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CAROL
Preparation for Maxiprep
- Prepared overnight cultures for maxi-prep tomorrow.
- Read through several modelling papers.
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CHINMOYEE
CLASS
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EMILY
Isolating Plamid, Nanodrop and Preparations for DNA Sequencing
Isolated plasmid from LuxOD47E overnight cultures using Sigma miniprep kit, lot # 035K6068, eluting in ddH2O. Learned how to use Nanodrop Spectrophotometer to determine the concentration of the DNA. Prepared DNA for DNA sequecning. The optimal concentration of DNA for DNA sequencing is 100 ng/ 1 kb. Our gene is 1362 base pairs and the concentration is 292.3 ng/uL, so we sent down 1.8 uL of DNA with 7.2 uL ddH2O.
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FAHD
Marketing and Outreach for June 9th 2009
Today, I contacted some Oil and Gas companies via e-mail and I will make follow up phone calls soon.
I also signed up for second life ™, which would be our biggest part of our outreach aspect of our project. I wanted to familiarize myself with the online virtual world so I can get more ideas on how to hold the ethics conference in second life ™
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IMAN
Descriptive Title of What You're Doing
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JAMIE
Descriptive Title of What You're Doing
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JEREMY
Preparation of luxPQ in TOPO for DNA Sequencing
Two colonies of luxPQ in the TOPO vector were sent for sequencing, one from this year and one from 2008. If luxPQ is present in either colony, then this colony will be proceeded with in the project. As per the University of Calgary DNA Sequencing requirements, there was 100ng/uL of DNA and water up to 10uL. Sequencing primers included primers annealing to the 5’ end and 3’ end of the multiple cloning site.
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KATIE
Do Not Group Deed Objects
Lost my entire PCR machine script included today and will have to start over since no one is able to access anything within the object. I have old versions of the scripts I was using so hopefully I will be able to update them quickly and integrate all scripts together since it is really not practical and I will also need to add more types of DNA. This will most likely involve:
- Adding a variable to keep track of what type of DNA has been added so that the correct product may be given to the avatar later
- Making the different products and putting them into the machine’s inventory
- Adding the names of the different types of DNA to a list that will be searched through to see what exists and what doesn’t
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KEVIN
Plasmid Isolation (miniprep)
The pBluescript were isolated from TOP10 cells by using Sigma's GenElute plasmid Miniprep kit (sigma). The pBluescript is needed to verify more competent cells in the future.
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MANDY
A Lesson Learned in Second Life
Do not group deed objects! Today I accidently lost Katie's PCR script while we played around with object ownership. We now have a better understanding at least of how to share building projects and scripts without losing the ability to modify or copy them. Sometimes, however, Second Life can still make us lose these 'permissions', so keeping copies of everything is a must!
Fahd and Prima got their first taste of Second Life today, and were able to complete an in-world survey about prefered Hotel ammenities for Hong Kong University in order to get us the Linden dollars we needed to upload the textures used in the Virtual Lab. Using these textures, I made more lab equipment, doors, and cupboards to make the environment more realistic and interesting.
Made multiple recolors of the logo so that it could be voted on by team members today (we had approximately 16 different shades of green!).
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PATRICK
Persistant Bugs
Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day.
Briefly became very excited at the idea of turning PDB models of proteins into ingame objects, instead of using spheres or other simple shapes, but this fell by the side.
Encountered some very persistant bugs in the scheme I was using for communication. I forget just what the problems were now, but just as soon as I had figured out why the RNAP wasn't getting the message I'd learn that the DNA parts were no longer learning each other's names properly...
I also had a conversation with someone from Brazil, through one of second life's universal translators. Yes, you heard me right, it is only 2009 and we have (primitive) universal translators! Look up the Hank Ramos Universal Translator, for more.
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PRIMA
Introduction to Second Life
I signed up in Second Life today. My avatar's name is Synthiya Shieldmaiden. I explored our island, sat on pretty much anything that was shaking or moving. I also met my Second Life team members and spoke to them using the local chat box. I also enjoyed flying in Second Life.
After couple horus of exploring, I completed an online survey to raise Lynden dollars for the Second Life team.
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STEFAN
Descriptive Title of What You're Doing
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VICKI
LuxOD47A plasmid isolation and preparation for sequencing
Plasmid isolation of competent LuxOD47A BBk cells
Purpose: to isolate plasmids from LuxOD47A cells that were cultured over the weekend
Protocol: refer to protocol page.
Concentration measurement of isolated plasmids
Purpose: to measure the concentration of the isolated plasmids with the Nanodrop spectrophotometer
Protocol: refer to protocol page.
Preparation of LuxOD47A in TOPO for sequencing
Protocol: refer to protocol page. 500 ng of DNA were inserted into the tube sent down for sequencing.
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