jpg\|thumb\|center\|550px]]

-		+	# The accession number was GenBank: AF016760.1.
-	#	+	# This sequence was from subject 1. GenBank and the Fasta both contain where the section of HIV came from.
-	#	+

Image:HIVSequences1.txt

2010-02-09T19:08:45Z

uploaded "[[Image:HIVSequences1.txt]]" Four HIV Sequences/ Proper file version

New page

Bobak Seddighzadeh Week 4

2010-02-09T19:08:15Z

New page

Part 2: GenBank

*What was the accession number of the sequence you chose? AF089154
* Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from? The HIV sequence was collected from subject 4. The sequence has a code that contains information about who the HIV was collected from. The code for this subject's particular sequence is S4V2-4 which indicates the clone is from subject four on his second visit, and its his fourth clone.
*

Image:Picture 3.jpg

2010-02-09T19:07:25Z

uploaded "[[Image:Picture 3.jpg]]" Fasta pic of gene

New page

Angela A. Garibaldi Week 4

2010-02-09T19:07:02Z

Part 2: GeneBank: add file

←Older revision		Revision as of 19:07, 9 February 2010
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	#Click on FASTA to get the FASTA format		#Click on FASTA to get the FASTA format
	#Copy and paste 6 sequences into a .txt file for easy access. In this way the entire descriptive name of the sequences along with their accession numbers are listed.		#Copy and paste 6 sequences into a .txt file for easy access. In this way the entire descriptive name of the sequences along with their accession numbers are listed.
		+
		+	[[Image:S14_Subject.txt \|List of (6) Subject 14 Sequences]]

User:Brian P. Josey/Notebook/2010/02/09

2010-02-09T19:04:58Z

Autocreate 2010/02/09 Entry for User:Brian_P._Josey/Notebook

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{|{{table}} width="800"
|-
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Project name</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>      </html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
|-
| colspan="2"|

==Entry title==
* Insert content here...


|}

__NOTOC__
[[category:OWWLabNotebookV1]]

Image:S14 Subject.txt

2010-02-09T19:03:37Z

uploaded "[[Image:S14 Subject.txt]]" Angela's list of 6 FASTA sequences of Subject 14 from the Marham study

New page

J'aime C. Moehlman's Week 4

2010-02-09T19:02:04Z

←Older revision		Revision as of 19:02, 9 February 2010
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	FASTA sequences on a word document:		FASTA sequences on a word document:
	[[Media:J'aimes Sequences.doc\| Example FASTA Sequences]]		[[Media:J'aimes Sequences.doc\| Example FASTA Sequences]]
		+
		+	===Activity 1: Part 3===
		+	#Created a workbench account with the user name of jmoehlman.
		+	#Saved my FASTA data into the Biology Workbench
		+	#Viewed the Help page for using the ClustalW tool in the nucleic tools.
		+	#*

Angela A. Garibaldi Week 4

2010-02-09T19:01:40Z

Starting Journal Week 4

New page

==Exploring HIV-1 Exercise==
===Part 2: GeneBank===
#Search NCBI site under GeneBank - Nucleotide with one of the codes used in the Markham paper for the subject's sequence of the env gene.
#The '''Accession number''' of the S14V4-8 sequence is GenBank: AF089617.1
#This first HIV sequence is from Subject 14 from Visit 4, Variant 8. The name code of the sequence in this case indicates who the HIV was collected from.
#Click on FASTA to get the FASTA format
#Copy and paste 6 sequences into a .txt file for easy access. In this way the entire descriptive name of the sequences along with their accession numbers are listed.

Ryan N. Willhite Week 3

2010-02-09T19:00:39Z

In-Class Activity:

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	==In-Class Activity==		==In-Class Activity==
		+	[[BIOL398-01/S10:Week 3]]

	What I know about HIV		What I know about HIV

Template:SBB10 ConstructionFiles RaffiH sbb33

2010-02-09T19:00:13Z

New page: '''Construction of Gentamicin resistance gene (sbb33) BglBrick Part''' PCR rh03F/rh05R on pLoxGen4 (576 bp, gp = A) PCR rh04F/rh06R on pLoxGen4 (284 bp, gp = B) ---- PCR rh03...

New page

'''Construction of Gentamicin resistance gene (sbb33) BglBrick Part'''
PCR rh03F/rh05R on pLoxGen4 (576 bp, gp = A)
PCR rh04F/rh06R on pLoxGen4 (284 bp, gp = B)
----
PCR rh03F/rh06R on A+B (bp 833, EcoRI/BamHI)
Sub into pBjk2741-Bca1144 (EcoRI/BamHI, 2170+910, L)
Product is pBjk2741-sbb33 {Promoter.rbs.GenR}
----
rh03F Forward EcoRI for BglBricking GenR ctctgGAATTCatgAGATCTctagcgcgtcgacataagcc
rh04F Removing the BglII site from GenR cgcgtagtgagatAtatatctatgatc
rh05R Removing the BglII site from GenR gatcatagatataTatctcactacgcg
rh06R Reverse BamHI for BglBricking GenR gcaaaGGATCCctagcgcgtcggccgggaag

Ryan N. Willhite Week 4

2010-02-09T18:59:57Z

add link to assignment

←Older revision		Revision as of 18:59, 9 February 2010
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	==In-Class Activity==		==In-Class Activity==
-		+	[[BIOL398-01/S10:Week 4]]
	===Activity 1, Part 2===		===Activity 1, Part 2===

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	* In order to get to the FASTA format, on he NCBI website the displau drop down menu allowed me to view the selected sequences in FASTA format.		* In order to get to the FASTA format, on he NCBI website the displau drop down menu allowed me to view the selected sequences in FASTA format.
	*uploaded file as (.txt), it is the FASTA file sequences from downloading sequences to the local hard drive.		*uploaded file as (.txt), it is the FASTA file sequences from downloading sequences to the local hard drive.
-		+	# [[Media:Wk4sequences.txt\|FASTA sequences]]
	* Ran into some trouble opening the FASTA file since there was no type it recognized. In order to overcome this issue, i saved as a .txt file extension and then opened it in notepad.		* Ran into some trouble opening the FASTA file since there was no type it recognized. In order to overcome this issue, i saved as a .txt file extension and then opened it in notepad.

Template:SBB10 ConstructionFiles RaffiH sbb09

2010-02-09T18:57:04Z

←Older revision		Revision as of 18:57, 9 February 2010
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-	'''Construction of sbb09 BglBrick Part'''	+	'''Construction of Tn5 3'TR (sbb09) BglBrick Part'''
	EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)		EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)
	Product is pBjk2741-sbb09 {Tn5 3'TR}		Product is pBjk2741-sbb09 {Tn5 3'TR}

Image:HIVSequences.txt

2010-02-09T18:57:03Z

uploaded "[[Image:HIVSequences.txt]]" Four different HIV sequences

New page

KP Ramirez Week 4

2010-02-09T18:56:24Z

←Older revision		Revision as of 18:56, 9 February 2010
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	come up with a question to email about what you felt should be asked in this paper?		come up with a question to email about what you felt should be asked in this paper?
		+
		+
		+	I began by loading up the Markham paper from PubMed then clicking on the nucleotides links. From there I could access GenBank. I noted that the links seemed to be invalid however I was able to access them through a different browser.
		+	==Assignment==
		+	• What was the accession number of the sequence you chose?
		+	*AF089141
		+	• Which subject of the study was that HIV sequence from? Which section of
		+	the record contains information about who the HIV was collected from?
		+
	{{Kevin A Paiz-Ramirez}}		{{Kevin A Paiz-Ramirez}}

Salomon Garcia: Week 4

2010-02-09T18:55:37Z

Activity 1 Part 1:

←Older revision		Revision as of 18:55, 9 February 2010
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	# What oher ways might you have searched?		# What oher ways might you have searched?
	# What other types of related information are available?		# What other types of related information are available?
-		+	[[Image:search 1.jpg\|thumb\|center\|550px\|Pubmed search]]

	# I searched for the original paper by typing in the entire title of the research paper into the search box and the window showed the paper that was written in 1998.		# I searched for the original paper by typing in the entire title of the research paper into the search box and the window showed the paper that was written in 1998.
	# Another way I could have searched for it was by doing an advanced search and using the authors name on the search.		# Another way I could have searched for it was by doing an advanced search and using the authors name on the search.
	# There were other information that was useful as was the information that described what HIV-1 is.		# There were other information that was useful as was the information that described what HIV-1 is.
-

	====Activity 1 Part 2====		====Activity 1 Part 2====

Template:SBB10 ConstructionFiles RaffiH sbb09

2010-02-09T18:55:19Z

←Older revision		Revision as of 18:55, 9 February 2010
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-	~~<pre>~~	+	'''Construction of sbb09 BglBrick Part'''
-	~~<b>~~Construction ~~File for~~ sbb09 BglBrick Part~~</b>~~	+	EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)
-	EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)	+	Product is pBjk2741-sbb09 {Tn5 3'TR}
-	Product is pBjk2741-sbb09 {Tn5 3'TR}	+	----
-	----	+	rh01F EIPCR construction of Tn5 3'TR basic part ccataAGATCTggttgagatgtgtataagagacagtcgacGGATCCtaactcgctcctcag
-	rh01F EIPCR construction of Tn5 3'TR basic part	+	rh02R Reverse BglII oligo for pBjk2741 EIPCR ccaatAGATCTcatGAATTCcacttcag
-	ccataAGATCTggttgagatgtgtataagagacagtcgacGGATCCtaactcgctcctcag	+
-	rh02R Reverse BglII oligo for pBjk2741 EIPCR	+
-	ccaatAGATCTcatGAATTCcacttcag	+
-	~~</pre>~~	+

User:Patricio Velez

2010-02-09T18:54:58Z

←Older revision		Revision as of 18:54, 9 February 2010
Line 1:		Line 1:
-	~~<!-- Delete~~ this ~~entire line as part of your first edit of~~ your user page --> ~~{{New~~ user}}	+	Please copy the source code from this page to your user page, fill in the answers and print out a copy for next time.<br>
		+	You do not need to keep the information on your user page once you've printed it out.
		+	==Registration/Questionnaire: 20.109 Spring 2010==

-	==~~Contact Info~~==	+	===Last Name===
-	~~[[Image:OWWEmblem.png\|thumb\|right\|Patricio~~ Velez ~~(an artistic interpretation)]]~~	+	Velez
		+	===First Name===
		+	Patricio

-	*Patricio Velez	+	===Preferred name (if not first)===
-	*MIT	+	PJ
-	*Address 1	+
-	*Address 2	+
-	*City, State, Country etc.	+
-	*[[Special:Emailuser/Patricio Velez\|Email me through OpenWetWare]]	+

-	~~I work in the [[Your Lab]] at XYZ University. I learned about [[OpenWetWare]] from My class., and I've joined because I am in~~ 20.~~109 and the class website is on openwetware..~~	+	===Course/Minor===
		+	Major: Course 20 (Biological Engineering); Potential Minor: 5(Chemistry)
		+	===Year of Graduation===
		+	2012
		+	===Telephone #===
		+	813-541-4025
		+	===Email===
		+	pjvelez@mit.edu
		+	===Potentially Relevant Background===

-	=~~=Education==~~	+	{\| border="1"
-	<!--~~Include info about your educational background~~-->	+	\|Have you taken/are you taking...
-	* Year, PhD, Institute	+	\|Answer yes/no/when
-	* Year, MS, Institute	+	\|-
-	* Year, BS, Institute	+	\|7.05/5.07 (Biochemistry)
		+	\|Yes; Spring 2010
		+	\|-
		+	\|7.06 (Cell Biology)
		+	\|No
		+	\|-
		+	\|7.03 (Genetics)
		+	\|No
		+	\|-
		+	\|7.02 (General Biology Lab)
		+	\| No
		+	\|-
		+	\| 5.310 (General Chemistry Lab)
		+	\|No
		+	\|-
		+	\|}

-	=~~=Research interests==~~	+	<br style="clear:both;"/>
-	~~<!-- Feel free to add brief descriptions to your research interests as well --~~>	+
-	~~# Interest 1~~	+
-	~~# Interest 2~~	+
-	~~# Interest 3~~	+

-	=~~=Publications==~~	+	{\| border="1"
-	~~<!-- Replace the PubMed ID's (~~"~~pmid=#######~~"~~) below~~ with ~~the PubMed ID's for your publications~~. ~~You can add or remove lines as needed -->~~	+	\|Do you have experience with...
-	~~<biblio>~~	+	\|Answer yes/no/type
-	~~#Paper1 pmid=6947258~~	+	\|-
-	~~#Paper2 pmid=13718526~~	+	\|Cell culture (microbial/mammalian/yeast?)
-	// ~~leave a comment about a paper here~~	+	\|No
-	~~#Book1 isbn=0879697164~~	+	\|-
-	~~</biblio>~~	+	\|Molecular biology (electrophoresis, PCR, etc)
		+	\|Yes : Minimal
		+	\|-
		+	\|}

-	==~~Useful links~~==	+	===Please briefly describe any previous laboratory experience===
-	*[[OpenWetWare:~~Welcome\|Introductory tutorial]]~~	+	None
-	*[[~~Help~~\|~~OpenWetWare help pages~~]]	+
		+	===Anything else you would like us to know?===
		+	I look forward to skills and habits required to work in a lab so I can apply them to my future endeavors.
		+
		+	===Commitment to academic integrity===
		+
		+	After you print out this page, please sign your name next to the following statement to indicate your agreement:
		+
		+	''I have read and understood the 20.109 [[20.109(S10):Statement_on_Collaboration_and_Integrity \| statement on collaboration and integrity]].''
		+
		+
		+	Patricio J. Velez

Image:Wk4sequences.txt

2010-02-09T18:54:01Z

uploaded "[[Image:Wk4sequences.txt]]" Sequences downloaded in FASTA format to hard drive. A summary of all saved in single file.

New page

Amanda N. Wavrin Week 4

2010-02-09T18:53:17Z

added FASTA example doc

New page

====Activity 1, Part 2: GenBank====
*Accesion number of chosen sequence: AF089135
*This sequence was from subject 3
*The definition tells us that the seguence was from S3V5-4
*[[Media:Sequences.doc|Example FASTA sequences]]

Michael R. Pina Week 4

2010-02-09T18:53:13Z

←Older revision		Revision as of 18:53, 9 February 2010
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	*The accession number of the sequence is AF016768.		*The accession number of the sequence is AF016768.
	*The sequence comes from subject 1; the definition section of the record contains this information as well as other information such as which visit.		*The sequence comes from subject 1; the definition section of the record contains this information as well as other information such as which visit.
		+	*The Biology Workbench does not seem the most user friendly, but it works just fine and gets the job done. I was able to align 4 sequences acquired from GenBank without any problems.

Image:Search 1.jpg

2010-02-09T18:52:53Z

uploaded "[[Image:Search 1.jpg]]"

New page

J'aime C. Moehlman's Week 4

2010-02-09T18:52:28Z

Activity 1: Part 2: added FASTA sequences

←Older revision		Revision as of 18:52, 9 February 2010
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	FASTA sequences on a word document:		FASTA sequences on a word document:
-	[[~~Image~~:J'aimes Sequences.doc \|Example FASTA Sequences]]	+	[[Media:J'aimes Sequences.doc\| Example FASTA Sequences]]

Alex J. George Week 4

2010-02-09T18:52:11Z

Upload FASTA file

←Older revision		Revision as of 18:52, 9 February 2010
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	* Accession Number of sequence: AF016767.2		* Accession Number of sequence: AF016767.2
	* This sequence was taken from the first visit of Subject 1. This information is given in the title of the sequence.		* This sequence was taken from the first visit of Subject 1. This information is given in the title of the sequence.
		+	[[Media:FASTA sequences.doc\| FASTA sequences]]

	{{Alex J. George}}		{{Alex J. George}}

J'aime C. Moehlman's Week 4

2010-02-09T18:51:24Z

Activity 1: Part 2:

←Older revision		Revision as of 18:51, 9 February 2010
Line 4:		Line 4:

	FASTA sequences on a word document:		FASTA sequences on a word document:
-	[[Image:J'aimes Sequences.doc\| Example FASTA Sequences]]	+	[[Image:J'aimes Sequences.doc \|Example FASTA Sequences]]

Template:SBB10 ConstructionFiles RaffiH sbb09

2010-02-09T18:51:19Z

←Older revision		Revision as of 18:51, 9 February 2010
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	<pre>		<pre>
-	~~'''~~Construction File for sbb09 BglBrick Part~~'''~~	+	<b>Construction File for sbb09 BglBrick Part</b>
	EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)		EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)
	Product is pBjk2741-sbb09 {Tn5 3'TR}		Product is pBjk2741-sbb09 {Tn5 3'TR}

Image:FASTA sequences.doc

2010-02-09T18:51:14Z

uploaded "[[Image:FASTA sequences.doc]]" 5 FASTA Sequences

New page

Ryan N. Willhite Week 4

2010-02-09T18:51:11Z

start journal 4

New page

==In-Class Activity==

===Activity 1, Part 2===

*The accession number from the sequence I chose was AF089153.
*The subject of the study was HIV-1 isolate S4V2-3 from USA envelope glycoprotein. The section of the record that contained information about who the HIV was collected from was in the subject.
* In order to get to the FASTA format, on he NCBI website the displau drop down menu allowed me to view the selected sequences in FASTA format.
*uploaded file as (.txt), it is the FASTA file sequences from downloading sequences to the local hard drive.

* Ran into some trouble opening the FASTA file since there was no type it recognized. In order to overcome this issue, i saved as a .txt file extension and then opened it in notepad.

Template:SBB10 ConstructionFiles RaffiH sbb09

2010-02-09T18:50:54Z

←Older revision		Revision as of 18:50, 9 February 2010
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		+	<pre>
	'''Construction File for sbb09 BglBrick Part'''		'''Construction File for sbb09 BglBrick Part'''
	EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)		EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)
Line 7:		Line 8:
	rh02R Reverse BglII oligo for pBjk2741 EIPCR		rh02R Reverse BglII oligo for pBjk2741 EIPCR
	ccaatAGATCTcatGAATTCcacttcag		ccaatAGATCTcatGAATTCcacttcag
		+	</pre>

Alex J. George Week 4

2010-02-09T18:50:51Z

New page: ===Activity 1: Searching NCBI=== ====Part 2: Genbank==== * Accessed Genbank records from the right-hand links of the Pubmed version of the article. * Accession Number of sequence: AF0167...

New page

===Activity 1: Searching NCBI===

====Part 2: Genbank====
* Accessed Genbank records from the right-hand links of the Pubmed version of the article.
* Accession Number of sequence: AF016767.2
* This sequence was taken from the first visit of Subject 1. This information is given in the title of the sequence.

{{Alex J. George}}

Image:Sequences.doc

2010-02-09T18:50:51Z

uploaded "[[Image:Sequences.doc]]"

New page

J'aime C. Moehlman's Week 4

2010-02-09T18:50:41Z

Activity 1: Part 2:

←Older revision		Revision as of 18:50, 9 February 2010
Line 4:		Line 4:

	FASTA sequences on a word document:		FASTA sequences on a word document:
-	[[Image:J'aimes Sequences.doc]]	+	[[Image:J'aimes Sequences.doc\| Example FASTA Sequences]]

Template:SBB10 ConstructionFiles RaffiH sbb09

2010-02-09T18:50:30Z

New page: '''Construction File for sbb09 BglBrick Part''' EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII) Product is pBjk2741-sbb09 {Tn5 3'TR} ---- rh01F EIPCR construction o...

New page

'''Construction File for sbb09 BglBrick Part'''
EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)
Product is pBjk2741-sbb09 {Tn5 3'TR}
----
rh01F EIPCR construction of Tn5 3'TR basic part
ccataAGATCTggttgagatgtgtataagagacagtcgacGGATCCtaactcgctcctcag
rh02R Reverse BglII oligo for pBjk2741 EIPCR
ccaatAGATCTcatGAATTCcacttcag

Image:S4V2-4.txt

2010-02-09T18:48:14Z

uploaded "[[Image:S4V2-4.txt]]" S4V2-4 sequence

New page

J'aime C. Moehlman's Week 4

2010-02-09T18:48:06Z

Activity 1: Part 2:

New page

===Activity 1: Part 2===
#Accession number of the chosen sequence: AF089139
#Subject: 3. The features section of the record talks about subject 3.

FASTA sequences on a word document:
[[Image:J'aimes Sequences.doc]]

SBB10 constructs

2010-02-09T18:46:15Z

←Older revision		Revision as of 18:46, 9 February 2010
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	[[Template:SBB10_ConstructionFiles_BenB_sbb05 \| Ben Bubenheim PiggieBac 5'TR (sbb05)]]<br>		[[Template:SBB10_ConstructionFiles_BenB_sbb05 \| Ben Bubenheim PiggieBac 5'TR (sbb05)]]<br>
	[[Template:SBB10_ConstructionFiles_BenB_sbb01 \| Ben Bubenheim N15 Protelomerase (sbb01)]]<br>		[[Template:SBB10_ConstructionFiles_BenB_sbb01 \| Ben Bubenheim N15 Protelomerase (sbb01)]]<br>
		+	<br>
		+	[[Template:SBB10_ConstructionFiles_RaffiH_sbb09 \| Raffi Hagopian Tn5 3'TR (sbb09)]]<br>
		+	[[Template:SBB10_ConstructionFiles_RaffiH_sbb33 \| Raffi Hagopian Gentamicin resistance gene (sbb33)]]<br>

Image:J'aimes Sequences.doc

2010-02-09T18:45:00Z

uploaded "[[Image:J'aimes Sequences.doc]]"

New page

BISC220/S10: Mod 1 Lab 3

2010-02-09T18:39:00Z

Protocol:

←Older revision		Revision as of 18:39, 9 February 2010
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	# Prepare 3.0 ml of the appropriate dilution of your purified fraction in Z buffer. Remember to mix the PF very well by vortexing before taking an aliquot for dilution. Label the enzyme dilution clearly and keep it and the PF stock solution on ice.		# Prepare 3.0 ml of the appropriate dilution of your purified fraction in Z buffer. Remember to mix the PF very well by vortexing before taking an aliquot for dilution. Label the enzyme dilution clearly and keep it and the PF stock solution on ice.
	# Prepare 5 ml of a 1:10 dilution of the substrate ONPG. The stock solution is at a concentration of 4 mg/ml. Label the substrate dilution clearly. Keep the diluted and undiluted substrate on ice.		# Prepare 5 ml of a 1:10 dilution of the substrate ONPG. The stock solution is at a concentration of 4 mg/ml. Label the substrate dilution clearly. Keep the diluted and undiluted substrate on ice.
-	# To perform the assay without inhbitior, prepare 10 assay tubes and 2 reagent blanks (2 identical #10 tubes) in 13 mm test tubes using the volumes and solutions indicated in the table that follows entitled “Uninhibited”. '''DO NOT ADD ENZYME UNTIL YOU START THE REACTION.'''	+	# To perform the assay without inhbitior, prepare 10 assay tubes and 2 reagent blanks (2 identical #11 tubes) in 13 mm test tubes using the volumes and solutions indicated in the table that follows entitled “Uninhibited”. '''DO NOT ADD ENZYME UNTIL YOU START THE REACTION.'''
-	# Equilibrate tubes 1-9 at 28°C for 5 minutes.	+	# Equilibrate tubes 1-10 at 28°C for 5 minutes.
	# Start the reaction by adding 100 µl (0.1 ml) of the diluted enzyme at 20 second intervals to each reaction tube but not the blanks (tubes #10). Vortex or invert to mix the reaction after the enzyme is added and return the tube to the water bath.		# Start the reaction by adding 100 µl (0.1 ml) of the diluted enzyme at 20 second intervals to each reaction tube but not the blanks (tubes #10). Vortex or invert to mix the reaction after the enzyme is added and return the tube to the water bath.
	# Stop the reaction by adding 1.0 ml of 1 M Na<sub>2</sub>CO<sub>3</sub> exactly 5 minutes after the addition of enzyme. Vortex each tube after adding stop buffer. Add stop buffer to the blanks at any time.		# Stop the reaction by adding 1.0 ml of 1 M Na<sub>2</sub>CO<sub>3</sub> exactly 5 minutes after the addition of enzyme. Vortex each tube after adding stop buffer. Add stop buffer to the blanks at any time.

Salomon Garcia: Week 4

2010-02-09T18:38:48Z

Activity 1 Part 1: part 2 questions added

←Older revision		Revision as of 18:38, 9 February 2010
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	====Activity 1 Part 1====		====Activity 1 Part 1====
-
	*Pubmed:		*Pubmed:
-
	# How did you searh for the PubMed entry?		# How did you searh for the PubMed entry?
	# What oher ways might you have searched?		# What oher ways might you have searched?
	# What other types of related information are available?		# What other types of related information are available?
		+
		+
		+	# I searched for the original paper by typing in the entire title of the research paper into the search box and the window showed the paper that was written in 1998.
		+	# Another way I could have searched for it was by doing an advanced search and using the authors name on the search.
		+	# There were other information that was useful as was the information that described what HIV-1 is.
		+
		+
		+	====Activity 1 Part 2====
		+	*GenBank:
		+	# What was the accession number of the sequence you chose?
		+	# Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from?
		+
		+
		+	#
		+	#

BISC220/S10: Mod 1 Lab 3

2010-02-09T18:33:07Z

Protocol:

←Older revision		Revision as of 18:33, 9 February 2010
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	# Prepare 3.0 ml of the appropriate dilution of your purified fraction in Z buffer. Remember to mix the PF very well by vortexing before taking an aliquot for dilution. Label the enzyme dilution clearly and keep it and the PF stock solution on ice.		# Prepare 3.0 ml of the appropriate dilution of your purified fraction in Z buffer. Remember to mix the PF very well by vortexing before taking an aliquot for dilution. Label the enzyme dilution clearly and keep it and the PF stock solution on ice.
	# Prepare 5 ml of a 1:10 dilution of the substrate ONPG. The stock solution is at a concentration of 4 mg/ml. Label the substrate dilution clearly. Keep the diluted and undiluted substrate on ice.		# Prepare 5 ml of a 1:10 dilution of the substrate ONPG. The stock solution is at a concentration of 4 mg/ml. Label the substrate dilution clearly. Keep the diluted and undiluted substrate on ice.
-	# To perform the assay without inhbitior, prepare 9 assay tubes and 2 reagent blanks (2 identical #10 tubes) in 13 mm test tubes using the volumes and solutions indicated in the table that follows entitled “Uninhibited”. '''DO NOT ADD ENZYME UNTIL YOU START THE REACTION.'''	+	# To perform the assay without inhbitior, prepare 10 assay tubes and 2 reagent blanks (2 identical #10 tubes) in 13 mm test tubes using the volumes and solutions indicated in the table that follows entitled “Uninhibited”. '''DO NOT ADD ENZYME UNTIL YOU START THE REACTION.'''
	# Equilibrate tubes 1-9 at 28°C for 5 minutes.		# Equilibrate tubes 1-9 at 28°C for 5 minutes.
	# Start the reaction by adding 100 µl (0.1 ml) of the diluted enzyme at 20 second intervals to each reaction tube but not the blanks (tubes #10). Vortex or invert to mix the reaction after the enzyme is added and return the tube to the water bath.		# Start the reaction by adding 100 µl (0.1 ml) of the diluted enzyme at 20 second intervals to each reaction tube but not the blanks (tubes #10). Vortex or invert to mix the reaction after the enzyme is added and return the tube to the water bath.
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	# Read your absorbances and make sure the enzyme dilution you used was appropriate before repeating the reactions with inhibitor. If the enzyme concentration is appropriate, absorbances will be largely within the linear range of the instrument and you will have clearly reached Vmax.		# Read your absorbances and make sure the enzyme dilution you used was appropriate before repeating the reactions with inhibitor. If the enzyme concentration is appropriate, absorbances will be largely within the linear range of the instrument and you will have clearly reached Vmax.
	# To assay the effect of IPTG on the reaction, repeat the assay using a putative inhibitor of the enzyme, IPTG. Prepare another set of 11 test tubes using the volumes and solutions indicated in the table entitled “Inhibited” that follows. '''DO NOT ADD THE ENZYME AT THIS TIME.'''		# To assay the effect of IPTG on the reaction, repeat the assay using a putative inhibitor of the enzyme, IPTG. Prepare another set of 11 test tubes using the volumes and solutions indicated in the table entitled “Inhibited” that follows. '''DO NOT ADD THE ENZYME AT THIS TIME.'''
-	# Equilibrate the 11 tubes at 28° for 5 minutes. Start the reaction by adding 100µl (0.1 ml) of enzyme dilution at 20 second intervals to each reaction tube ('''BUT NOT THE BLANKS'''). Stop the reactions exactly 5 minutes later by adding 1000µl (1.0 ml) of Na<sub>2</sub>CO<sub>3</sub>. Add stop buffer to the blanks too. Mix well by vortexing after each addition of enzyme or Na<sub>2</sub>CO<sub>3</sub>.	+	# Equilibrate the 12 tubes at 28° for 5 minutes. Start the reaction by adding 100µl (0.1 ml) of enzyme dilution at 20 second intervals to each reaction tube ('''BUT NOT THE BLANKS'''). Stop the reactions exactly 5 minutes later by adding 1000µl (1.0 ml) of Na<sub>2</sub>CO<sub>3</sub>. Add stop buffer to the blanks too. Mix well by vortexing after each addition of enzyme or Na<sub>2</sub>CO<sub>3</sub>.
	# Transfer all tubes to cuvettes making sure they are at least 2/3 to 3/4 filled. Zero the spectrophotometer at 420 nm using the reagent blanks. Read and record the absorbance of each assay.		# Transfer all tubes to cuvettes making sure they are at least 2/3 to 3/4 filled. Zero the spectrophotometer at 420 nm using the reagent blanks. Read and record the absorbance of each assay.
	<br><br>		<br><br>

User:Anthony Salvagno/Notebook/Research/2010/02/09/Tethering prior to BPS2010

2010-02-09T18:33:00Z

Results:

←Older revision		Revision as of 18:33, 9 February 2010
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	I definitely need a smartphone or maybe a live feed note taker program. Basically I don't want to drag the laptop around with me everywhere I need to to be able to get to take notes on OWW. Maybe I should look into getting the Droid asap, or maybe we can get a tablet pc soon. The iPad is a let down, but maybe the courier will be for real and awesome. Anyways...		I definitely need a smartphone or maybe a live feed note taker program. Basically I don't want to drag the laptop around with me everywhere I need to to be able to get to take notes on OWW. Maybe I should look into getting the Droid asap, or maybe we can get a tablet pc soon. The iPad is a let down, but maybe the courier will be for real and awesome. Anyways...
	:[[User:Steven J. Koch\|Steve Koch]] 00:50, 9 February 2010 (EST): What about the iphone that doesn't have a phone? (can't rememember what it's called, itouch?). How expensive are those?		:[[User:Steven J. Koch\|Steve Koch]] 00:50, 9 February 2010 (EST): What about the iphone that doesn't have a phone? (can't rememember what it's called, itouch?). How expensive are those?
		+
		+	So tethering did not work in this try. There were no stuck beads at all (except near the nail polish) in all 4 samples (2 with DNA, 2 without DNA). I spent at least 5 min looking around every sample and analyzing stuck beads, possible tethers, etc. I found no evidence for any of that. I think my slides were insufficiently clean (or too dirty) because I saw a lot of weird structures I wasn't able to recognize. They definitely were not clumps of beads. I don't think I'll have time today to do all this again so I'll try again tomorrow.
		+
		+	'''One interesting thing of note:''' In and near the nail polish I noticed lots of stuck beads. While this isn't so weird, what is weird is that the beads would stick only in bands. Like there would be a line of stuck beads and then a gap of nothing and then another line of stuck beads. The bands were probably like 5-10 beads thick (with little spaces between the beads) and were the entire sample in length (from tape to tape). I have never seen that before and thought it was interesting.
		+
	==In Other News==		==In Other News==
	I had this weird dream last night that I had to write a bunch of scripts for windows. One of which was the turn pictures b&w and invert them. Another one was to add gaussian blur to photos. There were more, but I can't remember what other scripts I had to write. I do want to do all this, but I need time and right now, I do not have this. After BPS though... we'll see!		I had this weird dream last night that I had to write a bunch of scripts for windows. One of which was the turn pictures b&w and invert them. Another one was to add gaussian blur to photos. There were more, but I can't remember what other scripts I had to write. I do want to do all this, but I need time and right now, I do not have this. After BPS though... we'll see!

Michael R. Pina Week 4

2010-02-09T18:23:49Z

New page: ===Part 2: GenBank=== *The accession number of the sequence is AF016768. *The sequence comes from subject 1; the definition section of the record contains this information as well as other...

New page

===Part 2: GenBank===
*The accession number of the sequence is AF016768.
*The sequence comes from subject 1; the definition section of the record contains this information as well as other information such as which visit.

BIOL398-01/S10

2010-02-09T18:23:02Z

Schedule: link to mylmuconnect for journal club slides

←Older revision		Revision as of 18:23, 9 February 2010
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	\| Feb 9		\| Feb 9
	\| [http://bioquest.org/bedrock/problem_spaces/hiv/Markham_1998.pdf Markham et al. (1998)], [http://www.jci.org/articles/view/34706/pdf Cohen et al. (2008) review], Exploring HIV Evolution Handout		\| [http://bioquest.org/bedrock/problem_spaces/hiv/Markham_1998.pdf Markham et al. (1998)], [http://www.jci.org/articles/view/34706/pdf Cohen et al. (2008) review], Exploring HIV Evolution Handout
-	\| Journal Club 1	+	\| Journal Club 1 slides are on [https://mylmuconnect.lmu.edu/webapps/login/ MyLMUConnect]

	[[BIOL398-01/S10:HIV Evolution \| HIV Evolution Project]]		[[BIOL398-01/S10:HIV Evolution \| HIV Evolution Project]]

←Older revision		Revision as of 18:46, 9 February 2010
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	[[Template:SBB10_ConstructionFiles_BenB_sbb05 \| Ben Bubenheim PiggieBac 5'TR (sbb05)]]<br>		[[Template:SBB10_ConstructionFiles_BenB_sbb05 \| Ben Bubenheim PiggieBac 5'TR (sbb05)]]<br>
	[[Template:SBB10_ConstructionFiles_BenB_sbb01 \| Ben Bubenheim N15 Protelomerase (sbb01)]]<br>		[[Template:SBB10_ConstructionFiles_BenB_sbb01 \| Ben Bubenheim N15 Protelomerase (sbb01)]]<br>
		+	<br>
		+	[[Template:SBB10_ConstructionFiles_RaffiH_sbb09 \| Raffi Hagopian Tn5 3'TR (sbb09)]]<br>
		+	[[Template:SBB10_ConstructionFiles_RaffiH_sbb33 \| Raffi Hagopian Gentamicin resistance gene (sbb33)]]<br>