Its been a pretty hectic week. I don't think one thing in particular has made it pretty hectic, but I've been working more and more this week, trying to push forward on PCR and my enrichment cultures, but honestly its a lot of time with not that much of a push forward. I'm starting to worry that although I've been rocking the preliminary experiments, I want to start doing a real experiment that will be directly applicable to my masters. In any regard, its been just a lot of time spinning my wheels.
I think whats making me feel like I've been so hectic, is that I've been away from home more and more, and relaxing less this week. John has his last class on Saturday, so he's been busting it to get everything done before Saturday, which means no free and fun time. So, I've been leaving the house at 8ish, getting some work in, sneaking out during the day for an afternoon yoga class or some time at the pool (or gym), then returning until 6 or 7 to get some more work done. Its a pretty sweet schedule actually, and I wish I would have thought of it earlier.
Exciting things, I want to take a class or two from the DELTA program here at UW. Its a pretty sweet program about teaching scientists how to teach, and how to engage students in the classroom. I was going to take the intro-level class this next spring, because the offerings in the fall didn't fit my schedule, and the summer class was offered when I was in Australia. Thanks to the lack of Australia trip, I am free to take the summer class. Easier said that done, however. So, by the time the trip was cancelled, the class was beyond full, and I e-mailed the program about being put on the waiting list. I was number 9. About a week ago, I got another e-mail from the program saying that the class starts on August 3rd, no one was dropped yet, and theres really no chance any of us would get in. Fast forward to yesterday, when I find out that indeed, someone has dropped, and no one else is able to fill the spot, so its mine!! Scary thing, starting class on Monday. Its three hours a day (9 to noon), three or four days a week for August.
I was looking over the syllabus, and its all about developing your teaching philosophy, and all that other mumbo-jumbo that I've been teasing John about having to do with his teaching classes. I think thats karma for you. But, I get to get a new notebook! I LOVE school supplies. I think thats the reason I'm still in school (even though i guess I'm technically about to start 18th grade, which is freaky deaky to realize how much of my life has been spent in school). I also need a new planner, which is again, more exciting for me that for most other people.
My local NPR station (WPR) has been spending more of the week focusing on sustainable foods, organic farming, buying local, and the real price we pay for what we eat. Its such an eye-opener, and on that note, I'm hitting up the Farmers Market tomorrow to get some veggies. Although I've had a pretty fluid off and on relationship with vegatarianism over the past 10 years or so of my life, I do feel this need to eat less meat. Which, in order to better control my thyroid problem and give me more energy I'm meeting with a nutritionist/dietitian next week. I'm actually pretty excited to talk about food.
So its almost 11, I'm going over to the SERF to run on a treadmill (I know, its beautiful and sunny outside, but I haven't been inside running in about 5 months, and the logistics of being able to shower and come back to school are unbeatable), then heading to some friends for a packing and saying good bye party before they more to Amherst...Freaking east coast.
I really want a vacation. Not the kind where I go to Alaska and see people and am energized the whole time, but one where I lie on the beach and do nothing for 3 or 4 days.
Friday, July 31, 2009
Sunday, July 26, 2009
Sunday, bloody Sunday.
So today has been a pretty lazy Sunday day: I LOVE it. I woke up pretty early (7AM)ish, made a killer eggs and potato breakfast, took a nice nap when John left for work, made roasted beets, potatoes and carrots with fresh peas for lunch, had some egg salad for dinner, randomly watched some TV, and took a shower. Note the lack of going into the office, going running, or even reading a paper. Aside from the lack of John time, its been a pretty sweet day.
Yesterday afternoon Kate, Andy and I drove to Mt. Horeb which aside from being the Mustard Capital of the world, has a healthy troll population, and some awesome roads for going on a nice long road ride. Although we only did around 30 miles, there were some hills, and it was beautiful out. Very beautiful. Afterwards I headed into lab to run a gel to check the status of the PCR I was up late running on Friday. The results were mixed, with my DSR genes amplifying, some of my DGGE amplifying, and none of my 16s amplifying (I think I forgot to add in the taq). Anyway, I'm excited to head in tomorrow and see if I tweak anything I'll get a better result.
I'll get up early tomorrow, pull and easy 5 miler, and then I want to hit up Yoga at lunchtime. This week is going to be super sweet: Harry Potter finally came out in IMAX, which I've been waiting for, and there will a sweet date sometime near in my future which involves some awesome Potter-ness. Also, two of the coolest people are moving to Massachusetts (stupid east coast), and there is a moving party on Friday. I have a follow up doctors appointment for my thyroid on Thursday, and some serious lab work to get done Monday through Wednesday. Although, I might see about sneaking out to walk around the zoo for a few hours on Tuesday.
I'm getting a little sad about all my new friends leaving. Its pretty hard to adjust into a new place, get everything settled in, and then BAM, people are moving away. Even crazier to me, is the fact that a week from tomorrow marks the one year mark for when John and I moved down here. That single-handedly makes this the shortest year of my life. I mean, I'm sure time has moved in a fairly linear consistent manner, but man, the times just flew by. Makes me worry about how future years are going to speedily progress.
On a side note, I'm trying to take a science and environmental journalism class in the fall. Its pretty writing intense, and its full right now. I contacted the instructor, and I can swing by on the first day of class and see about sneaking into the class. I've been thinking about going into science journalism and outreach, so I'm hoping that this class will give me a great opportunity to get my feet wet and see if I like it.
Yesterday afternoon Kate, Andy and I drove to Mt. Horeb which aside from being the Mustard Capital of the world, has a healthy troll population, and some awesome roads for going on a nice long road ride. Although we only did around 30 miles, there were some hills, and it was beautiful out. Very beautiful. Afterwards I headed into lab to run a gel to check the status of the PCR I was up late running on Friday. The results were mixed, with my DSR genes amplifying, some of my DGGE amplifying, and none of my 16s amplifying (I think I forgot to add in the taq). Anyway, I'm excited to head in tomorrow and see if I tweak anything I'll get a better result.
I'll get up early tomorrow, pull and easy 5 miler, and then I want to hit up Yoga at lunchtime. This week is going to be super sweet: Harry Potter finally came out in IMAX, which I've been waiting for, and there will a sweet date sometime near in my future which involves some awesome Potter-ness. Also, two of the coolest people are moving to Massachusetts (stupid east coast), and there is a moving party on Friday. I have a follow up doctors appointment for my thyroid on Thursday, and some serious lab work to get done Monday through Wednesday. Although, I might see about sneaking out to walk around the zoo for a few hours on Tuesday.
I'm getting a little sad about all my new friends leaving. Its pretty hard to adjust into a new place, get everything settled in, and then BAM, people are moving away. Even crazier to me, is the fact that a week from tomorrow marks the one year mark for when John and I moved down here. That single-handedly makes this the shortest year of my life. I mean, I'm sure time has moved in a fairly linear consistent manner, but man, the times just flew by. Makes me worry about how future years are going to speedily progress.
On a side note, I'm trying to take a science and environmental journalism class in the fall. Its pretty writing intense, and its full right now. I contacted the instructor, and I can swing by on the first day of class and see about sneaking into the class. I've been thinking about going into science journalism and outreach, so I'm hoping that this class will give me a great opportunity to get my feet wet and see if I like it.
Friday, July 24, 2009
Primers Primers everywhere and not a drop to drink
Today, (being this morning, afternoon, and fairly well into late tonight), has been spent diluting primers, and preforming PCR to see what I can see. Side note: just looked outside, and there is one hell of a thunderstorm raging on. It was pouring earlier, but abated long enough to make a quick run to home depot to get dinner with the boy (an easy 4 mile bike ride each way).
In any case, if PCR (Polymerase chain reaction: the way we copy DNA to do stuff with), was a zipper, primers would be the little crimped pieces of metal on the ends that tell the zipper where to start zipping, and where to stop zipping: they set the frame where the zipper can work. Also, to continue this analogy, PCR is like taking a zipper (a double helix of DNA), and heating it up so hot that the zipping mechanism and previously mentioned crimped metal ends falls off. This leaves two zipper strands. In PCR, the first step is to heat the DNA up so that it denatures (comes apart leaving 2 separate strands)...see the parallels?
Next, what we do is add primers to the DNA (or crimped metal ends to the zipper). This tells the DNA were we want it to replicate. These primers are pieces of DNA that are custom made so that they match up to certain segments of DNA that are present in all bacteria, or just some bacteria, which lets us be specific with what DNA we amplify. The other 2 important chemicals present in a PCR reaction, are the free nucleotides, the building blocks of DNA (think free individual zipper teeth), and Taq Polymerase, which is an enzyme that allows DNA to copy itself (for the zipper analogy, this equates to the zipper pull which physically connects the two sides of the zipper). The PCR reaction occurs at several different temperatures, which are cycled over and over again (more than 40 times) to grow DNA.
What happens is this:
First, the DNA is heated, this causes it to denature and separate into two strands (as mentioned earlier with the zipper)
Next, the temperature drops so that primers can attach to the DNA (think of putting those metal crimps on half of a zipper). This is called annealing.
After that, the temperature is raised again, and as this happens, DNA polymerase starts at the primers, and works along the DNA in one direction, grabbing free nucleotides from the liquid mixture, to match up to the DNA bases on the other side (imagine putting the zipper pull on the crimped metal end, and as you pull up to zip the half zipper, pieces of zipper are inserted into the other side of the pull to combine and make a complete zipper).
This cycle is repeated over and over again, each time doubling the DNA present in the reaction tube. Once this is done, then we run it on an agar gel (like jello), by applying an electric current that pulls the DNA along the charge (since DNA is negatively charged). This allows us to separate pieces of DNA that we amplified based on size.
My station is to the right: I picked out the awesome green contact paper to give it more of flair. i wanted to spray paint everything purple, but I decided that contact paper was the better option (err...I was told it was the better option)
Its still pouring rain, and I have another two hours until my PCR is done running. I'll come in and do the gel tomorrow. Hopefully there won't be anymore lightening as I still have to ride my bike home tonight.
In any case, if PCR (Polymerase chain reaction: the way we copy DNA to do stuff with), was a zipper, primers would be the little crimped pieces of metal on the ends that tell the zipper where to start zipping, and where to stop zipping: they set the frame where the zipper can work. Also, to continue this analogy, PCR is like taking a zipper (a double helix of DNA), and heating it up so hot that the zipping mechanism and previously mentioned crimped metal ends falls off. This leaves two zipper strands. In PCR, the first step is to heat the DNA up so that it denatures (comes apart leaving 2 separate strands)...see the parallels?
Next, what we do is add primers to the DNA (or crimped metal ends to the zipper). This tells the DNA were we want it to replicate. These primers are pieces of DNA that are custom made so that they match up to certain segments of DNA that are present in all bacteria, or just some bacteria, which lets us be specific with what DNA we amplify. The other 2 important chemicals present in a PCR reaction, are the free nucleotides, the building blocks of DNA (think free individual zipper teeth), and Taq Polymerase, which is an enzyme that allows DNA to copy itself (for the zipper analogy, this equates to the zipper pull which physically connects the two sides of the zipper). The PCR reaction occurs at several different temperatures, which are cycled over and over again (more than 40 times) to grow DNA.
What happens is this:
First, the DNA is heated, this causes it to denature and separate into two strands (as mentioned earlier with the zipper)
Next, the temperature drops so that primers can attach to the DNA (think of putting those metal crimps on half of a zipper). This is called annealing.
After that, the temperature is raised again, and as this happens, DNA polymerase starts at the primers, and works along the DNA in one direction, grabbing free nucleotides from the liquid mixture, to match up to the DNA bases on the other side (imagine putting the zipper pull on the crimped metal end, and as you pull up to zip the half zipper, pieces of zipper are inserted into the other side of the pull to combine and make a complete zipper).
This cycle is repeated over and over again, each time doubling the DNA present in the reaction tube. Once this is done, then we run it on an agar gel (like jello), by applying an electric current that pulls the DNA along the charge (since DNA is negatively charged). This allows us to separate pieces of DNA that we amplified based on size.
Anyway, thats what I'm running up in lab now. I am in the process of getting a new anaerobic station. Here is a picture of the one that everyone in lab uses
The tubes on the left are used to run gasses into syringes to make solutions anoxic. Gasses are passed through a reduced copper column to remove all traces of oxygen, then aseptically added to syringes or solutions so that anaerobic bacteria can live!
My station is to the right: I picked out the awesome green contact paper to give it more of flair. i wanted to spray paint everything purple, but I decided that contact paper was the better option (err...I was told it was the better option)Its still pouring rain, and I have another two hours until my PCR is done running. I'll come in and do the gel tomorrow. Hopefully there won't be anymore lightening as I still have to ride my bike home tonight.
TGIF?
I'm sweating up a storm right now. Seriously, pools of sweat are just poring down my face. I blame it on my morning run and bike ride to work in a relatively balmy 68 degree day. My morning run was supposed to be 5 miles, but I really wasn't feeling it, so I just did a out and back loop around the edge of Lake Mendota. I'll either ride the bike down to Home Depot tonight to meet John for his dinner break, or hit up the pool. The thing is, this is my "step back" week on my half marathon training plan to run a race at the end of august. Its nice to only be running 15 miles in one week, but part of me misses the 35 mile weeks I was running training for the Madison Marathon.
In lab, I'm working on PCR, this technique we use to amplify stretches of bacterial DNA, and coupling that to DGGE so I can explore the bacterial diversity of these enrichment cultures I've been working with the past few months. I'm a little nervous, just because I hear that it works really well the first few times, and then generally things hit the fan, and you can't get reproducible results when you're working with environmental samples, which would be LAME-O. Anyway, I'm going to spend a big chunk of today in lab re-hydrating the primers I ordered, and doing the PCR leg-work that I need to blast right though the DGGE next week.
Another lab plus, I'm getting my own anaerobic station, I'll have to post pictures of what it looks like, it will be super exciting, we just need to order some new parts for this piece of equipment that lets you control the gas flow rates (for H2, N2, and CO2).
By far, though, the most exciting thing happening today, is this awesome lunch I packed (err..the ingredients to make an awesome lunch and dinner). I have both a spinach, mozzarella and strawberry salad and a sourdough turkey sandwich with spinach, tomato and guacamole. Not to seem unenthusiastic or anything, but its really going to be one of the best parts of my day. Especially seeing as how John works until 11PM, and has class and work all day tomorrow (8 AM until 11:30 PM), and works sunday, so I'm pretty much on my own this weekend, which lets me get excited about my awesome meals and what I'm going to do in lab, instead of the normal fun things I have planned with the boy.
Yeah, I should probably get to work now.
In lab, I'm working on PCR, this technique we use to amplify stretches of bacterial DNA, and coupling that to DGGE so I can explore the bacterial diversity of these enrichment cultures I've been working with the past few months. I'm a little nervous, just because I hear that it works really well the first few times, and then generally things hit the fan, and you can't get reproducible results when you're working with environmental samples, which would be LAME-O. Anyway, I'm going to spend a big chunk of today in lab re-hydrating the primers I ordered, and doing the PCR leg-work that I need to blast right though the DGGE next week.
Another lab plus, I'm getting my own anaerobic station, I'll have to post pictures of what it looks like, it will be super exciting, we just need to order some new parts for this piece of equipment that lets you control the gas flow rates (for H2, N2, and CO2).
By far, though, the most exciting thing happening today, is this awesome lunch I packed (err..the ingredients to make an awesome lunch and dinner). I have both a spinach, mozzarella and strawberry salad and a sourdough turkey sandwich with spinach, tomato and guacamole. Not to seem unenthusiastic or anything, but its really going to be one of the best parts of my day. Especially seeing as how John works until 11PM, and has class and work all day tomorrow (8 AM until 11:30 PM), and works sunday, so I'm pretty much on my own this weekend, which lets me get excited about my awesome meals and what I'm going to do in lab, instead of the normal fun things I have planned with the boy.
Yeah, I should probably get to work now.
Wednesday, July 22, 2009
Splenda with Fiber, really people?
Today's been pretty chill for the most part. I've been hearing this faint ringing of fire-truck sounding sirens for the past 15 minutes, finally I look out my office window, and there is indeed, a fire truck with a handful of firefighters and some on-lookers doing some serious-looking talking in front of the atmospheric and ocean sciences building. Hmm...I have no idea whats going on, but I'm mainly just concerned with the fact it took me 15 minutes to turn my head slighly to the right and look out my window.
I've been really delving into reading the scientific literature lately. My down-time waiting for bacteiral cultures to grow couples with this new program called Papers (for mac), and launced me into a 5-paper a day habit I'd like to maintain for as long as I can. There is just so much to read, and I don't find a direct correlation between reading, remembering, and using that new-found knowledge in a paper. I don't yet anyway, but maybe sometime soon, as I become an older graduate student. I find it so amazing that the people around me (the professors and post-docs) can remeber hundreds of papers, who wrote them, and what the key points are. But, I hear that it comes with time and practice.
I'm working on trying to isolate iron-reducing colonies that I grew on an iron silicate mix I precipitated from a reduced state in artificial seawater which mimics what we think seawater in the archean would be compositionally (about 3.5 billion years ago). Anyway, I'm working with these enviromental enrichment (mixed) cultures and trying to see which iron they like to reduce, and what carbon source they like to pair that with. Its realy intresting work, but it involves spending a few hours innoculating tubes, letting them incubate while checking reduced iron every day or two, and letting them just grow for a week or two. There is substantial down time, which is spent for the most part either reading papers (as I've mentioned above), or watching the West Wing (or a Bravo reality TV show), and spending time with my Amazing boyfriend (who, as I write this is up to his eyeballs in school work and work of his own). So, the take home message, is that I really feel guilty when I have free time, because I keep thinking that every hour I don't read papers and try to get some education in now, is another hour its going to take me to finish my graduate work. The thing is, I'm not sure if thats true or not. I wish that my advisor had a 4th or 5th year graduate student that I could draft off of (to use a bike term, as it is tour de france time).
No matter, I'll keep plugging away, if for no other reason, than with John not at home, and with no one really here at Weeks hall, theres nothing better to do.
I've been really delving into reading the scientific literature lately. My down-time waiting for bacteiral cultures to grow couples with this new program called Papers (for mac), and launced me into a 5-paper a day habit I'd like to maintain for as long as I can. There is just so much to read, and I don't find a direct correlation between reading, remembering, and using that new-found knowledge in a paper. I don't yet anyway, but maybe sometime soon, as I become an older graduate student. I find it so amazing that the people around me (the professors and post-docs) can remeber hundreds of papers, who wrote them, and what the key points are. But, I hear that it comes with time and practice.
I'm working on trying to isolate iron-reducing colonies that I grew on an iron silicate mix I precipitated from a reduced state in artificial seawater which mimics what we think seawater in the archean would be compositionally (about 3.5 billion years ago). Anyway, I'm working with these enviromental enrichment (mixed) cultures and trying to see which iron they like to reduce, and what carbon source they like to pair that with. Its realy intresting work, but it involves spending a few hours innoculating tubes, letting them incubate while checking reduced iron every day or two, and letting them just grow for a week or two. There is substantial down time, which is spent for the most part either reading papers (as I've mentioned above), or watching the West Wing (or a Bravo reality TV show), and spending time with my Amazing boyfriend (who, as I write this is up to his eyeballs in school work and work of his own). So, the take home message, is that I really feel guilty when I have free time, because I keep thinking that every hour I don't read papers and try to get some education in now, is another hour its going to take me to finish my graduate work. The thing is, I'm not sure if thats true or not. I wish that my advisor had a 4th or 5th year graduate student that I could draft off of (to use a bike term, as it is tour de france time).
No matter, I'll keep plugging away, if for no other reason, than with John not at home, and with no one really here at Weeks hall, theres nothing better to do.
Welcome to me?
So I've been thinking about starting a blog. Well, I suppose its progressed from thinking about, to actually being started. I figure this will be a little something to chronicle my adventures in graduate school, from the science to the people (and some of the things in between). There is something so enticing about having a way to leave your own legacy, write the present on your terms, so at least you know whats being said about yourself.
This should be a low-maintenance side project, something to keep me distracted when papers that need to be read pile up, and lab protocols go awry. We'll see, you know what they say about the best laid plans of mice and men...
This should be a low-maintenance side project, something to keep me distracted when papers that need to be read pile up, and lab protocols go awry. We'll see, you know what they say about the best laid plans of mice and men...
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