BE.109:Lab tour - Revision history

Ilya: /* For next time */

2008-05-07T20:50:03Z

For next time

←Older revision		Revision as of 20:50, 7 May 2008
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	4. Complete the student registration/questionnaire to turn in next time [[Image:BE109StudentReg S06.doc\|Student Registration/Questionnaire]].		4. Complete the student registration/questionnaire to turn in next time [[Image:BE109StudentReg S06.doc\|Student Registration/Questionnaire]].

-	5. Register for an account on [[Main Page \| OpenWetWare]] ~~by emailing "admin AT openwetware DOT org" with "new account" in the subject line~~. Once you get an account familiarize yourself with the wiki by reading [[BE.109:OpenWetWare \| Using OpenWetWare]]. Put some information on your user page.	+	5. [[OpenWetWare:How to join\|Register for an account]] on [[Main Page \| OpenWetWare]]. Once you get an account familiarize yourself with the wiki by reading [[BE.109:OpenWetWare \| Using OpenWetWare]]. Put some information on your user page.

	6. Read the introduction for the [[BE.109:DNA engineering \| DNA engineering module]]: an experiment that you'll start next time.		6. Read the introduction for the [[BE.109:DNA engineering \| DNA engineering module]]: an experiment that you'll start next time.

Reshma P. Shetty: /* Introduction to our "back room" and tissue culture facility */

2006-02-07T23:54:09Z

Introduction to our "back room" and tissue culture facility

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	'''(Guided)'''		'''(Guided)'''

-	Our lab is beautifully equipped. We have a fume hood for work that generates hazardous vapors. We have a back room where dishes can be washed and material can be decontaminated. The backroom also has an icemaker, a sink with ultrapure water and several ~~CO2~~ tanks that feed into the incubators in the tissue culture facility.	+	Our lab is beautifully equipped. We have a fume hood for work that generates hazardous vapors. We have a back room where dishes can be washed and material can be decontaminated. The backroom also has an icemaker, a sink with ultrapure water and several CO<sub>2</sub> tanks that feed into the incubators in the tissue culture facility.

	The tissue culture facility has three hoods with germicidal lamps, six incubators for growing eukaryotic cells, two inverted microscopes, and a tabletop centrifuge. It also has a waterbath for warming up solutions and a refrigerator for keeping them cool.		The tissue culture facility has three hoods with germicidal lamps, six incubators for growing eukaryotic cells, two inverted microscopes, and a tabletop centrifuge. It also has a waterbath for warming up solutions and a refrigerator for keeping them cool.

Justinhlo: /* Introduction to pipetting */

2006-02-07T21:16:38Z

Introduction to pipetting

←Older revision		Revision as of 21:16, 7 February 2006
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	Someone will show you how to use your pipetmen and then you will use them to dilute a blue dye (0.01% Xylene Cyanol).		Someone will show you how to use your pipetmen and then you will use them to dilute a blue dye (0.01% Xylene Cyanol).
	#If you have never used pipetmen then you should practice by pipeting 800, 80 and 8 μl of the 0.01% XC stock into eppendorf tubes. XC is not hazardous but it will stain your clothes. Pipet each volume three times and visually inspect how well the volumes match.		#If you have never used pipetmen then you should practice by pipeting 800, 80 and 8 μl of the 0.01% XC stock into eppendorf tubes. XC is not hazardous but it will stain your clothes. Pipet each volume three times and visually inspect how well the volumes match.
-	#Using your P20, measure 10, 15 and 20 μl of the 0.01% XC stock solution into the bottom of three cuvettes. Using your P1000, add water to bring the final volume to 1 ml (=1000 ul).	+	#Using your P20, measure 10, 15 and 20 μl of the 0.01% XC stock solution into the bottom of three cuvettes. Using your P1000, add water to bring the final volume to 1 ml (=1000 μl).
	#Using your P200, measure 20, 50 and 100 μl of the 0.01% XC stock solution into the bottom of three more cuvettes. Using your P1000, add water to bring the final volume to 1 ml.		#Using your P200, measure 20, 50 and 100 μl of the 0.01% XC stock solution into the bottom of three more cuvettes. Using your P1000, add water to bring the final volume to 1 ml.
	#Using your P1000, measure 100, 200, and 400 μl of 0.01% XC solution into the bottom of three more cuvettes. Add water to bring the final volume to 1 ml.		#Using your P1000, measure 100, 200, and 400 μl of 0.01% XC solution into the bottom of three more cuvettes. Add water to bring the final volume to 1 ml.

Justinhlo: /* Part 1: Metric system */

2006-02-07T21:16:06Z

Part 1: Metric system

←Older revision		Revision as of 21:16, 7 February 2006
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	'''Practice problems:'''		'''Practice problems:'''
-	#The distance between two cells in 800 um. How many mm is that?	+	#The distance between two cells in 800 μm. How many mm is that?
	#The amount of sorbitol you want to weigh is 1.9 g. How many mg is that?		#The amount of sorbitol you want to weigh is 1.9 g. How many mg is that?
	#The volume you want to measure is 100 ml. How many liters is that?		#The volume you want to measure is 100 ml. How many liters is that?

Justinhlo: /* Part 3: Dilutions */

2006-02-07T21:15:14Z

Part 3: Dilutions

←Older revision		Revision as of 21:15, 7 February 2006
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	Many solutions are made by diluting concentrated stock solutions. Dilution factors of 1:2, 1:5, 1:10 and 1:100 are common. These dilutions are made by diluting one “part” stock with 1, 4, 9 or 99 “parts” water. For example, you could make 100 ml of a 0.5M sorbitol solution by mixing 10 ml of a 5M stock solution with 90 ml of water. This is a 1:10 dilution of the stock. The dilution factor can be converted to a fraction to determine the solution’s final concentration (5M x 1/10 = 0.5M).		Many solutions are made by diluting concentrated stock solutions. Dilution factors of 1:2, 1:5, 1:10 and 1:100 are common. These dilutions are made by diluting one “part” stock with 1, 4, 9 or 99 “parts” water. For example, you could make 100 ml of a 0.5M sorbitol solution by mixing 10 ml of a 5M stock solution with 90 ml of water. This is a 1:10 dilution of the stock. The dilution factor can be converted to a fraction to determine the solution’s final concentration (5M x 1/10 = 0.5M).

-	When the dilution factor is less obvious, the formula ~~C1V1~~ = ~~C2V2~~ can be used,	+	When the dilution factor is less obvious, the formula C<sub>1</sub>V<sub>1</sub> = C<sub>2</sub>V<sub>2</sub> can be used,
-	where C1 is the starting concentration of the stock solution,	+	where C<sub>1</sub> is the starting concentration of the stock solution,
-	C2 is the desired concentration,	+	C<sub>2</sub> is the desired concentration,
-	V1 is the volume of stock you’ll need (usually this is your unknown) and	+	V<sub>1</sub> is the volume of stock you’ll need (usually this is your unknown) and
-	V2 is the final volume you want to make. For example, to make 1000 ml of a 0.2M Tris from a 1.5M stock you would multiply 1.5M (V1) = 0.2M (1000) to find that you will need 133 ml of the stock. To determine how much water to add you would subtract V2 – V1, in this case 1000 ml –133 ml = 867 ml of water.	+	V<sub>2</sub> is the final volume you want to make. For example, to make 1000 ml of a 0.2M Tris from a 1.5M stock you would multiply 1.5M (V<sub>1</sub>) = 0.2M (1000) to find that you will need 133 ml of the stock. To determine how much water to add you would subtract V<sub>2</sub> – V<sub>1</sub>, in this case 1000 ml –133 ml = 867 ml of water.

	When solutions must be diluted several orders of magnitude, then serial dilutions are made. The concentrated stock is progressively diluted, for example using a 1:100 dilution as the new “stock” in another 1:100 dilution. Such a serial dilution produces a solution that is 10,000 times less concentrated than the starting material. One benefit to serial dilutions is that small volumes of each dilution can be made accurately. A drawback is that any pipetting or calculation error is propagated through every dilution.		When solutions must be diluted several orders of magnitude, then serial dilutions are made. The concentrated stock is progressively diluted, for example using a 1:100 dilution as the new “stock” in another 1:100 dilution. Such a serial dilution produces a solution that is 10,000 times less concentrated than the starting material. One benefit to serial dilutions is that small volumes of each dilution can be made accurately. A drawback is that any pipetting or calculation error is propagated through every dilution.

Justinhlo: /* Part 1: Metric system */

2006-02-07T21:12:56Z

Part 1: Metric system

←Older revision		Revision as of 21:12, 7 February 2006
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	#0.000000467		#0.000000467

-	The metric system and scientific notation go hand in hand, making unit conversions straightforward. For example 100 μl can be converted to ml by writing the starting volume in scientific notation (1.00 x 10<sup>2</sup> μl) and multiplying by the power of ten that separates the units (1 ml = 1 x 10<sup>3</sup> ul). Set up every equation so the units will cancel properly when you multiply through.	+	The metric system and scientific notation go hand in hand, making unit conversions straightforward. For example 100 μl can be converted to ml by writing the starting volume in scientific notation (1.00 x 10<sup>2</sup> μl) and multiplying by the power of ten that separates the units (1 ml = 1 x 10<sup>3</sup> μl). Set up every equation so the units will cancel properly when you multiply through.

	'''Practice problems:''' Be sure you can express your answers in scientific notation.		'''Practice problems:''' Be sure you can express your answers in scientific notation.

Justinhlo: /* Part 1: Metric system */

2006-02-07T21:12:22Z

Part 1: Metric system

←Older revision		Revision as of 21:12, 7 February 2006
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	10<sup>3</sup> = 1000 = 1000/1 = 10<sup>3</sup>/1 kilo (k-)		10<sup>3</sup> = 1000 = 1000/1 = 10<sup>3</sup>/1 kilo (k-)
	10<sup>0</sup> = 1 = 1/1 = 10<sup>0</sup>/1 base unit (-g, -l, -mole…)		10<sup>0</sup> = 1 = 1/1 = 10<sup>0</sup>/1 base unit (-g, -l, -mole…)
-	10<sup>-3</sup> = 0.001 = 1/1000 = 1/~~103~~ milli (m-)	+	10<sup>-3</sup> = 0.001 = 1/1000 = 1/10<sup>3</sup> milli (m-)
-	10<sup>-6</sup> = 0.000001 = 1/1000000 = 1/~~106~~ micro (u-)	+	10<sup>-6</sup> = 0.000001 = 1/1000000 = 1/10<sup>6</sup> micro (μ-)


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	#The amount of sorbitol you want to weigh is 1.9 g. How many mg is that?		#The amount of sorbitol you want to weigh is 1.9 g. How many mg is that?
	#The volume you want to measure is 100 ml. How many liters is that?		#The volume you want to measure is 100 ml. How many liters is that?
-	#Your reaction generates 0.1 ~~umoles~~ of product. How many mmoles is that?	+	#Your reaction generates 0.1 μmoles of product. How many mmoles is that?

	Scientific notation expresses numbers so there is one digit to the left of the decimal point and that number is multiplied by a power of ten. 2334 becomes 2.334 x 10<sup>3</sup> and 0.0041 becomes 4.1 x 10<sup>-3</sup>. Computations are easier with numbers in scientific notation and some numbers that are easier to write (602,214,199,000,000,000,000,000 versus 6.02 x 10<sup>23</sup>).		Scientific notation expresses numbers so there is one digit to the left of the decimal point and that number is multiplied by a power of ten. 2334 becomes 2.334 x 10<sup>3</sup> and 0.0041 becomes 4.1 x 10<sup>-3</sup>. Computations are easier with numbers in scientific notation and some numbers that are easier to write (602,214,199,000,000,000,000,000 versus 6.02 x 10<sup>23</sup>).
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	#0.000000467		#0.000000467

-	The metric system and scientific notation go hand in hand, making unit conversions straightforward. For example 100 ul can be converted to ml by writing the starting volume in scientific notation (1.00 x ~~102 ul~~) and multiplying by the power of ten that separates the units (1 ml = 1 x ~~103~~ ul). Set up every equation so the units will cancel properly when you multiply through.	+	The metric system and scientific notation go hand in hand, making unit conversions straightforward. For example 100 μl can be converted to ml by writing the starting volume in scientific notation (1.00 x 10<sup>2</sup> μl) and multiplying by the power of ten that separates the units (1 ml = 1 x 10<sup>3</sup> ul). Set up every equation so the units will cancel properly when you multiply through.

	'''Practice problems:''' Be sure you can express your answers in scientific notation.		'''Practice problems:''' Be sure you can express your answers in scientific notation.
-	#How many ml is 100 ul?	+	#How many ml is 100 μl?
	#How many mg is .023 g?		#How many mg is .023 g?
-	#How many mmoles is 250 ~~umoles~~?	+	#How many mmoles is 250 μmoles?

	===Part 2: Concentrations===		===Part 2: Concentrations===

Justinhlo: /* Introduction to pipetting */

2006-02-07T21:10:24Z

Introduction to pipetting

←Older revision		Revision as of 21:10, 7 February 2006
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	Someone will show you how to use your pipetmen and then you will use them to dilute a blue dye (0.01% Xylene Cyanol).		Someone will show you how to use your pipetmen and then you will use them to dilute a blue dye (0.01% Xylene Cyanol).
-	#If you have never used pipetmen then you should practice by pipeting 800, 80 and 8 ul of the 0.01% XC stock into eppendorf tubes. XC is not hazardous but it will stain your clothes. Pipet each volume three times and visually inspect how well the volumes match.	+	#If you have never used pipetmen then you should practice by pipeting 800, 80 and 8 μl of the 0.01% XC stock into eppendorf tubes. XC is not hazardous but it will stain your clothes. Pipet each volume three times and visually inspect how well the volumes match.
-	#Using your P20, measure 10, 15 and 20 ul of the 0.01% XC stock solution into the bottom of three cuvettes. Using your P1000, add water to bring the final volume to 1 ml (=1000 ul).	+	#Using your P20, measure 10, 15 and 20 μl of the 0.01% XC stock solution into the bottom of three cuvettes. Using your P1000, add water to bring the final volume to 1 ml (=1000 ul).
-	#Using your P200, measure 20, 50 and 100 ul of the 0.01% XC stock solution into the bottom of three more cuvettes. Using your P1000, add water to bring the final volume to 1 ml.	+	#Using your P200, measure 20, 50 and 100 μl of the 0.01% XC stock solution into the bottom of three more cuvettes. Using your P1000, add water to bring the final volume to 1 ml.
-	#Using your P1000, measure 100, 200, and 400 ul of 0.01% XC solution into the bottom of three more cuvettes. Add water to bring the final volume to 1 ml.	+	#Using your P1000, measure 100, 200, and 400 μl of 0.01% XC solution into the bottom of three more cuvettes. Add water to bring the final volume to 1 ml.
	#With a gloved hand or with a piece of parafilm over the lip of the cuvette, invert each cuvette several times to thoroughly mix the contents.		#With a gloved hand or with a piece of parafilm over the lip of the cuvette, invert each cuvette several times to thoroughly mix the contents.
	#Visually compare your dilutions to the reference ones. If time permits, you will read the absorbance of your dilutions in the spectrophotometer so do not throw them away.		#Visually compare your dilutions to the reference ones. If time permits, you will read the absorbance of your dilutions in the spectrophotometer so do not throw them away.

Nkuldell: /* For next time */

2006-01-30T20:51:10Z

For next time

←Older revision		Revision as of 20:51, 30 January 2006
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	4. Complete the student registration/questionnaire to turn in next time [[Image:BE109StudentReg S06.doc\|Student Registration/Questionnaire]].		4. Complete the student registration/questionnaire to turn in next time [[Image:BE109StudentReg S06.doc\|Student Registration/Questionnaire]].

-	5. Register for an account on [[Main Page \| OpenWetWare]] by emailing "admin AT openwetware DOT org" with "new account" in the subject line. Once you get an account familiarize yourself with the wiki by reading [[BE.109:OpenWetWare \| Using OpenWetWare]]. ~~Feel free to start putting~~ information on your user page.	+	5. Register for an account on [[Main Page \| OpenWetWare]] by emailing "admin AT openwetware DOT org" with "new account" in the subject line. Once you get an account familiarize yourself with the wiki by reading [[BE.109:OpenWetWare \| Using OpenWetWare]]. Put some information on your user page.

	6. Read the introduction for the [[BE.109:DNA engineering \| DNA engineering module]]: an experiment that you'll start next time.		6. Read the introduction for the [[BE.109:DNA engineering \| DNA engineering module]]: an experiment that you'll start next time.

Reshma P. Shetty: /* For next time */

2005-12-28T04:37:27Z

For next time

←Older revision		Revision as of 04:37, 28 December 2005
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	4. Complete the student registration/questionnaire to turn in next time [[Image:BE109StudentReg S06.doc\|Student Registration/Questionnaire]].		4. Complete the student registration/questionnaire to turn in next time [[Image:BE109StudentReg S06.doc\|Student Registration/Questionnaire]].

-	5. Register for an account on OpenWetWare ~~at http://openwetware.org/wiki/Main_Page~~ by emailing "admin AT openwetware DOT org" with "new account" in the subject line. Once you get an account familiarize yourself with the wiki by reading [[BE.109:OpenWetWare \| Using OpenWetWare]]. Feel free to start putting information on your user page.	+	5. Register for an account on [[Main Page \| OpenWetWare]] by emailing "admin AT openwetware DOT org" with "new account" in the subject line. Once you get an account familiarize yourself with the wiki by reading [[BE.109:OpenWetWare \| Using OpenWetWare]]. Feel free to start putting information on your user page.

-	6. Read the introduction for the DNA engineering module, an experiment that you'll start next time~~: http://openwetware~~.~~org/wiki/BE.109%3ADNA_engineering~~	+	6. Read the introduction for the [[BE.109:DNA engineering \| DNA engineering module]]: an experiment that you'll start next time.

	7. Learn a little about the Polymerase Chain Reaction (PCR) since you will perform these reactions next time. It is described in most biology textbooks so you could start there. Alternatively, the internet has some nice animations of the process, for example		7. Learn a little about the Polymerase Chain Reaction (PCR) since you will perform these reactions next time. It is described in most biology textbooks so you could start there. Alternatively, the internet has some nice animations of the process, for example
	*http://www.dnai.org/b/index.html (follow the links through “techniques” and "amplifying DNA”)		*http://www.dnai.org/b/index.html (follow the links through “techniques” and "amplifying DNA”)
	*or try: http://www.dnalc.org/shockwave/pcranwhole.html		*or try: http://www.dnalc.org/shockwave/pcranwhole.html

←Older revision		Revision as of 20:50, 7 May 2008
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	4. Complete the student registration/questionnaire to turn in next time [[Image:BE109StudentReg S06.doc\|Student Registration/Questionnaire]].		4. Complete the student registration/questionnaire to turn in next time [[Image:BE109StudentReg S06.doc\|Student Registration/Questionnaire]].

-	5. Register for an account on [[Main Page \| OpenWetWare]] ~~by emailing "admin AT openwetware DOT org" with "new account" in the subject line~~. Once you get an account familiarize yourself with the wiki by reading [[BE.109:OpenWetWare \| Using OpenWetWare]]. Put some information on your user page.	+	5. [[OpenWetWare:How to join\|Register for an account]] on [[Main Page \| OpenWetWare]]. Once you get an account familiarize yourself with the wiki by reading [[BE.109:OpenWetWare \| Using OpenWetWare]]. Put some information on your user page.

	6. Read the introduction for the [[BE.109:DNA engineering \| DNA engineering module]]: an experiment that you'll start next time.		6. Read the introduction for the [[BE.109:DNA engineering \| DNA engineering module]]: an experiment that you'll start next time.

←Older revision		Revision as of 20:51, 30 January 2006
Line 191:		Line 191:
	4. Complete the student registration/questionnaire to turn in next time [[Image:BE109StudentReg S06.doc\|Student Registration/Questionnaire]].		4. Complete the student registration/questionnaire to turn in next time [[Image:BE109StudentReg S06.doc\|Student Registration/Questionnaire]].

-	5. Register for an account on [[Main Page \| OpenWetWare]] by emailing "admin AT openwetware DOT org" with "new account" in the subject line. Once you get an account familiarize yourself with the wiki by reading [[BE.109:OpenWetWare \| Using OpenWetWare]]. ~~Feel free to start putting~~ information on your user page.	+	5. Register for an account on [[Main Page \| OpenWetWare]] by emailing "admin AT openwetware DOT org" with "new account" in the subject line. Once you get an account familiarize yourself with the wiki by reading [[BE.109:OpenWetWare \| Using OpenWetWare]]. Put some information on your user page.

	6. Read the introduction for the [[BE.109:DNA engineering \| DNA engineering module]]: an experiment that you'll start next time.		6. Read the introduction for the [[BE.109:DNA engineering \| DNA engineering module]]: an experiment that you'll start next time.