Over the last week Ben and I have been running experiments almost nonstop. We are testing DCQ at pH 6.2, 7.4, and 9.0. In addition to that we have one set in just water and the other with hydrogen peroxide to see if DCQ reacts with H2O2 when it is supposed to just react with HRP to react with TCP. Each run on the HPLC takes about four hours to run usually. But as predicted, the DCQ at pH 9.0 with H2O2, the reaction went incredible fast and DCQ was gone after 21 minutes. I was worried that it would be to fast to even get a reading in the HPLC at all.
There is definitely a some evidence here of pH dependency but it's not at all what we thought it would be. Theoretically pH 6.2 should be the most stable pH but it doesn't appear to be that way. So now it is exactly like the title of this blog. And we have to take a step back and look at this and know when to stop and publish something then continue. But for the time being the HPLC is keeping pretty busy and will be for the rest of the week.
Monday, July 27, 2009
Thursday, July 16, 2009
Life without Brad
This past week of research, Brad went on vacation. While I took some time off I still came in and did some work. It was interesting working without Brad being around. He has been micromanaging us and without out him around to do so me and Ben had to make some of our own decisions and do some problem solving on our own. It was great experience as an undergrad cause once you get out into the real world you will have to make your own decisions and decide things for yourself so I took this as a learning experience.
Also, I have been working on a paper(really informal) about TCP going to DCQ. A copy of this paper will go to the head of the North Carolina chemistry department because we are doing some similar things. And also none of his research students wanted to do HPLC work and it worked out cause I had most of the stuff he wanted to do already done. Not as exciting as other things perhaps but it's part of doing research and this is a stepping stone to gettin published which will help me alone when it comes time to go to Grad School.
Also, I have been working on a paper(really informal) about TCP going to DCQ. A copy of this paper will go to the head of the North Carolina chemistry department because we are doing some similar things. And also none of his research students wanted to do HPLC work and it worked out cause I had most of the stuff he wanted to do already done. Not as exciting as other things perhaps but it's part of doing research and this is a stepping stone to gettin published which will help me alone when it comes time to go to Grad School.
Tuesday, July 7, 2009
Nerds on the Run
Last week was a pretty interesting week for the B3. I spent the first part of my week looking at a ton of data, sorting it, making it look nice, and putting it all in one graph for easy comparison. After about two days of looking at the data and discussing the data collected, we went on a little break in town. We went and visited another professor of Monmouth who is head of the Education Department at Monmouth.(Sorry I am terrible with names and have a hard time remembering them) Who actually is about one year into bee keeping. That's right he keeps honey bees. This was pretty educational for all of us learning that different breeds of bees work differently and at different paces. And actually the whole process is pretty easy to do. Just collect your free honey once or twice a month, depending on the bees, and enjoy! This actually made me want to get some bees and get some honey of my own. What is misunderstood about the bees is how docile they are, and that could be depending on the breed of the bees. We even talked about the safety equipment and the professor didn't believe in it. As long as your slow and gentle the bees will leave you alone. We even talked about why bee keepers always wear white. Well I guess dark colors like black could make the bees think there is a bear trying to get there honey. Guess who wore black that day.
Also last Friday we took a little trip to Madison, Wisconsin to visit Om a student from Monmouth who is doing at REU in Madison. It was really neat because we actually got to see an NMR machine which is interesting because we read about them in books and learn to read the print outs but its neat actually getting to see one. But you can't get to close cause it can mess up your electronic devices as I found out. But it was all worth it. We even got to see a 900 NMR which are pretty rare in the world and for pictures see Brad's Blog.
I should talk about why I chose the title I did. Well as we were driving, on the four hour ride, we were listening to a podcast called basic brewing radio which talks about brewing and the methods and different techniques. Well my title came from us because we kept stopping the podcast to discuss the science or chemistry of what is actually happening. And Brad was the one who stopped us and said, "Good thing nobody is around to hear this. They would think we are a bunch of nerds." We all had a good laugh at it and new it was true. But even with that comment we kept stopping the podcast every once in a while and talking science about little things most people would never think about. It was fun though and educational. Maybe not for everyday life but it was fun for us.
Later on that day we went out to a hop farm in the country. And none of us realized how much went into this kind of farming. It was interesting as well cause the head farmer, if you will, actually has a science background and used to teach. So he could actually speak to us on a scientific level and explain things to us in a better way. It was a really great experience because you don't think how much science can go into these things of everyday life and as we learn these things we are expanding out minds and now thinking on a different level. So, in my opinion, this Liberal Arts in a way but a way more geared towards a specific focus. So these little side trips that get us out of the lab and get us a break from the data have been educational and not just something to give our minds a break. We are still thinking but thinking about something else. So with these little trips you wouldn't think could be related or broken down to a science have made us Nerds on the Run so to speak.
Also last Friday we took a little trip to Madison, Wisconsin to visit Om a student from Monmouth who is doing at REU in Madison. It was really neat because we actually got to see an NMR machine which is interesting because we read about them in books and learn to read the print outs but its neat actually getting to see one. But you can't get to close cause it can mess up your electronic devices as I found out. But it was all worth it. We even got to see a 900 NMR which are pretty rare in the world and for pictures see Brad's Blog.
I should talk about why I chose the title I did. Well as we were driving, on the four hour ride, we were listening to a podcast called basic brewing radio which talks about brewing and the methods and different techniques. Well my title came from us because we kept stopping the podcast to discuss the science or chemistry of what is actually happening. And Brad was the one who stopped us and said, "Good thing nobody is around to hear this. They would think we are a bunch of nerds." We all had a good laugh at it and new it was true. But even with that comment we kept stopping the podcast every once in a while and talking science about little things most people would never think about. It was fun though and educational. Maybe not for everyday life but it was fun for us.
Later on that day we went out to a hop farm in the country. And none of us realized how much went into this kind of farming. It was interesting as well cause the head farmer, if you will, actually has a science background and used to teach. So he could actually speak to us on a scientific level and explain things to us in a better way. It was a really great experience because you don't think how much science can go into these things of everyday life and as we learn these things we are expanding out minds and now thinking on a different level. So, in my opinion, this Liberal Arts in a way but a way more geared towards a specific focus. So these little side trips that get us out of the lab and get us a break from the data have been educational and not just something to give our minds a break. We are still thinking but thinking about something else. So with these little trips you wouldn't think could be related or broken down to a science have made us Nerds on the Run so to speak.
Friday, June 26, 2009
Data, Data, Data
This week has been an extremely busy week for us. I have doing a lot on the HPLC this week and I am know Ben has been running equations and the UV-vis as well.
After reading a journal article me and Brad decided to put our reaction of TCP + H2O2+ HRP to DCQ + (x) into di-ethyl either to stop the reaction in its place. But after a sort of failed attempt we managed to get a little bet of solution so we ran it in the HPLC and saw a peak when we stopped the reaction at about 10 seconds. This was interesting to see a new peak in something I thought I was starting to get a hold on. But because of the screw up and uncertainty of the data, we decided to try it again but with some slight changes and would be more prepaired this time.
So we raised the pH from 5 up to 7.4 so slow the reaction down some and we decided to take an allaquat every 30 seconds and put it into di-ethyl ether. In total we had eleven samples (one with TCP in dEE and no enzyme) and two standards. Of the eleven samples there were two things in the viles that were both going to be analyzed. The di-ethyl ether and the aquous solution at the bottom. So one by one I had to go through and extract what I needed and put them into viles and get them ready to be put in the HPLC. So now I have 24 different samples to run and we decide to run them twice. So I had to go through the HPLC and name 50 injections individually. And since there are two channels for each injection I have 100 things to look at and analyze. Not that you care I just want you to know how long and hard this is haha.
So the rest of the day and probably a few days next week will be spent looking at everything from one day of work. But hey, that's research.
After reading a journal article me and Brad decided to put our reaction of TCP + H2O2+ HRP to DCQ + (x) into di-ethyl either to stop the reaction in its place. But after a sort of failed attempt we managed to get a little bet of solution so we ran it in the HPLC and saw a peak when we stopped the reaction at about 10 seconds. This was interesting to see a new peak in something I thought I was starting to get a hold on. But because of the screw up and uncertainty of the data, we decided to try it again but with some slight changes and would be more prepaired this time.
So we raised the pH from 5 up to 7.4 so slow the reaction down some and we decided to take an allaquat every 30 seconds and put it into di-ethyl ether. In total we had eleven samples (one with TCP in dEE and no enzyme) and two standards. Of the eleven samples there were two things in the viles that were both going to be analyzed. The di-ethyl ether and the aquous solution at the bottom. So one by one I had to go through and extract what I needed and put them into viles and get them ready to be put in the HPLC. So now I have 24 different samples to run and we decide to run them twice. So I had to go through the HPLC and name 50 injections individually. And since there are two channels for each injection I have 100 things to look at and analyze. Not that you care I just want you to know how long and hard this is haha.
So the rest of the day and probably a few days next week will be spent looking at everything from one day of work. But hey, that's research.
Wednesday, June 24, 2009
To Iowa and Beyond
Last week was pretty eventful. Tuesday we spent most of the day making solutions and packing up equipment for out big trip to the University of Iowa. We met back up on Wednesday morning at about 7am, loaded the car, and were on our way. We stopped at the World's Largest Truck Stop because Brad thinks it's amazing, and it is pretty cool I have to admit. Then we get to Iowa City, park, and go into the basement of the one of the Med. School buildings where we met up with some pretty smart guys. (I am terrible with names so don't ask me, ask Brad) There were some pretty interesting conversations had and most of them were over my head but I pretended like I knew what they were talking about.
Anyway we gathered some data on the ESR, which I am still trying to figure out, and left a little early to go to Bio-research Company. There the talks continued and looks like we have a partnership with them. Some of the stuff we talked about I think would be pretty cool to start doing around here and the two guys we talked too were really smart but also down to earth.
Later after we checked in to our hotel I took the guys to Hu-Hot's a Mongolian place where you put everything you want in a bowl and they make it right in front of you. It's pretty cool. Then spent the rest of the night relaxing in the nice air conditioned Hotel.
The next day we continued running samples in the ESR and got some great graphs to show up. I didnt' really do a lot cause my knowledge of the ESR is really limited so I would just make up solutions when needed too. Also we met up with Matt Faron for lunch and it was good for me at least to hear about the transition from Monmouth to Grad School. Over all it was a great trip, I learned a lot about ESR and Grad School.
On Friday then we met up with Stephan a colaborator of Brad's from North Carolina. I got to have some one on one time with to discuss the data I had collected while Brad and Ben drove through some pretty harsh weather to get Brad and Stephen's kids.
Over all last week was overwelming. But for the better I think. Learning isn't always easy and there are going to be times you feel like a five year old at a fancy party. But you just have to stick it out and keep going and eventually you will become part of the party.
Anyway we gathered some data on the ESR, which I am still trying to figure out, and left a little early to go to Bio-research Company. There the talks continued and looks like we have a partnership with them. Some of the stuff we talked about I think would be pretty cool to start doing around here and the two guys we talked too were really smart but also down to earth.
Later after we checked in to our hotel I took the guys to Hu-Hot's a Mongolian place where you put everything you want in a bowl and they make it right in front of you. It's pretty cool. Then spent the rest of the night relaxing in the nice air conditioned Hotel.
The next day we continued running samples in the ESR and got some great graphs to show up. I didnt' really do a lot cause my knowledge of the ESR is really limited so I would just make up solutions when needed too. Also we met up with Matt Faron for lunch and it was good for me at least to hear about the transition from Monmouth to Grad School. Over all it was a great trip, I learned a lot about ESR and Grad School.
On Friday then we met up with Stephan a colaborator of Brad's from North Carolina. I got to have some one on one time with to discuss the data I had collected while Brad and Ben drove through some pretty harsh weather to get Brad and Stephen's kids.
Over all last week was overwelming. But for the better I think. Learning isn't always easy and there are going to be times you feel like a five year old at a fancy party. But you just have to stick it out and keep going and eventually you will become part of the party.
Friday, June 12, 2009
Basic research is what I am doing when I don't know what I am doing. Wernher von Braun (1912 - 1977)
The title is becoming truer every day as I have been finding out. But that's why we do research to figure out the unknown, and is why I enjoy doing it. Figuring out questions and understanding things to the fullest is a big passion for me from what I have learned already these past couple weeks.
Sorry for the delay in posting and updating but it has been a busy last couple of weeks. Last week we talked more in depth about our individual projects that will combine into the research Brad has planned for Ben and I. I will be looking at the interactions with cytochrome-c reacting with cardiolipin in apoptosis or as I like to think cell suicide. Apoptosis is an important part of a cell's life. If the cell is not capable of performing basic reactions any more it is in the way so it kills itself to save the overall organism it's apart of. But cytochrome-c plays an unusual part in this. Cytochrome-c acts as a peroxidase and oxidises cardiolipin and this starts in the inner membrane of the mitochondria which eventually moves out into the cytoplasm and starts the process of apoptosis. It is part of my job to figure out, in more detail, why or why doesn't this happen.
So after a lot of discussions we figured out the basic things we need to get to solve this mystery. We have ordered all our materials now through Sigma-Aldrich and Biorad. Next week we will actually be going to visit the University of Iowa and using there Electron Spin Resonance (ESR) to gather data on this and see some radicals that are formed.
While we are waiting for supplies to get in Brad has been volunteering our services to other various tasks around town. One afternoon we went out to Le Seur, where they are hoping to build an outdoor classroom for the college, and we were chipping away at a pile of branches. We made a pretty good dent I would have to say. Another day we went and helped a friend of Brad's move a piano from one house to another. It was a good break to use our muscles instead of our brains.
Now Brad is having us work on a little side project and a paper he has been working on for FIVE years. So I have been working on the HPLC gathering data for his paper. After a bad run Brad decided to switch the HPLC from running off methanol to ACN(ACN was a by product of the automobile industry but is no longer made because they are using a new plastic so ACN is no longer a bi-product) after me and Brad switched it to methanol earlier on this year. But the switch was worth it. After looking at some data I ran today some of the peaks on the HPLC came out clearer and stronger so it is easier to tell what is what and prove the products happening in the reaction Brad was looking at.
Over all this has been a really great week for me and I am continually learning. Looking forward to going to Iowa(my home state) and gathering more data and using the ESR(which is no easy task to read the graphs let me tell you, I am still trying to figure it out after two weeks). We are also stopping by a bio company to help establish relations to the college and meeting with one of Brad's collaborators from North Carolina (I think) next Friday. Next week looks pretty event full and I am looking forward to it.
Sorry for the delay in posting and updating but it has been a busy last couple of weeks. Last week we talked more in depth about our individual projects that will combine into the research Brad has planned for Ben and I. I will be looking at the interactions with cytochrome-c reacting with cardiolipin in apoptosis or as I like to think cell suicide. Apoptosis is an important part of a cell's life. If the cell is not capable of performing basic reactions any more it is in the way so it kills itself to save the overall organism it's apart of. But cytochrome-c plays an unusual part in this. Cytochrome-c acts as a peroxidase and oxidises cardiolipin and this starts in the inner membrane of the mitochondria which eventually moves out into the cytoplasm and starts the process of apoptosis. It is part of my job to figure out, in more detail, why or why doesn't this happen.
So after a lot of discussions we figured out the basic things we need to get to solve this mystery. We have ordered all our materials now through Sigma-Aldrich and Biorad. Next week we will actually be going to visit the University of Iowa and using there Electron Spin Resonance (ESR) to gather data on this and see some radicals that are formed.
While we are waiting for supplies to get in Brad has been volunteering our services to other various tasks around town. One afternoon we went out to Le Seur, where they are hoping to build an outdoor classroom for the college, and we were chipping away at a pile of branches. We made a pretty good dent I would have to say. Another day we went and helped a friend of Brad's move a piano from one house to another. It was a good break to use our muscles instead of our brains.
Now Brad is having us work on a little side project and a paper he has been working on for FIVE years. So I have been working on the HPLC gathering data for his paper. After a bad run Brad decided to switch the HPLC from running off methanol to ACN(ACN was a by product of the automobile industry but is no longer made because they are using a new plastic so ACN is no longer a bi-product) after me and Brad switched it to methanol earlier on this year. But the switch was worth it. After looking at some data I ran today some of the peaks on the HPLC came out clearer and stronger so it is easier to tell what is what and prove the products happening in the reaction Brad was looking at.
Over all this has been a really great week for me and I am continually learning. Looking forward to going to Iowa(my home state) and gathering more data and using the ESR(which is no easy task to read the graphs let me tell you, I am still trying to figure it out after two weeks). We are also stopping by a bio company to help establish relations to the college and meeting with one of Brad's collaborators from North Carolina (I think) next Friday. Next week looks pretty event full and I am looking forward to it.
Wednesday, May 27, 2009
First Timer
Hey, Blake here. This is my first blog I guess you could say but I am really excited about starting research with Brad and Ben. After a week break, when finals where done, I am back on campus and ready to start.
Day One was yesterday. Going over a lot of the basics while still learning! Learned about testing the pipets to make sure they are working properly then me and Ben made buffers two different ways. One easy way to figure out how to make a buffer was to google search Buffer Design and that will take you to a web site and after plugging in some information gives you a recipe on how to make your buffer.
Over all I would say it was a good first day here. Every0ne is excited for the rest of the summer. More to come though so keep checking every few days.
Day One was yesterday. Going over a lot of the basics while still learning! Learned about testing the pipets to make sure they are working properly then me and Ben made buffers two different ways. One easy way to figure out how to make a buffer was to google search Buffer Design and that will take you to a web site and after plugging in some information gives you a recipe on how to make your buffer.
Over all I would say it was a good first day here. Every0ne is excited for the rest of the summer. More to come though so keep checking every few days.
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