User:Linh N Le/Notebook/2009/08/28: Difference between revisions

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==Entry title==
==To Do==
* Insert content here...
* Write my last official notebook entry as a KochLab member :(
* We are running out of PEM, so I would like to make some more before I go
* We got motility working yesterday, so Andy may want to continue to pursue that


==Inventory==
*Brian had to leave, but i did give him a crash course on how to use the inventory page
*Most of the pages are self-explanatory
*Also note that chemicals and software inventory require an update to the google docs page
*The optics section of the inventory is blank
**My idea was to have it as a static page that just listed important opto-mechanics
**Perhaps we can have a check in-check out system so we can keep track of who took what where and when


==PEM==
* Andy, Brigette and I made 205ml of PEM a month or 2 ago and its getting low
* I will try to make 200ml more and follow the exact steps I took [http://www.openwetware.org/wiki/User:Linh_N_Le/Notebook/2009/06/22 last time]
* I will need NaOH and possibly HCL to titrate the buffer
** We should have plenty of normal soln left from earlier buffer makings
** We have 4 tubes of NaOH but no HCL, lets hope I dont screw up the titration
===Procedure===
*Following what I did last time, I want the following:
** 1mM MgCl2
** 1mM EGTA
** 80mM PIPES
*I am using the following chemicals:
**1M MgCl2 in 50mL falcon tube made 2 years ago ( we used it in the motility assay yesterday and it was fine)
***For 1mM in 200ml, I want .2ml (200uL)
**EGTA powder, working weight 380.35
**For 1mM in 200ml i need .07607g
**PIPES powder, working weight 302.37
**For 80mM in 200ml, I need 4.83792g
*I will wash out a 250ml glass bottle with DI water then use DI water to suspend the salts
**I will use the autoclaved DI water I made a month ago, that way we use it a up a bit since we have a fancy schmancy DI water machine
*I filled up the jar with ~150ml of DI h20, now to add the powders
*After addition of powders and washing it down with more DI water, I'm about 175ml
*Powder Concentrations used:
**200ul MgCl2
**.0768g EGTA
**4.8387g PIPES
*'''Note: I used the "DI Water" in the spray bottle. It may be tap water, Andy and I both dont know who filled it up with what. Last time I made buffers I used the water in the spray bottle, hopefully it still works
*Now to titrate
===Titration===
*Starting Ph
*added 25.8mL of 1M NaoH to get it to a Ph of 6.89
**Thats 12.9mM of NaoH in 200ml soln of PEM
==Test Drive==
*Andy is making motility stuff and is going to try my PEM, hope it all works!
*Andy got the motility to work!
==DI H<sub>2</sub>O==
*I went ahead and emptied out all the squeeze bottles that are labeled DI water and replaced it with the stuff from our DI water machine
==Final Note For KochLab==
*I would like to take a minute to thank each and every person in Koch Lab for this wonderful experience I have had over the past year and a half
*Koch: Thank you for teaching a really great Jr lab. It was how you handled that little lab that really made me want to work for you in a real one (and boy was I not disappointed). Even though you were still in a startup phase, you still allowed me to come in and work for you. Even though you don't think you gave me enough attention, you definitely met the need (and I'm amazed at how you juggle everything). I'm now spoiled on all future advisors
*Larry: You were the first grad student that I met in the lab, and luckily Pat joined at the same time to take all the abuse (j/k!). The lab experience would not have been anywhere near the same if you weren't around to jostle things up. I apologize if you felt you were the butt of one too many of my comics, but I appreciate that you can joke with me too sometimes.
*Ant: You were my mentor for the summer that I started and you were out of town for at least a week (what a first impression!). Joshing aside, you did do a great job showing me the ropes of the lab, helping me get things setup, and just otherwise guiding me along (even though I joked about you being my mentor, I really did appreciate it). You and Larry are quite a team, and I was glad that you let me into your circle
*Nas:Although we didn't really work that much together, you were always a happy guy. I don't know if you will read this, but let the record show that Nas was the most friendly and willing-to-help-y person I ever met. It was really neat to get to see the biologists in the lab; lending to the hybridization that I think is really the appeal and strength of biophysics. I do hope that you get your MD and work a good practice here
*Diego:Speaking of biologists, Diego is the main man. Although we didn't really interact too much, Diego did show me show me how Biologists and  Physicists can work together great! I also want to thank you for all the funny stories and help with graduate applications that you provided me.
**[[User:Ramalldf|Ramalldf]] 23:21, 29 August 2009 (EDT):Hey Linh, I forgot to add you to the email that I sent to the rest of Osley/Koch lab so I'll forward that to ya. Thanks for the note! I wish that I had had more of an opportunity to interact with you the summer that you started but I'm glad that OWW will let us keep in touch. It sounds like Koch and the other students trained you really well for this upcoming year so I'm sure that you'll rock at Ohio St. You always have a friend in this part of the country so don't be a stranger! :) P.S. I think that your comics were hilarious so continue making them, you might have the next Ph.D comics!
*Caleb:When Koch asked me "Do you know Caleb Morse?" I said "no" not knowing it was the same guy I saw at least 3 times a week when I tutored at CAPS. Caleb, you are a computer ''genius''! Thank you so much for helping me get the computers in line and being an overall cool guy. I enjoyed tutoring you in CAPS and it was all too amazing that we worked together for Koch
*Pat: Pat and I stated at the same time. Even though you are gone (and may not read this entry), thanks for being there as the other undergrad. Um, that may not sound as sincere as I want it to, but it was really great to have someone my age/level in the lab for me to relate to. It was also really fun to see you and Larry fight. We did have some fun times and I wish you the best as you also embark in grad school
*Andy: Oh Andy. I probably got on your nerves more times than you really cared for. Aside from that, thank you for "taking me under your wing" (I think it was voluntary, maybe Koch bribed you). You are one smart guy, and I'm glad that you took the time to share with me some of your knowledge. It was (and still is) hard to get the lab just they way you want it, but in the end, I think your changes are a great asset to the lab. You are an awesome teacher and have patience like few others (how many times have you surprised me by not blowing up at Larry). One more thing, I just want you to know that you have to coolest character in my comic.
*Brigette: I guess my computer will always think your named is misspelled. I'm sad that we didnt really get a chance to know each other as you just stared just as I left (and I'm sorry you're not in my comic yet, but I will try to fix that soon). Thanks for letting me help you with the projects, even though I got in the way more that anything. You are a really cool person and I'm amazed that KochLab got a female student. You'll bring some civility to this lab (maybe, maybe not), or at last a precedent to get more girls. I thought we worked well together and it was really fun to have a "lab partner" and someone just to gab with.
**[[User:Brigette D. Black|Brigette D. Black]] 03:35, 31 August 2009 (EDT): You didn't get in my way at all! I actually feel kind of bad I didn't have more for you to do, but I do insist you do one last comic. You really did help out quite a lot, and it was really nice to shoot the breeze while setting up and cleaning up. Your easy going personality helped a great deal when tensions were running high. I'm confident that you will do great in Ohio, and I wish you all the luck in the world (although I'm sure you will not need it). Thanks again for everything. We'll miss you, so make sure you come back and visit!
*Brian: Although you are new and we met only a couple times (and Koch denies that you are my replacement) I know you will do this lab some justice. You have a go-to attitude that I haven't seen in a long time and I know you will do some great things now that the lab has some momentum! Good luck, you'll need it!
*As a final thought, I have learned and grown so much since starting in this lab. I feel I'm more prepared for the rigors of grad school. It was amazing to see all the different personalities that are here and how you all still get along and work so great. Thank you all for allowing me to be a part of the lab and help it grow. I'm honored to be mentioned in papers and posters that you have written, and I feel I had an impact in the future of the lab. I'm sorry if I left anything out or if one person feels that their message is not as good as any other. I thank all of you for everything that you have done for me and all the time we have spent together (in and out of the lab). I am honored to not only feel like I was apart of a great lab, but somehow also friends with all of you. I will never forget any of you and hope to be able to come visit lots!
*''I will be in town until next Thursday if there is any last minute things that need my attention. My contact info is listed on my user page on the private wiki (including cell#)''
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Revision as of 00:35, 31 August 2009

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To Do

  • Write my last official notebook entry as a KochLab member :(
  • We are running out of PEM, so I would like to make some more before I go
  • We got motility working yesterday, so Andy may want to continue to pursue that

Inventory

  • Brian had to leave, but i did give him a crash course on how to use the inventory page
  • Most of the pages are self-explanatory
  • Also note that chemicals and software inventory require an update to the google docs page
  • The optics section of the inventory is blank
    • My idea was to have it as a static page that just listed important opto-mechanics
    • Perhaps we can have a check in-check out system so we can keep track of who took what where and when

PEM

  • Andy, Brigette and I made 205ml of PEM a month or 2 ago and its getting low
  • I will try to make 200ml more and follow the exact steps I took last time
  • I will need NaOH and possibly HCL to titrate the buffer
    • We should have plenty of normal soln left from earlier buffer makings
    • We have 4 tubes of NaOH but no HCL, lets hope I dont screw up the titration

Procedure

  • Following what I did last time, I want the following:
    • 1mM MgCl2
    • 1mM EGTA
    • 80mM PIPES
  • I am using the following chemicals:
    • 1M MgCl2 in 50mL falcon tube made 2 years ago ( we used it in the motility assay yesterday and it was fine)
      • For 1mM in 200ml, I want .2ml (200uL)
    • EGTA powder, working weight 380.35
    • For 1mM in 200ml i need .07607g
    • PIPES powder, working weight 302.37
    • For 80mM in 200ml, I need 4.83792g
  • I will wash out a 250ml glass bottle with DI water then use DI water to suspend the salts
    • I will use the autoclaved DI water I made a month ago, that way we use it a up a bit since we have a fancy schmancy DI water machine
  • I filled up the jar with ~150ml of DI h20, now to add the powders
  • After addition of powders and washing it down with more DI water, I'm about 175ml
  • Powder Concentrations used:
    • 200ul MgCl2
    • .0768g EGTA
    • 4.8387g PIPES
  • Note: I used the "DI Water" in the spray bottle. It may be tap water, Andy and I both dont know who filled it up with what. Last time I made buffers I used the water in the spray bottle, hopefully it still works
  • Now to titrate

Titration

  • Starting Ph
  • added 25.8mL of 1M NaoH to get it to a Ph of 6.89
    • Thats 12.9mM of NaoH in 200ml soln of PEM

Test Drive

  • Andy is making motility stuff and is going to try my PEM, hope it all works!
  • Andy got the motility to work!

DI H2O

  • I went ahead and emptied out all the squeeze bottles that are labeled DI water and replaced it with the stuff from our DI water machine

Final Note For KochLab

  • I would like to take a minute to thank each and every person in Koch Lab for this wonderful experience I have had over the past year and a half
  • Koch: Thank you for teaching a really great Jr lab. It was how you handled that little lab that really made me want to work for you in a real one (and boy was I not disappointed). Even though you were still in a startup phase, you still allowed me to come in and work for you. Even though you don't think you gave me enough attention, you definitely met the need (and I'm amazed at how you juggle everything). I'm now spoiled on all future advisors
  • Larry: You were the first grad student that I met in the lab, and luckily Pat joined at the same time to take all the abuse (j/k!). The lab experience would not have been anywhere near the same if you weren't around to jostle things up. I apologize if you felt you were the butt of one too many of my comics, but I appreciate that you can joke with me too sometimes.
  • Ant: You were my mentor for the summer that I started and you were out of town for at least a week (what a first impression!). Joshing aside, you did do a great job showing me the ropes of the lab, helping me get things setup, and just otherwise guiding me along (even though I joked about you being my mentor, I really did appreciate it). You and Larry are quite a team, and I was glad that you let me into your circle
  • Nas:Although we didn't really work that much together, you were always a happy guy. I don't know if you will read this, but let the record show that Nas was the most friendly and willing-to-help-y person I ever met. It was really neat to get to see the biologists in the lab; lending to the hybridization that I think is really the appeal and strength of biophysics. I do hope that you get your MD and work a good practice here
  • Diego:Speaking of biologists, Diego is the main man. Although we didn't really interact too much, Diego did show me show me how Biologists and Physicists can work together great! I also want to thank you for all the funny stories and help with graduate applications that you provided me.
    • Ramalldf 23:21, 29 August 2009 (EDT):Hey Linh, I forgot to add you to the email that I sent to the rest of Osley/Koch lab so I'll forward that to ya. Thanks for the note! I wish that I had had more of an opportunity to interact with you the summer that you started but I'm glad that OWW will let us keep in touch. It sounds like Koch and the other students trained you really well for this upcoming year so I'm sure that you'll rock at Ohio St. You always have a friend in this part of the country so don't be a stranger! :) P.S. I think that your comics were hilarious so continue making them, you might have the next Ph.D comics!
  • Caleb:When Koch asked me "Do you know Caleb Morse?" I said "no" not knowing it was the same guy I saw at least 3 times a week when I tutored at CAPS. Caleb, you are a computer genius! Thank you so much for helping me get the computers in line and being an overall cool guy. I enjoyed tutoring you in CAPS and it was all too amazing that we worked together for Koch
  • Pat: Pat and I stated at the same time. Even though you are gone (and may not read this entry), thanks for being there as the other undergrad. Um, that may not sound as sincere as I want it to, but it was really great to have someone my age/level in the lab for me to relate to. It was also really fun to see you and Larry fight. We did have some fun times and I wish you the best as you also embark in grad school
  • Andy: Oh Andy. I probably got on your nerves more times than you really cared for. Aside from that, thank you for "taking me under your wing" (I think it was voluntary, maybe Koch bribed you). You are one smart guy, and I'm glad that you took the time to share with me some of your knowledge. It was (and still is) hard to get the lab just they way you want it, but in the end, I think your changes are a great asset to the lab. You are an awesome teacher and have patience like few others (how many times have you surprised me by not blowing up at Larry). One more thing, I just want you to know that you have to coolest character in my comic.
  • Brigette: I guess my computer will always think your named is misspelled. I'm sad that we didnt really get a chance to know each other as you just stared just as I left (and I'm sorry you're not in my comic yet, but I will try to fix that soon). Thanks for letting me help you with the projects, even though I got in the way more that anything. You are a really cool person and I'm amazed that KochLab got a female student. You'll bring some civility to this lab (maybe, maybe not), or at last a precedent to get more girls. I thought we worked well together and it was really fun to have a "lab partner" and someone just to gab with.
    • Brigette D. Black 03:35, 31 August 2009 (EDT): You didn't get in my way at all! I actually feel kind of bad I didn't have more for you to do, but I do insist you do one last comic. You really did help out quite a lot, and it was really nice to shoot the breeze while setting up and cleaning up. Your easy going personality helped a great deal when tensions were running high. I'm confident that you will do great in Ohio, and I wish you all the luck in the world (although I'm sure you will not need it). Thanks again for everything. We'll miss you, so make sure you come back and visit!
  • Brian: Although you are new and we met only a couple times (and Koch denies that you are my replacement) I know you will do this lab some justice. You have a go-to attitude that I haven't seen in a long time and I know you will do some great things now that the lab has some momentum! Good luck, you'll need it!
  • As a final thought, I have learned and grown so much since starting in this lab. I feel I'm more prepared for the rigors of grad school. It was amazing to see all the different personalities that are here and how you all still get along and work so great. Thank you all for allowing me to be a part of the lab and help it grow. I'm honored to be mentioned in papers and posters that you have written, and I feel I had an impact in the future of the lab. I'm sorry if I left anything out or if one person feels that their message is not as good as any other. I thank all of you for everything that you have done for me and all the time we have spent together (in and out of the lab). I am honored to not only feel like I was apart of a great lab, but somehow also friends with all of you. I will never forget any of you and hope to be able to come visit lots!
  • I will be in town until next Thursday if there is any last minute things that need my attention. My contact info is listed on my user page on the private wiki (including cell#)
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