I've practice my presentation about five times to myself. I'm not a very good public speaker, considering I don't have a lot of experience in that area, so I'm going to try to practice as much as possible today. I feel like I'm going to have to speak quickly to make the 8 minute mark . . . in fact I've practiced and averaged about 7 minutes each time. I just feel like I can't cut anymore information out without cheating the project and leaving the audience hanging.
I'm trying not to be so nervous about the presentation but I still am anyway. I hope I can connect with the audience like Scott Cochran wants all of us to do. I think I know what I'm going to wear; I have that at least.
Tuesday, January 31, 2012
Monday, January 30, 2012
Winding down. But not really.
So today we had our second and last meeting. Scott Cochran came and talked with us (not to, with!) about good presentation skills. I am not much of an extrovert, so I'm not naturally good at giving presentations. Public speaking actually makes my mouth go dry and my heart beat out of my chest. I did give a presentation on work I did with the GGC last fall, so I wasn't incredibly worried about this presentation because of my prior experience. But turns out there are a lot of things you can do wrong when giving a presentation. It was all good advice, but I'm a lot more nervous now, exponentially so.
Before the meeting and earlier in the day, I submitted my paper and sent my presentation to Dr. Schwartz to see what suggestions he had. He promptly emailed me back, and gave said suggestions. I am currently waiting on some information from Melanie before I finalize (and practice the living daylights out of) my presentation. I'm a bit worried about the time limits but I'm going to have to find a way to cram all of my information into the presentation.
Before the meeting and earlier in the day, I submitted my paper and sent my presentation to Dr. Schwartz to see what suggestions he had. He promptly emailed me back, and gave said suggestions. I am currently waiting on some information from Melanie before I finalize (and practice the living daylights out of) my presentation. I'm a bit worried about the time limits but I'm going to have to find a way to cram all of my information into the presentation.
Friday, January 27, 2012
Writing away!
Today I worked on my paper again. I have so many resources for the work I did that it gets confusing sometime to write about the right exon or right mutation. This is especially true because of the nature of the research. A lot of times I will have to look at a sequence of something and figure out what exon it's talking about, or try to locate a mutation among hundreds of the same four letters over and over in different combinations . . . A, C, T, G. Eventually I figure things out.
I wanted to get my paper finalized tonight but I'm not sure it's going to happen since I went to Clemson to support my teammates at their (sort of) first indoor meet of the season. I haven't been to practice in a really long time because of an injury so I felt it was important for me to come and support them. I'm considering bringing my computer to the meet tomorrow to work on it in between events.
I wanted to get my paper finalized tonight but I'm not sure it's going to happen since I went to Clemson to support my teammates at their (sort of) first indoor meet of the season. I haven't been to practice in a really long time because of an injury so I felt it was important for me to come and support them. I'm considering bringing my computer to the meet tomorrow to work on it in between events.
Thursday, January 26, 2012
Well this feels strange.
It feels so very strange to be done with my research! Of course I still have to do the paper and the presentation, but man, I just wish I could keep going. I love doing research, the possibility of finding some previously unknown piece of information that could potentially lead to more information is something special.
I drove to the center, bringing back all their supplies that I borrowed. I arrived a little after 9:00, which is when the weekly lab meeting starts, so I went upstairs and unpacked the things I had brought back. I had to take a lot of labeling tape off of tubes and dishes and racks and boxes in the process; a lot of what I had borrowed I labeled as property of the GGC so I wouldn't forget it. After that was finished I got to analyzing the last four sequences. Since I ran out of ExoSap on Exon 6, I had to load the last 8 samples from that Exon onto the last few sequencing plates. I also analyzed those. It was a bit tricky to find those samples among the other 70 samples per each sequencing plate. I completed the mutations chart for Exons vs. patients on the computer and in the binder for this gene.
I also talked to Melanie about a few details about the gene and the procedure, and then I was ready to leave. It was sad the last time I left the GGC this past summer, and it was sad this time as well. I'm going to miss stopping in regularly! But I've already decided that I'm going to try to come visit everyone there this summer. I'm really grateful for the opportunities they've given me.
I drove to the center, bringing back all their supplies that I borrowed. I arrived a little after 9:00, which is when the weekly lab meeting starts, so I went upstairs and unpacked the things I had brought back. I had to take a lot of labeling tape off of tubes and dishes and racks and boxes in the process; a lot of what I had borrowed I labeled as property of the GGC so I wouldn't forget it. After that was finished I got to analyzing the last four sequences. Since I ran out of ExoSap on Exon 6, I had to load the last 8 samples from that Exon onto the last few sequencing plates. I also analyzed those. It was a bit tricky to find those samples among the other 70 samples per each sequencing plate. I completed the mutations chart for Exons vs. patients on the computer and in the binder for this gene.
I also talked to Melanie about a few details about the gene and the procedure, and then I was ready to leave. It was sad the last time I left the GGC this past summer, and it was sad this time as well. I'm going to miss stopping in regularly! But I've already decided that I'm going to try to come visit everyone there this summer. I'm really grateful for the opportunities they've given me.
Wednesday, January 25, 2012
Writing my paper
Today I just started writing my paper. I feel like it's sooooo late to start, and I hate being rushed, but I've been consumed up until this point with work. I have to go back to the GGC one more time to analyze my last four sequences and bring back all the supplies I have left over at the Wofford lab.
Anyway, back to my paper. I went to a coffee shop in Spartanburg, The Coffee Bar, which is a really good place to work. I saw Alex Hubbard there (shout out) working diligently as well. He's doing an independent research interim also. I'm really glad I finally got to start my paper, because I've just felt it hanging over my head. Since I can sum up my results in an Excel Spreadsheet, I'm going to provide as much background info on the work I'm doing, and the work of the GGC, as possible. I'm trying to stick to the outline I made, and hope that the paper really reflects how much time I've spent on this project/any findings that I have. I think the presentation will come fairly easily after I write the paper. I presented my research from the summer at the end of last semester, so I will probably stick to a format close to that powerpoint since I think it went well.
Anyway, back to my paper. I went to a coffee shop in Spartanburg, The Coffee Bar, which is a really good place to work. I saw Alex Hubbard there (shout out) working diligently as well. He's doing an independent research interim also. I'm really glad I finally got to start my paper, because I've just felt it hanging over my head. Since I can sum up my results in an Excel Spreadsheet, I'm going to provide as much background info on the work I'm doing, and the work of the GGC, as possible. I'm trying to stick to the outline I made, and hope that the paper really reflects how much time I've spent on this project/any findings that I have. I think the presentation will come fairly easily after I write the paper. I presented my research from the summer at the end of last semester, so I will probably stick to a format close to that powerpoint since I think it went well.
Tuesday, January 24, 2012
Last sequences submitted!
Today I was at the center again. I got my last four plates (exons) ready to be submitted for sequencing. Not only does this involve getting the Dye-Ex plates ready, loading them with my samples, drying the samples down, resuspending them, and denaturing them, but some paperwork goes along with it. You have to make a chart of how your plate is loaded, and you have to create a corresponding excel spreadsheet with the sample names. It's all very specific! But I have quite gotten the hang of it this interim, certainly moreso than I did this summer. I think it is because I am acting more independently now in the research (at least the motions) than I was this summer; this of course has to do with the isolation aspect in working at Wofford's lab by myself. It's a very valuable experience!
I also analyzed four of the sequences, which I submitted yesterday. I made notes on anything that I found and submitted them to Melanie. Everything about this gene goes in a binder, and each exon has its own tab. This is generally how things are organized at the center. I had a few notebooks that I was keeping up this summer as I worked on a few different genes. It is especially useful because you can look back on how you carried out a reaction (what temperatures, times, etc.) and see how it turned out. I've learned the power of keeping good notes because of this practice.
I also analyzed four of the sequences, which I submitted yesterday. I made notes on anything that I found and submitted them to Melanie. Everything about this gene goes in a binder, and each exon has its own tab. This is generally how things are organized at the center. I had a few notebooks that I was keeping up this summer as I worked on a few different genes. It is especially useful because you can look back on how you carried out a reaction (what temperatures, times, etc.) and see how it turned out. I've learned the power of keeping good notes because of this practice.
Monday, January 23, 2012
Busy bee
I went to the center today, and it was quite the busy day. For the first part of the day, I got all of the remaining exons ready to be sequenced up to the BigDyeFast step. By 3:00 I had submitted four plates of samples for sequencing. Tomorrow I will submit the last four. I also analyzed four sequences while I was at the center. This took the last couple of hours that I was at the center.
When analyzing sequences I compare 10-15 of the samples to the regular transcript of the gene, and anything that doesn't match the transcript shows up in red. Most of the time it's an "ambiguity code" like a Y or a W, and you have to look at the colors of the wave signals to see what the base is. If it's not an ambiguity code and you see a base change, you still probably need to check the waves to make sure the sample isn't messy looking.
If an SNP is found, I think the next step would be to screen the "normal population" DNA plates. Hopefully I'm able to locate some sort of mutation within this gene!
When analyzing sequences I compare 10-15 of the samples to the regular transcript of the gene, and anything that doesn't match the transcript shows up in red. Most of the time it's an "ambiguity code" like a Y or a W, and you have to look at the colors of the wave signals to see what the base is. If it's not an ambiguity code and you see a base change, you still probably need to check the waves to make sure the sample isn't messy looking.
If an SNP is found, I think the next step would be to screen the "normal population" DNA plates. Hopefully I'm able to locate some sort of mutation within this gene!
Sunday, January 22, 2012
O Also!
My dad took a few pictures of me working. I'll post some below. You'll also see them in the presentation if you are present.
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| Taking samples out of the PCR machine after amplification |
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| About to load a gel |
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| Loading the gel |
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| Taking some sample |
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| After the gel has been run, going to take a picture! |
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| Taking the picture out of the camera |
Working on the Weekend
Yesterday I showed my parents the lab. They really liked it, for this I am glad. I ran a gel on Exons 13 and 14, which turned out a little streaky but my gel was a tad bit old. It was from the beginning of the week but I figured I could get away with using it one more time.
Today I created an outline for my paper, and started looking for sources/reference materials. I am having some issues tracking down articles on one of the syndromes that is associated with this gene. There is one article that I was really curious about, and I clicked on about 20 different links trying to gain access to a pdf. No luck! O well, I will have to obtain my information elsewhere I do believe. Completing this paper and presentation are going to be difficult because I still have a copious amount of work to do at the center to acquire results. The hard work will be well worth it though. I love learning more about the field of genetics. As a side note, I'm taking a Human Genetics class this next semester with Dr. Moss (and a class on current topics in biology, which will surely include some talk of genetics). I'm pretty excited about it, not gonna lie.
'Til tomorrow!
Today I created an outline for my paper, and started looking for sources/reference materials. I am having some issues tracking down articles on one of the syndromes that is associated with this gene. There is one article that I was really curious about, and I clicked on about 20 different links trying to gain access to a pdf. No luck! O well, I will have to obtain my information elsewhere I do believe. Completing this paper and presentation are going to be difficult because I still have a copious amount of work to do at the center to acquire results. The hard work will be well worth it though. I love learning more about the field of genetics. As a side note, I'm taking a Human Genetics class this next semester with Dr. Moss (and a class on current topics in biology, which will surely include some talk of genetics). I'm pretty excited about it, not gonna lie.
'Til tomorrow!
Friday, January 20, 2012
Last two exons amplified . . . *sigh*
It seems like it's been a long road to this point, even though it's only been two weeks. I transferred a couple of exosap'd exons to 96 well plates, and then amplified the last two exons. I'm going to run the gel on those tomorrow, and hopefully they will turn out well. If not I definitely have time to reamplify before I go to the center again.
When I do go to the center, I will have A LOT to accomplish. So far I've submitted six plates for sequencing, two of which I've analyzed the results already. This being said I will have to analyze four plates next visit. Also, I will be bringing exons seven through 12 exosap'd. Thus I will have to run six BigDyeFast PCRs, and get six plates ready for sequencing. I will also have to ExoSap, BigDyeFast, and get plates ready for exons 13 and 14. Then exons 7-14 have been submitted for sequencing, I will have to analyze those eight plates of samples. I'm going to assume this will take at least three trips to the center. I'm going to be a busy girl next week! (Not that this is irregular.)
There are a few things that I've learned while working in the lab. I'll list a few of them for you.
1) Tubes are hard to deal with in masses.
2) Especially those with domed caps.
3) Don't even attempt to paint your nails while working with tubes. Your nails will be bent back, broken, and immediately chipped.
4) You CAN get calluses on your thumbs.
5) Sharpies don't work as well as the permanent markers from the GGC.
6) I'm not sure Pandora has that time limit per month anymore; I've listened to it nonstop for at least 8 hours everyday. Otherwise, I've somehow managed to trick them.
7) I find working in a lab to be a bit relaxing, even though I have to race the clock in preparing the reactions.
8) Multi-channel pipettes save lives. (Ok, maybe not literally, but still.)
9) Tour groups think anyone working alone in a lab is an alien.
10) Doing science-y things pays off. Mark Olencki will come take your picture!
When I do go to the center, I will have A LOT to accomplish. So far I've submitted six plates for sequencing, two of which I've analyzed the results already. This being said I will have to analyze four plates next visit. Also, I will be bringing exons seven through 12 exosap'd. Thus I will have to run six BigDyeFast PCRs, and get six plates ready for sequencing. I will also have to ExoSap, BigDyeFast, and get plates ready for exons 13 and 14. Then exons 7-14 have been submitted for sequencing, I will have to analyze those eight plates of samples. I'm going to assume this will take at least three trips to the center. I'm going to be a busy girl next week! (Not that this is irregular.)
There are a few things that I've learned while working in the lab. I'll list a few of them for you.
1) Tubes are hard to deal with in masses.
2) Especially those with domed caps.
3) Don't even attempt to paint your nails while working with tubes. Your nails will be bent back, broken, and immediately chipped.
4) You CAN get calluses on your thumbs.
5) Sharpies don't work as well as the permanent markers from the GGC.
6) I'm not sure Pandora has that time limit per month anymore; I've listened to it nonstop for at least 8 hours everyday. Otherwise, I've somehow managed to trick them.
7) I find working in a lab to be a bit relaxing, even though I have to race the clock in preparing the reactions.
8) Multi-channel pipettes save lives. (Ok, maybe not literally, but still.)
9) Tour groups think anyone working alone in a lab is an alien.
10) Doing science-y things pays off. Mark Olencki will come take your picture!
Thursday, January 19, 2012
Nooooo! My exosap!
I ran out of Exosap again. Well, I still have 100 microliters left, but to do one exon it takes 4x35 microliters, which is more than 100 last time I checked. Alas, I will not be able to bring in everything to BigDyeFast and sequence. I'll have to do the last two exons at the center. These things happen I suppose.
P.S. I'm not in the lab right now, I just remembered that I wanted to post about this at some point.
P.S. I'm not in the lab right now, I just remembered that I wanted to post about this at some point.
Getting closer to the finish line, sort of?
Today I realized how much quicker my pace is now that I'm kind of in the swing of things. I only have Exons 13 and 14 to amplify, run a gel on and exosap. I have to exosap exon 7 (the first try, since the second amplification with less primer didn't even work), exon 10, and exon 12.
I somehow forgot to exosap exon 10 and moved straight to 11. I guess that's what having a multitude of tiny tubes does to you. I've decided to make use of the white board and start writing what I have left to do so I can cross off tasks as they are completed.
My parents might visit me soon so that I can show them my lab. I hope they like it! I feel like such a big girl working in here by myself with all this DNA.
Worrisome notification of the day: I'm running out of 10 microliter pipette tips. I basically need 70 more since I can use the other pipette tips for everything except the initial amplification. Thirty-five patients multiplied by 2 exons = 70 tips needed! I've rummaged through the lab I'm in and the supply room, but I think I'm going to have to ask one of the biology professors tomorrow. For today I'll try to finish exosap'ing what I have amplified and run on gels.
I somehow forgot to exosap exon 10 and moved straight to 11. I guess that's what having a multitude of tiny tubes does to you. I've decided to make use of the white board and start writing what I have left to do so I can cross off tasks as they are completed.
My parents might visit me soon so that I can show them my lab. I hope they like it! I feel like such a big girl working in here by myself with all this DNA.
Worrisome notification of the day: I'm running out of 10 microliter pipette tips. I basically need 70 more since I can use the other pipette tips for everything except the initial amplification. Thirty-five patients multiplied by 2 exons = 70 tips needed! I've rummaged through the lab I'm in and the supply room, but I think I'm going to have to ask one of the biology professors tomorrow. For today I'll try to finish exosap'ing what I have amplified and run on gels.
Wednesday, January 18, 2012
Back in the lab
Today I Exosap'd Exons 8 and 9 and transferred them to plates. I made sure to orient the DNA samples in such a way that it would speed up the process of loading them into the trays for sequencing. Any little thing to speed up the process helps! I also did an amplification on Exon 10, the next exon in line to be sequenced. In addition, I ran a second amplification on Exon 7. In my last gel the primer dimer was VERY bright. Too bright compared to the DNA band. I added less primer to this amplification, so hopefully it will be more successful.
Since I am at a break of sorts (while two of the PCR machines are in use) I am going to the Student Athlete/Artist exhibit in the Student Life center. When I get back I will run the two amplifications on a gel and try to amplify Exon 11 and 12. If the gel turns out alright I will probably start tomorrow off with exosaping Exons 7 and 10. I'm glad I'm starting to move through the Exons quicker . . . although I'm still not sure if I'll be able to finish everything in time! If I can't then my presentation and paper will just have to be about the process of working between labs, the steps I took to sequence what I could, and any results I acquire.
Speaking of results, the only base change(s) I found from Exon 1 and 2 are insignificant. Melanie emailed me; she will explain how she came to that conclusion next time I go to the center. The more experience I can get with this type of research, the better!
Since I am at a break of sorts (while two of the PCR machines are in use) I am going to the Student Athlete/Artist exhibit in the Student Life center. When I get back I will run the two amplifications on a gel and try to amplify Exon 11 and 12. If the gel turns out alright I will probably start tomorrow off with exosaping Exons 7 and 10. I'm glad I'm starting to move through the Exons quicker . . . although I'm still not sure if I'll be able to finish everything in time! If I can't then my presentation and paper will just have to be about the process of working between labs, the steps I took to sequence what I could, and any results I acquire.
Speaking of results, the only base change(s) I found from Exon 1 and 2 are insignificant. Melanie emailed me; she will explain how she came to that conclusion next time I go to the center. The more experience I can get with this type of research, the better!
Tuesday, January 17, 2012
Full day
Today has been quite the full day. I'm exhausted. My morning started at 6:30 with transferring products from a lot of little tubes into plates, since they are easier to transport. I then commenced the drive to Greenwood, where I ran three PCR reactions.
At the GGC, you sign up for PCR slots so that you can get your reaction ready and immediately put it in the machine. Otherwise the reaction may be ruined as the ingredients could prematurely take their course or denature or degrade. And you should always check to make sure that the slot you signed up for is open. I did just this, but when I brought my first two plates up to the machines, someone had decided that they were going to take my slot. Luckily some others opened up such that I could utilize them. After putting those in the machine, I went to prepare my third plate. I came back, and someone was in my spot AGAIN. I had to go to the back and use the older machine, which I hope is still working properly. It's so important for everyone in a lab to be organized and coordinated; the lab will not run smoothly otherwise. Working at the GGC this summer really opened my eyes to that. Having been exposed to only classroom labs before that, I had no idea the organization that had to be in place. In a classroom, the teacher basically directs all the procedures.
I also got four plates ready for submission to the sequencer. The process takes a little over an hour to complete, so I could only get two done before 3:00, when the plates are taken over to the building with the sequencer. I had the option to leave around 3:30 and just get my next two plates ready for sequencing next time, but since I am on a huge time crunch I stayed until 5 to get those plates ready. It was one of the first times I did the processing sequence by myself. I never knew what to do without instruction before, but after having performed all the steps by myself once I knew what to do.
I looked over the first two exons I put in the sequencer. Rather, I looked over 140 sequences of DNA and compared them to the original exon sequences. This process took awhile. Any anomalies I saw, I highlighted and printed out. I then left these for Melanie. One, or both of us, is going to look to see if the base changes could change the amino acid for the protein, and then if that change is likely to be detrimental to the proteins' function.
I dropped some stuff off in the lab upon returning to Wofford; new polymerase, buffer, dNTPs, etc. have to be frozen/refrigerated. Tomorrow I will continue working on amplifying and exosaping the samples for each exon.
At the GGC, you sign up for PCR slots so that you can get your reaction ready and immediately put it in the machine. Otherwise the reaction may be ruined as the ingredients could prematurely take their course or denature or degrade. And you should always check to make sure that the slot you signed up for is open. I did just this, but when I brought my first two plates up to the machines, someone had decided that they were going to take my slot. Luckily some others opened up such that I could utilize them. After putting those in the machine, I went to prepare my third plate. I came back, and someone was in my spot AGAIN. I had to go to the back and use the older machine, which I hope is still working properly. It's so important for everyone in a lab to be organized and coordinated; the lab will not run smoothly otherwise. Working at the GGC this summer really opened my eyes to that. Having been exposed to only classroom labs before that, I had no idea the organization that had to be in place. In a classroom, the teacher basically directs all the procedures.
I also got four plates ready for submission to the sequencer. The process takes a little over an hour to complete, so I could only get two done before 3:00, when the plates are taken over to the building with the sequencer. I had the option to leave around 3:30 and just get my next two plates ready for sequencing next time, but since I am on a huge time crunch I stayed until 5 to get those plates ready. It was one of the first times I did the processing sequence by myself. I never knew what to do without instruction before, but after having performed all the steps by myself once I knew what to do.
I looked over the first two exons I put in the sequencer. Rather, I looked over 140 sequences of DNA and compared them to the original exon sequences. This process took awhile. Any anomalies I saw, I highlighted and printed out. I then left these for Melanie. One, or both of us, is going to look to see if the base changes could change the amino acid for the protein, and then if that change is likely to be detrimental to the proteins' function.
I dropped some stuff off in the lab upon returning to Wofford; new polymerase, buffer, dNTPs, etc. have to be frozen/refrigerated. Tomorrow I will continue working on amplifying and exosaping the samples for each exon.
Monday, January 16, 2012
Good news . . . bottle has been opened.
I got one of my friends to open it for me. It was really frustrating to have something so simple halt my work, especially since I have been working long hours and nonstop to try to get all of the work done. I don't really have time to spare.
I made a new gel and buffer solution before lunch so that the gel could solidify. I loaded the gel with some samples from Exons 6 through 9 and I'm running it now. In the meantime I consolidated my tubes since I am running low on boxes to put the tubes in, AGAIN. I also counted out and numbered tubes for the next two Exosap PCRs I'm going to run.
I'm only running two PCRs at a time because I haven't tried the third machine and at this point in the game it would be just as efficient to run two PCRs as it would be to run three. That way, if the third PCR machine here isn't working properly I can avoid wasting time and PCR ingredients. Working in the lab is all about efficiency right now! I also have to make a list of what to bring back from the GGC next. I'm running low on dNTPs and ExoSap and well . . . pretty much everything except the polymerase buffer. I've got plenty of that! I'll let you know how my gel turns out in a little bit.
I made a new gel and buffer solution before lunch so that the gel could solidify. I loaded the gel with some samples from Exons 6 through 9 and I'm running it now. In the meantime I consolidated my tubes since I am running low on boxes to put the tubes in, AGAIN. I also counted out and numbered tubes for the next two Exosap PCRs I'm going to run.
I'm only running two PCRs at a time because I haven't tried the third machine and at this point in the game it would be just as efficient to run two PCRs as it would be to run three. That way, if the third PCR machine here isn't working properly I can avoid wasting time and PCR ingredients. Working in the lab is all about efficiency right now! I also have to make a list of what to bring back from the GGC next. I'm running low on dNTPs and ExoSap and well . . . pretty much everything except the polymerase buffer. I've got plenty of that! I'll let you know how my gel turns out in a little bit.
Onward! That is, if I can get this bottle open.
So I did some work over the weekend. I exosap'd two exons, and transferred those to 96 well plates because those are easier to transport than a million little tubes. Yesterday I amplified up DNA for three of the exons. The next amplification is in the PCR machine right now. I need to make a gel and buffer to run a few samples on to make sure everything amplified correctly, but I can't get this bottle of TBE buffer open. My research is literally at a standstill because I can't get this bottle open. My hand is beet red from trying. Any tips or tricks? They would be greatly appreciated.
Friday, January 13, 2012
First sequence submitted
I brought a few plates for sequencing today, I hope they turn out well! I figured that the big dye fast process takes too long at Wofford, so I did two plates with that at the center today. I really enjoy working at the center so I don't mind the drive.
Thursday, January 12, 2012
Trip Tomorrow?
This is going to be a really quick blog, but I've been so busy in the lab! I determined today that the final step in getting the amplified DNA product ready for sequencing is too difficult to do here at Wofford with the equipment available, so I am going up to the center tomorrow to try to put my first sequencing plate in for this gene. I've heard that it may snow tomorrow, if so I may be stuck here. If that happens to be the case I'll just amplify more exons!
Wednesday, January 11, 2012
I think my thumbs are bruised.
So much PCR! Thus, so many tubes. And those suckers hurt my thumbs when I have to open and close them so often. But as far as actual progress goes, I started doing PCR on the exons. I ran a gel on Exon 1 to make sure everything was ok . . . there was a lot of primer dimer so I cut the amount down again for my next batch. We'll see how that one turns out. I've got the 3rd and 4th exons cooking in the thermal machine right now. Here are some pretty gel pictures for you; the bright band is primer dimer, the lighter one is the actual DNA.
My work day in the lab is from about 9am to 7 or 8pm so far. The funny thing is I don't even mind! I guess I just really enjoy this stuff.
Tuesday, January 10, 2012
Frazzled, but learning the ropes
This is the area in which I run my gels
This is the area in which I put together my mix to amplify DNA
Monday, January 9, 2012
Upside Down and Backwards
Everything that I did in the GGC lab today was just that. I was a little rusty getting back to doing things; I put the PCR plates in backwards on accident and then later ran my gel upside down for about a minute before realizing it. Everything turned out alright though! I did my temperature gradient on the primers with a random male's DNA, then ran the PCR products on a gel. After this, I packed up all my materials for the research and drove back to Wofford. I don't think I've EVER been so careful driving. So much DNA and research material . . . it's precious cargo. Once I got back I labeled and put up everything that needed to be refrigerated/frozen. I also wrote down an inventory of everything I brought. To succeed with this research, I must be organized!
That's all for today, hopefully tomorrow I can get a lot done with initial PCR and gels. I'm off to make a protocol and schedule!
That's all for today, hopefully tomorrow I can get a lot done with initial PCR and gels. I'm off to make a protocol and schedule!
Sunday, January 8, 2012
I've got a fly on my face!
Ok so I titled this entry as so because when Dr. Moss was helping me set everything up today in the lab I helped his clean out some fruit fly bottles. We were using paint brushes and at one point I accidently pushed the plastic netting back, let go, and thus catapulted a few fruit fly larvae onto my face. This, I thought, is the life of a bio major. It made me laugh.
Anyway, I've decided I'm going to make a protocol to carry around with me in the lab so that I can reference it while I'm doing my work. This will help avoid mistakes, I do believe, which during the scientific process can be costly and time-consuming. And we all know how limited time and money are! I'll check back with you tomorrow when I drive to the GGC again to pick up all my supplies and do a temperature gradient on the various primers.
Anyway, I've decided I'm going to make a protocol to carry around with me in the lab so that I can reference it while I'm doing my work. This will help avoid mistakes, I do believe, which during the scientific process can be costly and time-consuming. And we all know how limited time and money are! I'll check back with you tomorrow when I drive to the GGC again to pick up all my supplies and do a temperature gradient on the various primers.
Friday, January 6, 2012
Challenges already!
Today I traveled to the GGC to get the materials to start working . . . but there was much more preparation in store than just grabbing some polymerase and fleeing the scene. Upon arrival Melanie and I immediately set up a binder for the gene I'm working on. The binder is already fat with information, and I haven't even started working! She explained to me why this gene was chosen for screening; afterward we set to finding all the tubes of patient DNA we're going to use.
All the tubes of DNA are kept in a cold room. And I mean cold. After trying to pull singular tubes out of all the different boxes off of different racks off of different shelves, we decided to just take the racks out of the cold room and pull tubes from there. This helped us avoid freezing. Next came the sorting and aliquoting. It was tedious work, but it's so important to get everything sorted correctly. The primers came in around lunch time. My last task was to dilute and aliquot those.
Back at Wofford I went to the lab I'm working in to make sure I had key card access. I surveyed the equipment I'm going to use and pondered how I'm going to get all my work done in the short amount of time I have. Strategy is the name of the game! As with any research project, thinking several steps ahead is a must. I also found out today that I have to do gels after every PCR. This makes sense, and I like making gels. I just have to consult the biology professors again for instructions on what I can use here at Wofford for making and running them. I realized this is a part of real world research: having to accommodate for a different lab in which availability and variety of equipment may vary. This is going to be a learning experience, and I can't wait for it.
All the tubes of DNA are kept in a cold room. And I mean cold. After trying to pull singular tubes out of all the different boxes off of different racks off of different shelves, we decided to just take the racks out of the cold room and pull tubes from there. This helped us avoid freezing. Next came the sorting and aliquoting. It was tedious work, but it's so important to get everything sorted correctly. The primers came in around lunch time. My last task was to dilute and aliquot those.
Back at Wofford I went to the lab I'm working in to make sure I had key card access. I surveyed the equipment I'm going to use and pondered how I'm going to get all my work done in the short amount of time I have. Strategy is the name of the game! As with any research project, thinking several steps ahead is a must. I also found out today that I have to do gels after every PCR. This makes sense, and I like making gels. I just have to consult the biology professors again for instructions on what I can use here at Wofford for making and running them. I realized this is a part of real world research: having to accommodate for a different lab in which availability and variety of equipment may vary. This is going to be a learning experience, and I can't wait for it.
Thursday, January 5, 2012
First day! Well, sort of . . .
So today the research interim group had its first (of two) meetings. We all went around in a circle and told about our projects. I was really surprised at how complicated and interesting the projects are going to be! This is not to say that a Wofford student would ever attempt to glide through interim on a self-proposed project that a goldfish could easily complete, but some of the projects blew my mind a little bit. I especially enjoyed hearing about the research projects for the humanities. Just because I'm eternally dedicated to science doesn't mean I don't appreciate a good dose of art or literature or history. This is a liberal arts institute after all! It's a good situation to be in, surrounded by such a wealth of knowledge and variety of interests.
As for advances on my project, today Dr. Moss showed me around in the lab space I have been so graciously lent for interim. I shall be returning to Room 101, where I had my genetics lab course. I get to play with the PCR machine and the vortex and the centrifuge and micropipettes . . . see how fun biology is? I suppose it's less playing and more utilization, considering the seriousness of the matter. My situation is no longer that of a student trying to successfully gel electrophorese their own DNA. Research that the Greenwood Genetic Center does legitimately helps people! I truly appreciate the opportunities that have been given to me by both Wofford and the GGC. I can't wait to start my work tomorrow, when I travel to Greenwood for my first weekly visit.
As for advances on my project, today Dr. Moss showed me around in the lab space I have been so graciously lent for interim. I shall be returning to Room 101, where I had my genetics lab course. I get to play with the PCR machine and the vortex and the centrifuge and micropipettes . . . see how fun biology is? I suppose it's less playing and more utilization, considering the seriousness of the matter. My situation is no longer that of a student trying to successfully gel electrophorese their own DNA. Research that the Greenwood Genetic Center does legitimately helps people! I truly appreciate the opportunities that have been given to me by both Wofford and the GGC. I can't wait to start my work tomorrow, when I travel to Greenwood for my first weekly visit.
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