Hey all!
I am home with the family this weekend. So great to see everyone and pet my puppy! When I am here, it is hard to imagine how I get along without them all. Keith is doing a great job as the single parent and everything seems to be going just fine.
Back at work, I had some frustrating days. Ben Rodriguez showed us a program called Oligo 6 that searches for primers - little bits of a DNA sequence that doesn't have a lot of CG combos, or repeats, and that occur on either side of an "interesting" area of DNA we would like to study. Of course, there are more things, like length, and what is the middle and all kinds of temp readings and stuff that you have to take into account. So - we are supposed to find some possible good primers, and they will order them and we will see if we can use them to duplicate the DNA. One problem - we don't have access to this program in the lab. We can try to find a pirated version to install on our own laptops (Phoenix is very good at finding those on Chinese websites), but even when I gave in to that, can't get the program to work right on my machine. When I can find primers, can't get the info to copy - so I will have a good possibility staring right at me on my screen, the program will freeze up, and I will have to shut it down and lose all my info. Same thing with problems with the open source R programming language - everyone else (Phoenix) is breezing along - my computer keeps telling me it can't open this package, or read this file - even with Phoenix sitting there typing on the keyboard to try to fake it out into not knowing that it is me that needs the information! This is not only on my laptop, but also on a school computer, whereas it works fine for Phoenix on both. So the computers are still allergic to my fingers on the keyboards, and I went home feeling pretty miserable.
BUT, the next day we worked back in the lab, and that is a much happier place for me. We took primers that have all ready been proven to work, and did PCR with COBRA testing- PCR is a long and exact method of combine a bunch of stuff into tiny test tubes, and then using a machine to heat them and cool them several times to get DNA to grow between the primers. And that was really neat. We use centrifuges and vortexers (spinners and shakers) and lots and lots of pipetting. Then we made a gel, and injected our resulting PCR material mixed with dye into small wells in the gel, and put it into a machine that pulls the dye one way and the DNA the other. Then off to a fancy UV photography machine that captures the information of how well the DNA performed at the different temperatures we set for the PCR. That is supposed to give us an answer about the best temperature to use for that particular primer. We will use this test again on new primers that they ordered to figure out what will work best. Then we move on and do other things with the primers - to be told to us next week. I am not sure if I like the lab work better because I really love it, or if it is because it is new to me, and I haven't had a history of getting frustrated on it like I have computers.
The fellow that is training us in the lab is named Joseph Lui. He is a very nice fellow - one of the few people I have worked with that is older than me! Of course, he is Asian, like 90% of the rest of the lab folks - he is from Taiwan.
Jacob came for a visit last week and it was great to have him with me. When you have a bunch of boys, you can have the problem of treating them as a group. It is when you get time with them one at a time that you really appreciate their individuality and personality. I enjoyed showing him around, but he thinks my job looks really boring, so I don't think I inspired a budding scientist. Of course, I was down in the computer lab the day he came in - not my favorite part of the job either. He says Ohio has better pizza than NC (specifically Donatos pizza), and I showed him the "Wonder Kroger" that has all kinds of departments inside, and several different kinds of orange soda he has never tried (orange soda is Jacob's favorite), and Easton Mall, which was really neat. We saw "A-Team" at the theater there and it was really good. Made some good memories - wish I had thought to take some pictures!!
Well, better get a move on my day. Keith had to go down to the church and play piano for the July 4th pancake breakfast this morning - I slept in to recover from my 4 am rising yesterday to go to the airport. I will be returning to Ohio Monday night to start up again on Tues.
Have a happy and safe 4th!
Leslie
Saturday, July 3, 2010
Wednesday, June 23, 2010
Wed June 23rd
Yesterday we worked really hard in the lab. So far, we have cultured cells, watched them, and divided them. Monday we took the cells and dissolved them to get the DNA released, and then put them in test tubes. The ultimate goal is to make RNA out of the DNA, and then cDNA (complementary) out of that. We can use that to make lots of copies of the areas we are interested in, and use that to generate data to examine and measure. Yesterday we got a lot closer to our goal - we took the DNA and made RNA from it, and measured it for purity and amount of RNA. Then we treated it and incubated it to start making the RNA - almost there!
Then the leader of the program came over and told us that she has a different project she wants us to work on, so we will not even be doing anything with Michael anymore. Sigh - SO, new project, details to follow, I guess.
The classes with esoteric and mysterious titles have started. Statistical Phylogenetics ended up being a lot like genealogy, only with genes and viruses. You try to find a common ancestor in the terms of the arrangement of your A C G T on the strand, and identify where something mutates and forms a node - or the line branches off. Looking at different lines, you try to determine which are most similar, or made with the fewest changes in the original strand. You want to see how long it took to change, to hopefully predict when it will change in the future. Of course, this is done with lots and lots of lines of A C G T's that are all compared, one by one, by the computer. The project they are going to do to examine this, is to compare the genome of a bunch of different kinds of flightless birds - ostriches, kiwi, etc, that all live on different continents and see if they can figure out from the genome if that was one mutation that caused flightlessness, or if it happened several times in different places. I thought that sounded really interesting.
Yesterday we looked at Bioinformatics - which is basically analyzing biological data with a computer. He showed us different data bases that are available to go out and look at, that have genes and things mapped out.
Today's lecture is on Chemogenomics - and it is about to start.
Have a good day!
Leslie
Then the leader of the program came over and told us that she has a different project she wants us to work on, so we will not even be doing anything with Michael anymore. Sigh - SO, new project, details to follow, I guess.
The classes with esoteric and mysterious titles have started. Statistical Phylogenetics ended up being a lot like genealogy, only with genes and viruses. You try to find a common ancestor in the terms of the arrangement of your A C G T on the strand, and identify where something mutates and forms a node - or the line branches off. Looking at different lines, you try to determine which are most similar, or made with the fewest changes in the original strand. You want to see how long it took to change, to hopefully predict when it will change in the future. Of course, this is done with lots and lots of lines of A C G T's that are all compared, one by one, by the computer. The project they are going to do to examine this, is to compare the genome of a bunch of different kinds of flightless birds - ostriches, kiwi, etc, that all live on different continents and see if they can figure out from the genome if that was one mutation that caused flightlessness, or if it happened several times in different places. I thought that sounded really interesting.
Yesterday we looked at Bioinformatics - which is basically analyzing biological data with a computer. He showed us different data bases that are available to go out and look at, that have genes and things mapped out.
Today's lecture is on Chemogenomics - and it is about to start.
Have a good day!
Leslie
Saturday, June 19, 2010
Week 2 finished-
Wow- busy day on Friday! We started out down in the computer lab, working on MatLab, and I was also working on my graphs with Excel- which is a little different on my Mac. Trying to get the data I want to show up where I want was pretty frustrating - and I didn't get it done, so I will have to try to work on it this weekend some. I know there HAS to be a way to get all the pieces of info in there - I can draw it on a piece of paper - why can't I make it happen on the computer?
In MatLab we are trying to normalize the data we have, so three different files have pieces of information we need - the sequence depth is the total numbers of sequences on the entire chromosome 17 ( over 212000), and that is on one file. The region is the spot where transcription starts for one gene, and then you go out 5000 base pairs on each side, and we have a region for each gene (on chr 17 that is 1905 genes), and that is on another file. And the length of the gene is measured from the spot on the chromosome where the gene starts to where it ends - on another file. We put all those together to calculate a "normal" number for the gene expression compared to all the other gene expressions. So, in this program I have to figure out how to pull out the info that we need, and get it to all work together to give the results we need and save them. Then, I supposed we are going to do the same thing with the other cell line and compare them to see if there are any big differences.
Then we went upstairs to the wet lab where Micheal was extracting RNA from cells. We watched as he put in acid to break down the cells and did the process to get the RNA out. After that, he showed us how to split the cells that we were growing - a long process with many chemicals and a centrifuge, before we put the new cell samples back into the dishes and incubate. Never having done anything like this before I came here, I really need to get the basic idea of a clean zone about my sample down. I am never supposed to have my hand wave in the air above my sample, and beware of anything touching anything else. Someday Steven Spielberg or George Lucas can design a holographic sleeve you can assign around what you are supposed to keep clear of to remind you - that would help! We also were shown "The Cold Room", which is where you work with samples that need to stay at low temps. It is 4 degrees Celsius in there - which would feel pretty great at times, like after walking out to the parking lot to my car in the heat!
Keith came in last night for a visit - yay! So I am planning on some relaxation and fun, and brain down-time! Next week we will be taking classes in the morning, and going to the lab in the afternoon. Michael seems determined to get max productivity out of us - and I am learning a whole bunch from him. Of course, when you start with no knowledge at all like I am, you have no where to go but up!!
See you next week-
Leslie
In MatLab we are trying to normalize the data we have, so three different files have pieces of information we need - the sequence depth is the total numbers of sequences on the entire chromosome 17 ( over 212000), and that is on one file. The region is the spot where transcription starts for one gene, and then you go out 5000 base pairs on each side, and we have a region for each gene (on chr 17 that is 1905 genes), and that is on another file. And the length of the gene is measured from the spot on the chromosome where the gene starts to where it ends - on another file. We put all those together to calculate a "normal" number for the gene expression compared to all the other gene expressions. So, in this program I have to figure out how to pull out the info that we need, and get it to all work together to give the results we need and save them. Then, I supposed we are going to do the same thing with the other cell line and compare them to see if there are any big differences.
Then we went upstairs to the wet lab where Micheal was extracting RNA from cells. We watched as he put in acid to break down the cells and did the process to get the RNA out. After that, he showed us how to split the cells that we were growing - a long process with many chemicals and a centrifuge, before we put the new cell samples back into the dishes and incubate. Never having done anything like this before I came here, I really need to get the basic idea of a clean zone about my sample down. I am never supposed to have my hand wave in the air above my sample, and beware of anything touching anything else. Someday Steven Spielberg or George Lucas can design a holographic sleeve you can assign around what you are supposed to keep clear of to remind you - that would help! We also were shown "The Cold Room", which is where you work with samples that need to stay at low temps. It is 4 degrees Celsius in there - which would feel pretty great at times, like after walking out to the parking lot to my car in the heat!
Keith came in last night for a visit - yay! So I am planning on some relaxation and fun, and brain down-time! Next week we will be taking classes in the morning, and going to the lab in the afternoon. Michael seems determined to get max productivity out of us - and I am learning a whole bunch from him. Of course, when you start with no knowledge at all like I am, you have no where to go but up!!
See you next week-
Leslie
Thursday, June 17, 2010
Thur June 17th
Today I spent my morning up in the lab - lots of fun! We worked in the culture area, with shields and airflow control, and I used the new skills I learned to make a batch of media to grow cultures in. Very precise measurements of several different ingredients, all combined to make stuff to keep cancer cells happy and thriving. My mentor upstairs, Michael, is very knowledgeable and is teaching me a lot. He is going to assign us some genes to investigate to help further his research. If we end up lucky enough to find some that turn out interesting, we will get credit on the paper he publishes! We observed as he treated two different cell lines with different chemicals to see how they change.
After that, we went downstairs to the computer area and I did more tutorials on MatLab, and then Cenny took us over and explained the files we are going to use and what she wants us to do with them. By the time she was done, my brain was about to explode! So, I took lots of notes, and I hope things will sink in overnight. Trying to visualize how all the graphs relate to one another is conceptually hard enough, and then I have to figure out how to program with MatLab to get the parts of the different files together and interacting with each other. Phoenix seems to do better than I in that - but I guess she said she has had experience in similar projects in school, and I have never done anything like this - at least that is what I keep reassuring my aging, and aching brain!
Today I also I have some homework to do. I never learned metric measurements in school - back then, that was for those silly folks overseas. So now I have catch up to do in that area. And a quiz tomorrow to prove that I studied it! Plus I still have to learn Excel and how to graph my pipette measurements - I think I like taking measurements better than graphing them. But both are very important in research, and I know that learning these things now will really pay off later.
For now tho - time to rest the gray matter!
Bye for now-
Leslie
After that, we went downstairs to the computer area and I did more tutorials on MatLab, and then Cenny took us over and explained the files we are going to use and what she wants us to do with them. By the time she was done, my brain was about to explode! So, I took lots of notes, and I hope things will sink in overnight. Trying to visualize how all the graphs relate to one another is conceptually hard enough, and then I have to figure out how to program with MatLab to get the parts of the different files together and interacting with each other. Phoenix seems to do better than I in that - but I guess she said she has had experience in similar projects in school, and I have never done anything like this - at least that is what I keep reassuring my aging, and aching brain!
Today I also I have some homework to do. I never learned metric measurements in school - back then, that was for those silly folks overseas. So now I have catch up to do in that area. And a quiz tomorrow to prove that I studied it! Plus I still have to learn Excel and how to graph my pipette measurements - I think I like taking measurements better than graphing them. But both are very important in research, and I know that learning these things now will really pay off later.
For now tho - time to rest the gray matter!
Bye for now-
Leslie
Wednesday, June 16, 2010
Wed June 16th
Hi ho, all!
Yay, I finally got up into the lab! Today I learned how to run the autoclave - that is a sterilizer that is kind of like a huge computerized pressure cooker... wonder if it would do a good job on roast and potatoes? Then I learned pipetting and measured tiny bits of water into a little dish on a very sensitive scale and recorded the weights. Next I get to make a graph of all the results and measure the deviations of the weights - hopefully getting the results clustered as close together as possible. "Get to" is optimistic positive talk for "have to".
Also, today I was given my own petri dish of breast cancer cells - I have to change the media they grow in every 2-3 days, and divide the cells when they grow too crowded. Kind of like caring for a malignant chia-pet. I looked at them through a digital microscope - it was crazy. They are all different sizes, and shapes. Regular body cells would all be uniform - you can look at one and pretty much predict what the rest are going to look like. Not so with the cancer cells- they were all over the board. Time went a lot faster up there too -
Happy days to you!
Leslie
Yay, I finally got up into the lab! Today I learned how to run the autoclave - that is a sterilizer that is kind of like a huge computerized pressure cooker... wonder if it would do a good job on roast and potatoes? Then I learned pipetting and measured tiny bits of water into a little dish on a very sensitive scale and recorded the weights. Next I get to make a graph of all the results and measure the deviations of the weights - hopefully getting the results clustered as close together as possible. "Get to" is optimistic positive talk for "have to".
Also, today I was given my own petri dish of breast cancer cells - I have to change the media they grow in every 2-3 days, and divide the cells when they grow too crowded. Kind of like caring for a malignant chia-pet. I looked at them through a digital microscope - it was crazy. They are all different sizes, and shapes. Regular body cells would all be uniform - you can look at one and pretty much predict what the rest are going to look like. Not so with the cancer cells- they were all over the board. Time went a lot faster up there too -
Happy days to you!
Leslie
Tuesday, June 15, 2010
Tues June 15
Well, I made a mistake in yesterday's post. It was histone levels, not methylation levels that I was tracing. ( I know that you all were laughing up your sleeves at my oops. ) The methylation is actually going to come in when I am in the wet lab. Not sure exactly the difference yet - but the black spiky lines apparently are what they were looking for, and what was recorded on the graph. In any case, I found and graphed the oncogenes - 8 of them! Apparently genes only happen once on a chromosome, so - 8 graphs, and a quick writeup listing of all the genes I looked for.
Today I got my first taste of MatLab, and I did OK! My normal reaction of freaking out when a new computer program and language is staring me in the face did not last a whole long time- luckily I found a very helpful tutorial website to help me walk through it. I was able to actually achieve my goal of isolating chromosome 17 data today - which really surprised my mentor. She thought it would take me a lot longer, seeings how this was my first experience with it, and I was feeling my way around on my own. I was rejoicing! Pretty quietly, but rejoicing none-the-less.
Tomorrow I get to do autoclave and pipette training upstairs in the lab - and we are having a online meeting with all the other students and mentors, as well as the very nice people who are funding this adventure.
Hope you all are having a fun and relaxing summer!
Leslie
Today I got my first taste of MatLab, and I did OK! My normal reaction of freaking out when a new computer program and language is staring me in the face did not last a whole long time- luckily I found a very helpful tutorial website to help me walk through it. I was able to actually achieve my goal of isolating chromosome 17 data today - which really surprised my mentor. She thought it would take me a lot longer, seeings how this was my first experience with it, and I was feeling my way around on my own. I was rejoicing! Pretty quietly, but rejoicing none-the-less.
Tomorrow I get to do autoclave and pipette training upstairs in the lab - and we are having a online meeting with all the other students and mentors, as well as the very nice people who are funding this adventure.
Hope you all are having a fun and relaxing summer!
Leslie
Monday, June 14, 2010
Monday June 14th-
Today I got to get started on work! I feel like I actually accomplished something today. I am looking for specific genes that can cause regular cells to start mutating into cancer cells - called oncogenes - and finding them on the map of the two DNA lines. One cell line is a "regular" breast cancer cell, and the other one has a resistance to tamoxifen - a drug to treat it. Then I look for spikes in the methylation levels around the location of the gene, and compare the two. The theory is, if the cell lines have different levels in the methylation, perhaps that gene is part of the reason there is a resistance. So, I research for the kinds of genes, search for them on the genome finder, and take screen shots of the graphs that apply. Not sure what happens after that, but at least I am moving forward!
Didn't get up to the lab today- maybe tomorrow. And we have a meeting to nail down what our projects are before the web meeting on Wed. Did laundry today- I am supposed to go out and run errands, but don't feel like it. In my summer of self indulgence, think I am not gonna!
Bonsoir-
Didn't get up to the lab today- maybe tomorrow. And we have a meeting to nail down what our projects are before the web meeting on Wed. Did laundry today- I am supposed to go out and run errands, but don't feel like it. In my summer of self indulgence, think I am not gonna!
Bonsoir-
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