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Friday, June 29, 2007
Linda again
Last week, I found out that my BSA versus BSA+mucin procedure was successful; according to the nifty plate well cell reader device, the BSA+mucin biofilm samples had 0.084, 0.111, 0.251, and 0.100 concentrations of bacteria while the BSA had all lower ones: 0.023, 0.042, 0.047, and 0.037. However the 0.251 reading was a bit extraneous, and I'm attributing it to the micro pipette-bubble accident that probably contaminated that particular cell. Whoops. Afterwards, I uploaded my data onto Prism, where it fashioned really spectacular graphs and analyzed my data so thoroughly and speedily that I felt rather old.
This week, I began doing some preliminary data-collection relating to my project. The mission? To gather 0 weeks data for colony diameter in AF317, MG1655, and Fufu bacteria from 5 different mouse cecums, as diameter directly correlates with rate of growth. I must say that when I started, I thought it would be simple enough: just smear some bacteria onto a plate and twiddle your thumbs for an hour or two until they finished growing. Not so. Add in several hours of prep plus thawing, vortexing, incubating, labelling, massing, extracting Fufu from cecum sacs with a two-inch pipette tip, sterilizing, autoclaving, remassing, calculating and adjusting concentrations, more vortexing, diluting, spreading, and clean-up. The most amazingly tedious aspect was the diluting, as 8 dilutions were necessary for each of the 7 bacteria and each time a new micro pipette tip was needed as well as vortexing. By the end of the diluting process, around 3 hours, I think I became a little nonchalant in the dilutions...which I think led to the fact that there grew a mysterious new strain of bacteria in one of bacteria plates. Thankfully, the rest seemed entirely normal and proliferating and usable, but from now on, I resolve to keep my wits about me and take a quick break if I start to get feckless instead of risking sabotaging all my hard work. This reminds me of a hilarious yet slightly embarrassing little episode that happened that day. It was around noon and I was busy pipetting my way along, when my PI Bill comes up and asks me how long I'll be. I tell him I still have a few left to do, so maybe 30 minutes or so. Then he says "why don't you take a break from working on that?", and then proceeds to talk to the others congregated in our little lab hall. So I plop off my chair and go to lunch. An hour later, Mary Lou, my mentor, goes "There you are! We've been looking for you!" Apparently Bill had wanted me to take a break from pipetting so he could show me how to scan and photoshop plates. Everyone had stood around hypothesizing that I had an overactive bladder and was hanging around in the bathroom, until they realized that I could not possibly be in it for that long of a time. Now whenever someone speaks to me, I make sure to paraphrase exactly what they say back...in case of a misunderstanding.
This week, I began doing some preliminary data-collection relating to my project. The mission? To gather 0 weeks data for colony diameter in AF317, MG1655, and Fufu bacteria from 5 different mouse cecums, as diameter directly correlates with rate of growth. I must say that when I started, I thought it would be simple enough: just smear some bacteria onto a plate and twiddle your thumbs for an hour or two until they finished growing. Not so. Add in several hours of prep plus thawing, vortexing, incubating, labelling, massing, extracting Fufu from cecum sacs with a two-inch pipette tip, sterilizing, autoclaving, remassing, calculating and adjusting concentrations, more vortexing, diluting, spreading, and clean-up. The most amazingly tedious aspect was the diluting, as 8 dilutions were necessary for each of the 7 bacteria and each time a new micro pipette tip was needed as well as vortexing. By the end of the diluting process, around 3 hours, I think I became a little nonchalant in the dilutions...which I think led to the fact that there grew a mysterious new strain of bacteria in one of bacteria plates. Thankfully, the rest seemed entirely normal and proliferating and usable, but from now on, I resolve to keep my wits about me and take a quick break if I start to get feckless instead of risking sabotaging all my hard work. This reminds me of a hilarious yet slightly embarrassing little episode that happened that day. It was around noon and I was busy pipetting my way along, when my PI Bill comes up and asks me how long I'll be. I tell him I still have a few left to do, so maybe 30 minutes or so. Then he says "why don't you take a break from working on that?", and then proceeds to talk to the others congregated in our little lab hall. So I plop off my chair and go to lunch. An hour later, Mary Lou, my mentor, goes "There you are! We've been looking for you!" Apparently Bill had wanted me to take a break from pipetting so he could show me how to scan and photoshop plates. Everyone had stood around hypothesizing that I had an overactive bladder and was hanging around in the bathroom, until they realized that I could not possibly be in it for that long of a time. Now whenever someone speaks to me, I make sure to paraphrase exactly what they say back...in case of a misunderstanding.
Monday, June 25, 2007
We'll be visiting your labs!
This week Robin and I are going to start doing lab visits. We'll come by each of your labs to see how you're doing, meet your mentor, and give you a chance to tell us more about your project. This is an informal meeting and will last 15-30 mins. We're eager to hear more about your lab experiences and to literally see what you're doing in the lab! We'll send out individual scheduling info later.
Sunday, June 24, 2007
Second Week
Early in the week things in my lab slowed down a bit. On Tuesday, most of the people who work in my lab left for Virginia to collect more fish so I had a shorter day in lab. Wednesday though, work picked up again. After doing the usual work in the lab, dosing eggs with different PAHs and looking at eggs that had been dosed a few days before, we ended the day by dissecting the fish that had brought in Tuesday night. This had to be done almost immediately after the fish were brought in so they wouldn't be given a chance to flush out the chemicals in their system that we were testing for. Five of us in the lab set up an assembly line to disect the fish. I was at the very beginning. After taking them out of their tank I put the fish in ice cold water. Usually when putting the fish to sleep they use an anesthetic but this time we couldn't as it might interfere with the chemicals already present in their system. Since fish are cold-blooded, the cold water slowed them down so they wouldn't move, but were still alive so we could take blood (which needs the heart to be pumping). My other job was doing the blood smears after Cole had drawn their blood.
We disecting fish on Wednesday and Thursday morning as well. Thursday I got to see what the fish looked like once they'd cut it open to look at the liver, heart and other organs. It was fascinating, even after the fish had been dead for a few minutes, you could still see heart pumping.
Thursday afternoon and Friday I did more typical work in the lab. We looked at fish embryos under the microscope and judged their heart development after they had been induced with different chemicals. I also spawned fish again and screened the eggs, pulling out the good ones to use in my experiment. Friday afternoon I dosed those eggs, and tomorrow, Monday, I'll get to look at their development.
We disecting fish on Wednesday and Thursday morning as well. Thursday I got to see what the fish looked like once they'd cut it open to look at the liver, heart and other organs. It was fascinating, even after the fish had been dead for a few minutes, you could still see heart pumping.
Thursday afternoon and Friday I did more typical work in the lab. We looked at fish embryos under the microscope and judged their heart development after they had been induced with different chemicals. I also spawned fish again and screened the eggs, pulling out the good ones to use in my experiment. Friday afternoon I dosed those eggs, and tomorrow, Monday, I'll get to look at their development.
Second Week of ADHD Research
I had a wonderful day at the lab on Monday, June 18. First, I met with my principal investigator, Dr. Allison Ashley-Koch. We talked about an overview of my project. Unfortunately, the single nucleotide polymorphisms as well as the assays have not arrived yet. In addition, they were running low on ADHD DNA, so they have to wait until the DNA bank refills it before I could start on my project. As a result, I spent my day shadowing Chris, my mentor. This was a great introduction to me, attempting to learn more about the various instruments that they use in the lab. Moreover, with this practice, I will be more prepared when I start doing my own work on the ADHD DNA. Chris showed me how to use the Taqman recipe, which is used to figure out how much master mix, water, and assays should be added in accordance with the number of DNA samples. Next, I had to pipette the master mix onto the micro-well plates containing the DNA of patients enrolled in the Caregiver study. We then ran them on the PCR machine. After lunch, watched the Biomek robot transfer DNA into the micro-well plates. It was so fascinating to see how precise the machine worked. Lastly, we looked at the results from the Taqman plates earlier that day, and they were all quite successful.
Tuesday was another fun day in the lab. After speaking with Dr. Allison in the morning, I went to the third floor lab of the Center for Human Genetics Building. Chris asked me to pipette the Taqman recipe unto the micro-well plates containing DNA of patients enrolled in the Hostility study. However, before doing that I first had to make the recipe by adding water, master mix, and 20x assay. It was thrilling to do nearly the entire process by myself. After having to pipette two plates, I placed them in the centrifuge and took them upstairs to the PCR machine so that they can be ran for forty cycles. I was actually able to work the machine by myself (with instructions and Chris’ assistance of course =)). Then, I had to do the Taqman again, except this time, I used a different assay. This is because I was trying to find a different single nucleotide polymorphism (SNP) in the DNA. Upon returning from lunch, I created folders on the computer for my data to be stored in when we scan the plates. I also tried to find the gene and chromosome of the SNP that I was trying to observe. When I finished, it was time to take the plates out of the PCR machine so that they can be scanned using the 7900 machine. We then went to the computer to look at the data that we produced. None of the NTC controls were amplified, so we were able to submit the data to the clinical people for analysis. Finally, to end my day, we used the Biomek robot again. Overall, I was thrilled to be able to learn new techniques.
On Wednesday, June 20, I came to my lab and proceeded to the Post PCR refrigerator to get the plates that I prepared the day before. Chris allowed me to scan the plates by myself. Fortunately, I remembered most of the process that he showed me the prior. After scanning, he asked me to do the Taqman for the C-plates for Hostility. Since not all of the micro-wells contained DNA samples, I had to look at the chart to see where to pipette the Taqman recipe. I carefully completed that tedious process and centrifuged my resulting plates. Next, I ran the plates onto the PCR machine. When I returned after lunch, I did some more Taqman on DNA from patients enrolled in the Hostility study. Upon completion, I ended up with about fourteen plates. I went upstairs to store the plates in the cold room. This was a great day of practice and precision.
I had a rewarding day at the lab on Thursday. All of the plates that I ran on the PCR machine the prior were successful. I then looked at the results on the computer and none of the NTC controls amplified. After which, Chris showed me the DNA sequencing machine, wherein he uses a restriction enzyme to find a single nucleotide polymorphism in an insertion deletion. This is completed using micro satellites. He then asked me to do some more Taqman. I finished the list of assays needed to be run. Upon completion, I felt proud that I completed about twenty micro-well plates. Moreover, I am happy to say that my ID badge finally works, which means that I’ll be able to access most of the doors in the Center for Human genetics Building !!!
Finally Friday was more of an analyzing day. First, I scanned twelve plates unto the computer so that they can be run through on the 7900 machine. After a few minutes of waiting, I placed the plates in the cold room and analyzed the results to see if my PCR from the previous day was successful. To analyze the results, we used the program SDS 2.2.2. It generated graphs of the data, which is then submitted to a statistician for further evaluation. As it turned out, all of the plates that I completed were great. When I finished looking at the data that I produced, Chris showed me some useful tools in trying to find known mutations. There is a website called http://genome.ucsc.edu/ that is very helpful in doing so. We also used the Biomek robot to prepare for the PCR. Chris promised to show me how to use the PCR on Monday, so I’m very thrilled for that. Overall, this week was wonderful !!!!!
Tuesday was another fun day in the lab. After speaking with Dr. Allison in the morning, I went to the third floor lab of the Center for Human Genetics Building. Chris asked me to pipette the Taqman recipe unto the micro-well plates containing DNA of patients enrolled in the Hostility study. However, before doing that I first had to make the recipe by adding water, master mix, and 20x assay. It was thrilling to do nearly the entire process by myself. After having to pipette two plates, I placed them in the centrifuge and took them upstairs to the PCR machine so that they can be ran for forty cycles. I was actually able to work the machine by myself (with instructions and Chris’ assistance of course =)). Then, I had to do the Taqman again, except this time, I used a different assay. This is because I was trying to find a different single nucleotide polymorphism (SNP) in the DNA. Upon returning from lunch, I created folders on the computer for my data to be stored in when we scan the plates. I also tried to find the gene and chromosome of the SNP that I was trying to observe. When I finished, it was time to take the plates out of the PCR machine so that they can be scanned using the 7900 machine. We then went to the computer to look at the data that we produced. None of the NTC controls were amplified, so we were able to submit the data to the clinical people for analysis. Finally, to end my day, we used the Biomek robot again. Overall, I was thrilled to be able to learn new techniques.
On Wednesday, June 20, I came to my lab and proceeded to the Post PCR refrigerator to get the plates that I prepared the day before. Chris allowed me to scan the plates by myself. Fortunately, I remembered most of the process that he showed me the prior. After scanning, he asked me to do the Taqman for the C-plates for Hostility. Since not all of the micro-wells contained DNA samples, I had to look at the chart to see where to pipette the Taqman recipe. I carefully completed that tedious process and centrifuged my resulting plates. Next, I ran the plates onto the PCR machine. When I returned after lunch, I did some more Taqman on DNA from patients enrolled in the Hostility study. Upon completion, I ended up with about fourteen plates. I went upstairs to store the plates in the cold room. This was a great day of practice and precision.
I had a rewarding day at the lab on Thursday. All of the plates that I ran on the PCR machine the prior were successful. I then looked at the results on the computer and none of the NTC controls amplified. After which, Chris showed me the DNA sequencing machine, wherein he uses a restriction enzyme to find a single nucleotide polymorphism in an insertion deletion. This is completed using micro satellites. He then asked me to do some more Taqman. I finished the list of assays needed to be run. Upon completion, I felt proud that I completed about twenty micro-well plates. Moreover, I am happy to say that my ID badge finally works, which means that I’ll be able to access most of the doors in the Center for Human genetics Building !!!
Finally Friday was more of an analyzing day. First, I scanned twelve plates unto the computer so that they can be run through on the 7900 machine. After a few minutes of waiting, I placed the plates in the cold room and analyzed the results to see if my PCR from the previous day was successful. To analyze the results, we used the program SDS 2.2.2. It generated graphs of the data, which is then submitted to a statistician for further evaluation. As it turned out, all of the plates that I completed were great. When I finished looking at the data that I produced, Chris showed me some useful tools in trying to find known mutations. There is a website called http://genome.ucsc.edu/ that is very helpful in doing so. We also used the Biomek robot to prepare for the PCR. Chris promised to show me how to use the PCR on Monday, so I’m very thrilled for that. Overall, this week was wonderful !!!!!
Week Two!
The latter half of this week, I started the fun and TBS-filled process of staining brain tissue to identify new neurons by a protein that they contain. It's a pretty interesting process, and a delicate one! The brain tissue is paper-thin, and must be transfered from filter to filter and vial to vial. And, of course, it must be rinsed in TBS three times after every move for five minutes at a time. My mentor and I took a peek at an un-covered piece of tissue on Friday right after we finished staining it with Vector Grey, and so far it looks fantastic. Monday, I will be arranging the brains in a particular order on gel-coated slides and cover-slipping them. Arranging them is very challenging, and I hope I do well!
I have also met a few other people in the lab this week. There are a few graduate students, who have just gone to California for a big conference, and a few undergraduate students from a different summer research program at Duke. Some are in the MOB program (not sure what that stands for!), and one is a Duke senior working on a big project that will be presented in San Diego in November. There is also a Howard Hughes undergraduate, though I have not had the chance to meet her just yet. All around me there is interesting work going on, and I've been looking in during my many TBS rinses!
I have also met a few other people in the lab this week. There are a few graduate students, who have just gone to California for a big conference, and a few undergraduate students from a different summer research program at Duke. Some are in the MOB program (not sure what that stands for!), and one is a Duke senior working on a big project that will be presented in San Diego in November. There is also a Howard Hughes undergraduate, though I have not had the chance to meet her just yet. All around me there is interesting work going on, and I've been looking in during my many TBS rinses!
Hey guys, Allie here. This week started off with my first lab meeting on Monday. It was really interesting with everyone there talking about their own progress and also discussing how to answer some new questions in the lab. For most of the week I went on entering data from flow charts on patient's NK cells. Several of the records went back to 2006 so the data had to be re-gated for my specific study. Jen taught me how to use a program called FlowJo, which lets you interpret the data straight from the flow cytometry lab, which was fun.
When I wasn't working on data analysis Dr. Devlin and Dr. Markert spent time teaching me about other important concepts in the lab. Patients with atypical DiGeorge are born with some T cells, but because the babies are athymic the T cells can't recognize self from non-self. These T cells are likely to bind with self antigens and proliferate. The result is large oligoclonal populations and a terrible rash for the patient. Spectratyping is a tool that uses RNA to show you the diversity of the T cell receptors. An atypical patient might show a large T cell population but with spectratyping you'd find they had only a few oligoclonal populations, as opposed to a normal very diverse population.
On Friday, David, the undergrad, brought his samples to the DNA sequencing lab so I tagged along. Instead of just dropping off the tubes with the lab, we got to sequence it ourselves which involved combining the DNA with a mix of primers, enzymes and nucleotides (some fluorescent) and loading the samples into the machine, the very very expensive machine. The actual process was a little anticlimactic but learning about the how the process and machinery all worked was interesting. All in all it was another good week. Soon I'll get to do more bench work along with the continuing data analysis, so I'm looking forward to that. Hope everyone is having a great weekend!
When I wasn't working on data analysis Dr. Devlin and Dr. Markert spent time teaching me about other important concepts in the lab. Patients with atypical DiGeorge are born with some T cells, but because the babies are athymic the T cells can't recognize self from non-self. These T cells are likely to bind with self antigens and proliferate. The result is large oligoclonal populations and a terrible rash for the patient. Spectratyping is a tool that uses RNA to show you the diversity of the T cell receptors. An atypical patient might show a large T cell population but with spectratyping you'd find they had only a few oligoclonal populations, as opposed to a normal very diverse population.
On Friday, David, the undergrad, brought his samples to the DNA sequencing lab so I tagged along. Instead of just dropping off the tubes with the lab, we got to sequence it ourselves which involved combining the DNA with a mix of primers, enzymes and nucleotides (some fluorescent) and loading the samples into the machine, the very very expensive machine. The actual process was a little anticlimactic but learning about the how the process and machinery all worked was interesting. All in all it was another good week. Soon I'll get to do more bench work along with the continuing data analysis, so I'm looking forward to that. Hope everyone is having a great weekend!
it happened
Hello everyone! It's Maya again. So this week started off interestingly enough. Monday, I was mostly writing and reading/becoming familiar with procedures that I would do later in the week and discussing with Brandy, one of the people working at the lab with me, when we would receive the mice for the project. Tuesday, we carried out the beginning of a procedure I had been investigating the day before, to extract DNA from mice tails. Wednesday, I played guitar for all of you (yay what fun!) and finished the procedure. Thursday, I didn't do very much. I counted cells and talked with Brandy about summer plans. Then, on friday, it happened. We finally disected the mouse, which wasn't particularly drastic, but I had been dreading it for quite some time. I may sound like a pansy, but honestly, I'm not particularly psyched about the whole surgery gig, so watching my mentor TV cut the crap out of a mouse wasn't the most amazing thing in the world. In the whole procedure, we extracted the spleen, the kidneys, the brain, the testes, and bones for bone marrow. The bone marrow test did not work due to excess fat on the bones increasing the inability to strip the bones clean. We executed the kidney and spleen tests and will carry on with those on Monday when we will, yet again, disect another mouse, of which I will have pictures! Well that's all for now!
Cheers!
Cheers!
Friday, June 22, 2007
insert intriguing title here
Uh, so, week two... More squishing aphids, more PCR, more gels. Next week I'll be doing something new though. I'm going to be trying a different type of gel, and the process is called DGGE. It involves a polyacrylamide gel that has a gradient of denaturing agent in it, because when you do the PCR, you use these special kind of primers called clamp primers that hold the DNA together at the specific gene of interest, or something to that effect. The grad student I'm working with isn't really that familiar with it and I'm even less so, so I guess we'll both be figuring it out a little more once the time comes to try it out. It's supposed to be really good at seperating bands that are only a few base pairs different. Anyway, I could probably also do a better job of explaining if it wasn't so late, but I kind of wanted to troll for more votes for the duct tape thing while I'm at it... because it's ridiculous how far behind I am now. So yeah, some more votes would be nice...
Plant Nerd
At the beginning of the week, Carrie showed me how to set up a 96-well tray for PCR with single EST markers. I found that it's really hectic when I'm making multiple cocktails, each with a different primer, and then realize that I'm running low on Taq, primers, dNTPs, or buffer...all at once. Anyway, I actually finished the PCRs with all of the primers that I'll be using in my project, but I still have the microsatellites to do. With the PCR results, I ran gels and found that most of them all had bands, which made me really happy! Once, when I was microwaving the agarose + buffer solution, I got caught up in talking to someone and forgot about the beaker! So the solution spilled over... but thankfully, it wasn't anything serious. I remembered that safety video and told one of the lab people what happened (even though I was completely mortified), but she was really nice and told me how to clean it up =]. After checking for the germination of the remaining seeds, David and I collected seeds from plants that had fruited and selfed those that hadn't been crossed yet. During that time, I had a chance to ask David about his "life path", and I found out that he had a fascinating story to tell. Then up in the lab, I went to Google Maps and found the locations of all of the tilingii and guttatus populations that I'm studying, and I made my own map for my poster. Oh, speaking of posters - today, we dug out old posters that various people from the lab had made, and David showed me how there is a variety of ways to set them up. Along with that, I heard/read about the fascinating research of past and present lab members. It's been a busy but fun-filled week...
I've been thinking - I've always considered myself an animal-person (my house = perpetually overcrowded zoo / animal hospital), and I am...but this summer, I realized how incredibly amazing/intruiging/unbelievably complex plants are! Since I was young, my parents bought flat after flat of plants from Lowe's and also rescued unwanted ones from various people moving back to Japan, and I had always wondered what it was about plants that fascinated my parents. I viewed plants as boring because no matter how hard I worked, they never seemed to interact with me - they don't play fetch, hop onto my lap, beg for carrots, or curl up in my hair. But I realized this summer that plants aren't just those green, crunchy, photosynthesizing "things" that we eat in salads - they are incredibly diverse and have so many different mechanisms for survival that have evolved throughout their history. I'm kind of disappointed about not realizing this earlier...It's kind of like when you're in the same class with a person for a whole year, but you never really get to know her until the last day when you realize how charismatic she truly is...and then you want to hit yourself for not taking the opportunity to get to know her better when you had had the chance to for the whole year. But I'm happy because I have the rest of my hopefully long life to get to know plants better.
I can't believe it's already been two weeks! I've now begun stopping to examine random plants while I'm running and looking at the distance between the anther and stamen (I'm really interested in that trait!), and I'm now performing experiments with the various begonias, Saint Paulias, and Torenias around my house to see if I can cross-polinate and/or self them. I feel like such a plant nerd...and I love it!
I've been thinking - I've always considered myself an animal-person (my house = perpetually overcrowded zoo / animal hospital), and I am...but this summer, I realized how incredibly amazing/intruiging/unbelievably complex plants are! Since I was young, my parents bought flat after flat of plants from Lowe's and also rescued unwanted ones from various people moving back to Japan, and I had always wondered what it was about plants that fascinated my parents. I viewed plants as boring because no matter how hard I worked, they never seemed to interact with me - they don't play fetch, hop onto my lap, beg for carrots, or curl up in my hair. But I realized this summer that plants aren't just those green, crunchy, photosynthesizing "things" that we eat in salads - they are incredibly diverse and have so many different mechanisms for survival that have evolved throughout their history. I'm kind of disappointed about not realizing this earlier...It's kind of like when you're in the same class with a person for a whole year, but you never really get to know her until the last day when you realize how charismatic she truly is...and then you want to hit yourself for not taking the opportunity to get to know her better when you had had the chance to for the whole year. But I'm happy because I have the rest of my hopefully long life to get to know plants better.
I can't believe it's already been two weeks! I've now begun stopping to examine random plants while I'm running and looking at the distance between the anther and stamen (I'm really interested in that trait!), and I'm now performing experiments with the various begonias, Saint Paulias, and Torenias around my house to see if I can cross-polinate and/or self them. I feel like such a plant nerd...and I love it!
Hi guys!This week, I've been prepping for my project, which is the study of transfer rates of plasmids between bacteria in batch bioreactors. A bioreactor (that one is quite complicated-->) is a vessel where environmental conditions like the amounts of different gases, flowrates, temperature, and pH can all be controlled; but for our experiment, we are going to use bottles with vaccum seals instead. Next week, in the bioreactors, we are going to test six different concentrations of bacteria. We have already made triplicates of each combination of bacteria so that if one sample is faulty, then we still have two other ones to study, and we'll study how they're similar to or different from each other, of course. Right now, I have 34 bottles of solutions waiting to be inoculated with the bacteria on monday. I'll come in on sunday to watch my mentor prepare the bacteria so that I can learn how for later; something I've learned this week is that scientific research has no time constraints! Anyway, today, I also have to make a calibration curve comparing different amounts of toluene.
The graph will become our standard, and the measurements we obtain from the bioreactors will be compared to the calibration curve. The optimal slope should be .999; hopefully we'll get that number today. My mentor Ruoting told me that I'll be very busy next week with the 34 bioreactors, so I'll be having an extremely productive few days in the lab! I'm really excited to see how the data turns out because we'll be testing to see whether an E-Coli conjugate with P. Putida's plasmid exists.Have a lovely weekend,
Annie
PCR power
Yes, so I am still working on my project, which will involve 27 primer pairs and 12 sea urchin individuals. If you do the math, that's 324 different base pair sequences. Here's the process: PCR, gel electrophoresis, DNA purification, specs, and sequencing. For 324 different tubes. Needless to say, it will take some time, but I am almost finished PCRing all the tubes. Yesterday, I did an 8 by 12 plate of PCR reaction. Once we could get it to work, I used an automatic pipette to alloquate the primer master mixes into the 96 tubes. Surprisingly, PCR involves more math than I thought. It wasn't difficult, but I was actually forced to use a calculator. WHen I am creating the PCR master mixes, sometimes I feel like I'm cooking, putting together a recipe.. 4 ul of sugar, 25 ul of water, and 750 ul of baking soda. Delicious. But like cooking, you have to be careful about not putting in the correct amount of each ingredient. PCR is a reaction that involves a lot of different components, and depending on how many tubes you have, you master mix will be correspondingly bigger or smaller. The lab even has its own blender- the tabletop vortex that mixes up the ingredients to make everything homogenous. Of course, all this "biological cooking" hasn't changed my mind about kitchen cooking... I still avoid it at all costs, but I am learning that scientists have to be alert and focused to get specific reactions like PCR right. If you're not careful, you could spoil the batch and waste ingredients while you're at it. Overall, it's been an interesting week.
Thursday, June 21, 2007
In the Field- Ecology
Hey everyone!
I started the week off with a shopping trip to Sears, Lowes and many more hardware stores to buy products for Eileen's project. Then, I spent more time helping out Eileen (a grad student) with her chambers that collect gases given off by plants. Wednesday and Thursday I stayed at the field most of the day to help install the chambers. I also helped Dr. Wright collect data on mono culture (one species of a plant) plants and if they had more herbivory than many species of a plant. We are still working on that project. I had lots of fun so far this week and I hope everyone is having a blast as well.
Baninder
I started the week off with a shopping trip to Sears, Lowes and many more hardware stores to buy products for Eileen's project. Then, I spent more time helping out Eileen (a grad student) with her chambers that collect gases given off by plants. Wednesday and Thursday I stayed at the field most of the day to help install the chambers. I also helped Dr. Wright collect data on mono culture (one species of a plant) plants and if they had more herbivory than many species of a plant. We are still working on that project. I had lots of fun so far this week and I hope everyone is having a blast as well.
Baninder
Tuesday, June 19, 2007
Nicole and the "Drunken Mouse"
Today was the very first day that I analyzed open field data of the mice that had been injected with 40 mg of cocaine. The tapes run fo
r about an hour, most times featuring two mice for convenience, and the analyst is supposed to focus on just decoding one mouse behavior at a time. When I began watching the mice, of course their behavior was "different", even strange, but as I approached the time to analyze that small brown mouse in arena 20, the adjectives strange and different became better suited for use in understatements.
Post-injection, the mouse would sit up on its hind legs and rock from foot to foot as if it was "tippy", which is the word designated to describe this behavior in decoding. After rocking and leaning his/her head against the glass walls of the arena surroundings for a few seconds, she would proceed to play it cool as her little mouse body would erratically fall into the center of the arena. She had a lack of balance in her walk, sniff, and stance that could best be imagined if compared to an ad on the effects of alcohol consumption at its worse....
r about an hour, most times featuring two mice for convenience, and the analyst is supposed to focus on just decoding one mouse behavior at a time. When I began watching the mice, of course their behavior was "different", even strange, but as I approached the time to analyze that small brown mouse in arena 20, the adjectives strange and different became better suited for use in understatements. Post-injection, the mouse would sit up on its hind legs and rock from foot to foot as if it was "tippy", which is the word designated to describe this behavior in decoding. After rocking and leaning his/her head against the glass walls of the arena surroundings for a few seconds, she would proceed to play it cool as her little mouse body would erratically fall into the center of the arena. She had a lack of balance in her walk, sniff, and stance that could best be imagined if compared to an ad on the effects of alcohol consumption at its worse....
Monday, June 18, 2007
Number Systems in Babies and Adults
Today turned out to be full of talks about development in children and adults. In the morning, Dr. Brenda Armstrong (who, funny enough, taught my mom in medical school) gave us a talk about how the in-utero heart changes after the baby is born. I was fascinated, and although I don't think I will ever go into pediatric cardiology, Dr. Armstrong's talk reminded me of how incredible our bodies are. Our bodies go through incredible changes in a span of seventy or so years. Not only physically, but developmentally.
The thing that I am most interested in scentifically right now is early childhood development. Anyone who knows me is aware that I love kids. I babysit regularly; it is not just a job but an important part of my life. I have worked in the preschool at Friends School for a community service credit, and learned how to deal with kids that have simple A.D.D. or even selective mutism. Last year I interned at Frank Porter Grahm both in the childcare center with the two and three year olds (again, learning about development while working with kids who had DiGeorges and high functioning autism) as well as on a research project, First School, which looks at ways to improve education in children ages three though eight.
Working in Dr. Brannon's lab fits right in with that line of interest. Today Sara, my mentor, told me about the two ways babies and adults process number. The first system is the analogue system, which is essentially the approximation system. If there are 20 peanuts on the table, you might approximate that there are about 15-25 peanuts. If there are 200 peanuts on the table, that margin of error goes up to say, 150-250 peanuts. It also describes if you hold two weights of different sizes in your hand. With a one to two ratio, you would have no problem saying which was heavier. With a 51 lb weight and a 52 lb weight you might have more trouble.
The object tracking system is the other system that we use. Most adults can keep track of about four things. Sara had me do a little test online (Here it is if you want to try-keep track of the dots that blink at the beginning-http://research.yale.edu/perception/oba/MOT.mov). Although four is the limit for most adults, people like air-traffic controllers can track up to nine or so objects on a screen. Infants, on the other hand, we think can only track three. Infants could distinguish one from three, or two from three, but not three from six. Somehow, that conversion between analogue and infant tracking failed. We are now doing studies that look more into this. Although it is somewhat confusing, as I learn more about it I understand it better.
As usual, the lemurs are quite adorable. I found out today that their names are themed according to species. The ring-tailed lemurs are Greek names (Aracus, Licinius, Teres), the mongoose lemurs Mexican (Miguel, Pedro, Rosalinda, Guillermo), the blue eyed lemurs after blue-eyed movie stars (Tarantino, Witherspoon, etc.). The list goes on. For those of you interested, the website: http://lemur.duke.edu/
The thing that I am most interested in scentifically right now is early childhood development. Anyone who knows me is aware that I love kids. I babysit regularly; it is not just a job but an important part of my life. I have worked in the preschool at Friends School for a community service credit, and learned how to deal with kids that have simple A.D.D. or even selective mutism. Last year I interned at Frank Porter Grahm both in the childcare center with the two and three year olds (again, learning about development while working with kids who had DiGeorges and high functioning autism) as well as on a research project, First School, which looks at ways to improve education in children ages three though eight.
Working in Dr. Brannon's lab fits right in with that line of interest. Today Sara, my mentor, told me about the two ways babies and adults process number. The first system is the analogue system, which is essentially the approximation system. If there are 20 peanuts on the table, you might approximate that there are about 15-25 peanuts. If there are 200 peanuts on the table, that margin of error goes up to say, 150-250 peanuts. It also describes if you hold two weights of different sizes in your hand. With a one to two ratio, you would have no problem saying which was heavier. With a 51 lb weight and a 52 lb weight you might have more trouble.
The object tracking system is the other system that we use. Most adults can keep track of about four things. Sara had me do a little test online (Here it is if you want to try-keep track of the dots that blink at the beginning-http://research.yale.edu/perception/oba/MOT.mov). Although four is the limit for most adults, people like air-traffic controllers can track up to nine or so objects on a screen. Infants, on the other hand, we think can only track three. Infants could distinguish one from three, or two from three, but not three from six. Somehow, that conversion between analogue and infant tracking failed. We are now doing studies that look more into this. Although it is somewhat confusing, as I learn more about it I understand it better.
As usual, the lemurs are quite adorable. I found out today that their names are themed according to species. The ring-tailed lemurs are Greek names (Aracus, Licinius, Teres), the mongoose lemurs Mexican (Miguel, Pedro, Rosalinda, Guillermo), the blue eyed lemurs after blue-eyed movie stars (Tarantino, Witherspoon, etc.). The list goes on. For those of you interested, the website: http://lemur.duke.edu/
Linda
Hey guys!
A little about myself:
I am pretty much the most clumsy and uncoordinated person ever; I bump into things and bruise easily. Fortunately, this has not proved to be catastrophic in my lab yet (little do they know). I fear bugs and tsetse flies and tapeworms and generally all parasitic protozoa. Around new people, I tend to be reserved, polite, and friendly. With people I know well, I'm generally hyperactive-crazy, incoherent, and hilarious. I loved to pounce on my friends in fits of tigger-worthy joy from behind...up until I was side-stepped one day, and thereby fell to the ground on my bum with an audible thump and acquired the condition known as coccydynia (inflammation of the tailbone, self-diagonsed off medecinenet.com). I can find the most random things hilariously funny and I love to laugh and make other people laugh, even if its at me and my awkward antics or germophobicness or hypochondriacness. I love to get lost in a good book, and I am impatiently anticipating the arrival of the last Harry Potter book! I love to reminise about Arizona, sunsets, moutains, and stress-free days. I love swimming, because it's a no-contact sport and I love to break it down to club music when I think no one is watching. And as a final caution, I have a voracious appetite for everything that does not contain trans fat or carcinogenic grill marks, so hide your food.
About my lab!:
I am working in the Experimental Surgery department in the Medical Sciences Research Building with Dr. William (Bill) Parker as my mentor. The project I will be working on involves a mouse that has been living in a sterile bubble for the duration of two years. It has not been exposed to any pathogens or bacteria, except for a certain strain of e. coli bacteria that has been dripped into a spout extending from the bubble structure. After this period however, two different strains of e. coli were discovered: a fast-growing strain and a slow-growing strain. The hypothesis I will be testing is that when inside the small intestines of the mouse, these bacteria had been growing at the same rate. From a broader perspective, this experiment could possibly further tap into the pool of knowledge regarding bacteria behavior and evolution.
So far, I have been learning some laboratory techinques and procedures from Mary Lou so that I will be well prepared for the experiment. I have entered the realm of preparing mucin (mucus from a pig's intestines) and BSA (Bovine Serum Albumin Fraction), running dialysis, concocting media cocktails, incubating a certain mysterious "bacteria 315", and preparing stick well cell cultures to test the bacteria growth on BSA versus BSA+ Mucin. Hopefully everything will turn out right!
Ta ta for now!
A little about myself:
I am pretty much the most clumsy and uncoordinated person ever; I bump into things and bruise easily. Fortunately, this has not proved to be catastrophic in my lab yet (little do they know). I fear bugs and tsetse flies and tapeworms and generally all parasitic protozoa. Around new people, I tend to be reserved, polite, and friendly. With people I know well, I'm generally hyperactive-crazy, incoherent, and hilarious. I loved to pounce on my friends in fits of tigger-worthy joy from behind...up until I was side-stepped one day, and thereby fell to the ground on my bum with an audible thump and acquired the condition known as coccydynia (inflammation of the tailbone, self-diagonsed off medecinenet.com). I can find the most random things hilariously funny and I love to laugh and make other people laugh, even if its at me and my awkward antics or germophobicness or hypochondriacness. I love to get lost in a good book, and I am impatiently anticipating the arrival of the last Harry Potter book! I love to reminise about Arizona, sunsets, moutains, and stress-free days. I love swimming, because it's a no-contact sport and I love to break it down to club music when I think no one is watching. And as a final caution, I have a voracious appetite for everything that does not contain trans fat or carcinogenic grill marks, so hide your food.
About my lab!:
I am working in the Experimental Surgery department in the Medical Sciences Research Building with Dr. William (Bill) Parker as my mentor. The project I will be working on involves a mouse that has been living in a sterile bubble for the duration of two years. It has not been exposed to any pathogens or bacteria, except for a certain strain of e. coli bacteria that has been dripped into a spout extending from the bubble structure. After this period however, two different strains of e. coli were discovered: a fast-growing strain and a slow-growing strain. The hypothesis I will be testing is that when inside the small intestines of the mouse, these bacteria had been growing at the same rate. From a broader perspective, this experiment could possibly further tap into the pool of knowledge regarding bacteria behavior and evolution.
So far, I have been learning some laboratory techinques and procedures from Mary Lou so that I will be well prepared for the experiment. I have entered the realm of preparing mucin (mucus from a pig's intestines) and BSA (Bovine Serum Albumin Fraction), running dialysis, concocting media cocktails, incubating a certain mysterious "bacteria 315", and preparing stick well cell cultures to test the bacteria growth on BSA versus BSA+ Mucin. Hopefully everything will turn out right!
Ta ta for now!
Sunday, June 17, 2007
Hey everyone! My name is Susannah Butters and I'm a rising junior at Carolina Friends School, a small Quaker school in Durham. This summer I will be working in Dr. Richard Di Giulio's lab in the Nicholas School of the Environment and Earth Sciences.
It has been a whirlwind first week. On Monday, the first day, instead of being picked up by the usual one escort to take me to the lab I'd be working in, four people arrived. They were all quite enthusiastic and got me excited about spending the summer working with them. Once I arrived at the lab, I was given a tour and an introduction to what they do and what I'd be studying for the next seven weeks. They research how polycyclic aromatic hydrocarbons (PAHs) affect the aryl hydrocarbon receptor (AHR) pathway in zebrafish and killifish.
By the second day, they had me working with a graduate student studying zebrafish hatchlings. These hatchlings had been dosed with PAHs and we looked at them under a microscope, noting the impact of the PAHs. We were especially focused on the zebrafishes' development of pericardial edemas from their exposure to PAHs.
Another day I got to help spawn killifish. To do this, you hold the females and rub their stomachs with your thumb to make their eggs come out onto your gloved hand. You add the eggs to a jar and then fertilize them with a male fish. The first time that I got to help with this though, we came across a surprise. The person I was working with, Cole, was spawning a female fish and got two already fertilized eggs among many regular ones. Everyone in the lab assured me that this never happens. Eggs are supposed to be fertilized only after they leave the mother. They looked at these two eggs under a microscope and figured that it had been about a week since they were fertilized. It's a mystery to everyone in the lab as to how this happened and I'm interested to see what we discover about them as tests are run as they get older. For now, they are living in the lab and have been nicknamed Jesus Fish 1 and Jesus Fish 2.
I'm very excited to be working in this lab. It's already proven to be a very interesting week.
It has been a whirlwind first week. On Monday, the first day, instead of being picked up by the usual one escort to take me to the lab I'd be working in, four people arrived. They were all quite enthusiastic and got me excited about spending the summer working with them. Once I arrived at the lab, I was given a tour and an introduction to what they do and what I'd be studying for the next seven weeks. They research how polycyclic aromatic hydrocarbons (PAHs) affect the aryl hydrocarbon receptor (AHR) pathway in zebrafish and killifish.
By the second day, they had me working with a graduate student studying zebrafish hatchlings. These hatchlings had been dosed with PAHs and we looked at them under a microscope, noting the impact of the PAHs. We were especially focused on the zebrafishes' development of pericardial edemas from their exposure to PAHs.
Another day I got to help spawn killifish. To do this, you hold the females and rub their stomachs with your thumb to make their eggs come out onto your gloved hand. You add the eggs to a jar and then fertilize them with a male fish. The first time that I got to help with this though, we came across a surprise. The person I was working with, Cole, was spawning a female fish and got two already fertilized eggs among many regular ones. Everyone in the lab assured me that this never happens. Eggs are supposed to be fertilized only after they leave the mother. They looked at these two eggs under a microscope and figured that it had been about a week since they were fertilized. It's a mystery to everyone in the lab as to how this happened and I'm interested to see what we discover about them as tests are run as they get older. For now, they are living in the lab and have been nicknamed Jesus Fish 1 and Jesus Fish 2.
I'm very excited to be working in this lab. It's already proven to be a very interesting week.
Lots of PCRs
This first week has gone by so fast. The undergrads in my lab tell me that 7 weeks will go by like 2 days. Now I have only 5 weeks left to do my project. Although I have a vague idea about what my project will be, I don't really have a hypothesis or specific question I am answering. I am simply investigating a bunch of different genes, PCRing them, sequencing them, and then noticing any point mutations, or SNPs, that fall out of it. Since sea urchins are have a high crossing-over frequencing, and therefore have a good deal of mutations. For my project, I will be looking at 12 individuals and 27 primer sequences that will create 27 different bp sequences anywhere from 100 to 1500 bp in length. These sequences are all coding sequences in the skeletogenic network of Strongylocentrotus purpuratus, a gene network that has been heavily researched and controls the development of the sea urchin's skeleton. I am looking at each of the 27 sequences in each individual, if I have time, in order to find any interesting mutation or mutations that this particular population has in common. Since each individual has 2 copies of its genetic material, I am actually sequencing 24 x 27 sequences of DNA, and that means 12 x 27 different PCRs. To make things quicker and easier, I am doing 4 individuals with 4 primers at a time, so that I do 16 PCRs at a time.
I also learned to use the spec machine on Friday. This allows you to look at how efficient the DNA purification after PCR was. It measures the concentration of DNA vs. protein, as well as the content of DNA vs. other junk that you don't want. You pipette a tiny droplet of the mixture onto a small metal surface and the machine uses light rays to read the DNA concentration in the water.
Overall, I had a very exciting week. I have learned so much, and gotten so much experience. It was a rush of different protocols and vocabulary, and I can't wait to learn more next week and the rest of this summer!
I also learned to use the spec machine on Friday. This allows you to look at how efficient the DNA purification after PCR was. It measures the concentration of DNA vs. protein, as well as the content of DNA vs. other junk that you don't want. You pipette a tiny droplet of the mixture onto a small metal surface and the machine uses light rays to read the DNA concentration in the water.
Overall, I had a very exciting week. I have learned so much, and gotten so much experience. It was a rush of different protocols and vocabulary, and I can't wait to learn more next week and the rest of this summer!
Wandering Old Rats
Hi! My name is Sophia Cao, and I am a rising senior at Cedar Ridge High School in Hillsborough. At Cedar Ridge, I'm in the International Baccalaureate Diploma Programme, which is basically AP level classes smushed together with some big essays/projects and a Theory of Knowledge course in a program with a really long name. Erica did this program too in high school!
I play a lot of sports, and I'm usually in one for at least 2 or so seasons a school year. I've done Cross Country, Swimming, and Track, and I'm starting tennis in the summer/fall. And I am totally open to playing tennis with someone who knows how some weekend!
I also enjoy listening to and finding music, most of my favorite bands being of the British indie sort, though I really like almost everything and I enjoy dabbling in a variety of genres (even opera, minimally!) Oh and you should check this video out--it's this absolutely amazing opera performance by this mobile phone salesman from Wales. Most of you have probably already seen it, but if you haven't, it's worth seeing. http://youtube.com/watch?v=1k08yxu57NA
My lab this year deals in neuroscience. I work with Melissa Glenn, a postdoc in Dr. Christina Williams' lab. I'm coming in at the end stages of a 2-year study on the effects of prenatal choline exposure levels on neurogenesis, memory, and explorative tendencies in aging rats who have been exposed to different levels of choline during the prenatal stages. So far, I've done everything from observing rat maze tests to watching perfusions and brain extractions, to moving delicate slices of rat brains into appropriate containers. The research that this lab does really has the potential to be quite revolutionary. Eventually, it is plausible that research like this can help improve quality of life drastically for the aging population. These old rats (90-something in rat years) and their seemingly random wanderings have the capacity to change lives! Who would have thought?
It looks like I'm in for an exciting summer! I'm really happy that I am a part of this possibly groundbreaking study.
I play a lot of sports, and I'm usually in one for at least 2 or so seasons a school year. I've done Cross Country, Swimming, and Track, and I'm starting tennis in the summer/fall. And I am totally open to playing tennis with someone who knows how some weekend!
I also enjoy listening to and finding music, most of my favorite bands being of the British indie sort, though I really like almost everything and I enjoy dabbling in a variety of genres (even opera, minimally!) Oh and you should check this video out--it's this absolutely amazing opera performance by this mobile phone salesman from Wales. Most of you have probably already seen it, but if you haven't, it's worth seeing. http://youtube.com/watch?v=1k08yxu57NA
My lab this year deals in neuroscience. I work with Melissa Glenn, a postdoc in Dr. Christina Williams' lab. I'm coming in at the end stages of a 2-year study on the effects of prenatal choline exposure levels on neurogenesis, memory, and explorative tendencies in aging rats who have been exposed to different levels of choline during the prenatal stages. So far, I've done everything from observing rat maze tests to watching perfusions and brain extractions, to moving delicate slices of rat brains into appropriate containers. The research that this lab does really has the potential to be quite revolutionary. Eventually, it is plausible that research like this can help improve quality of life drastically for the aging population. These old rats (90-something in rat years) and their seemingly random wanderings have the capacity to change lives! Who would have thought?
It looks like I'm in for an exciting summer! I'm really happy that I am a part of this possibly groundbreaking study.
Attention-Deficit/ Hyperactivity Disorder
Hello everyone! To formally introduce myself, my name is Alexa Nicole Celerian. I am a rising junior from Josephine Dobbs Clement Early College High School. It is an amazing school located at the heart of North Carolina Central University. I was born in the Philippine Islands, and I resided there for more than ten years. Throughout my childhood years, I learned how to speak four different languages. I enjoy sports; however, my most favorite is swimming. I have a family of four consisting of my mother, father, and a 14-year-old brother. My family is my inspiration. In the near future, I aspire of becoming a successful cardiologist. As a child, I have always dreamt of becoming a medical doctor. I love working with people, especially children; so, I might even consider the field of pediatric cardiology. I feel that the Howard Hughes Program will provide me with a greater body of knowledge.
My first week in the program was extremely interesting. There was so much to learn and I have never been exposed to so many lab instruments/ technologies in the past. On Monday, my Principal Investigator, Dr. Allison Ashley-Koch, cordially greeted me. We then walked to the Center of Human Genetics, the area wherein I will be primarily doing my research. During my first day, I had to sign a Confidentiality form, and then Dr. Allison began introducing me to my project. It involves trying to find out if environmental factors such as smoking, lead exposure, alcohol use, and so forth, heightens the risk or is related to Attention- Deficit/ Hyperactivity Disorder (AD/HD). I read about the basics of Genetics in medicine to gain a better understanding of the subject. In addition, I read more about assessing AD/HD. I learned that AD/HD involves hyperactive-impulsive or inattentive symptoms that caused impairment and were present before seven years of age. Overall, it was a day of trying to understand the concept of the main subject I was trying to research.
Tuesday was another exciting day! It mostly dealt with the clinical side of research. After meeting with Dr. Allison, I was introduced to Linda Exelbierd, who is the AD/HD study coordinator. She is in-charge with consenting the patients and informing them of the benefits/ risks of their study participation. The proband is usually a child under the age of twelve who has AD/HD. She tries to consent as many of the proband’s family member to see the history of AD/HD within that family. To participate in the study, the family often has to go through many steps. They have to answer many questionnaires, developmental histories, and general information. In addition, they have to be checked for their attention span as well as have their blood samples are drawn. The process then repeats after two years. Linda actually showed me several pedigrees of patients she inputted in the computer. It was interesting to see the various generations affected with AD/HD. After meeting with Linda, I was introduced to Shelley Keats, another clinical employee. She inputs questionnaire data into the computer and she is also present during family meetings. As a matter of fact, I may be able to observe a family meeting when they have one! One very striking thing that we talked about was a disorder known as Trichotillomania, wherein people pull their hairs or pick their skin excessively to the point of baldness. According to Shelley, patients whom she has spoken to in the past told her that they do not feel any pain when they pull their hairs or pick their skin. Tuesday was very intriguing.
Next came Wednesday. The highlight of that day was surely getting an I.D. badge. It made me feel “Official” !! After that, Melanie Kail and a fellow personnel showed me how they put patient data into the computer. Melanie will help me organize my data after working in the lab. We looked through the data and queried the factors that might affect AD/HD. We analyzed the results and placed it in a spreadsheet. Unfortunately, we didn’t see much correlation but it might have just been due to the fact that we did not have that big of a population size. One significant thing though is that all the children whose mothers drank while pregnant were affected. I was asked to observe a clinical meeting as well. They were mostly talking about regulations dealing with accessing patient files. Then, for the rest of the day, I completed several IRB modules as well as Online Safety Training Sessions.
On Thursday, I met with Dr. Allison again in the morning and she and I talked about my first week as well as the activities that I participated in during the morning with the Howard Hughes Program. We read about the role of dopamine transporter (DAT) genotype and maternal prenatal smoking on children with AD/HD. Dopamine transporter is the system that helps neurons with transporting messages/ impulses. The journal stated that children with two copies of the DAT allele and had prenatal smoke exposure had greater hyperactive-impulsive scores compared to its contrary. For the rest of the day, I completed some more safety training and I read more excerpts from journals.
Lastly, Friday was perhaps the best part of my week. Dr. Allison was teaching me about the structure of a DNA. I then attended a session with Julie Rochelle as well as other new personnel in the Center for Human Genetics. She discussed lab safety rules, the dress code, and other ethics rules. Next, I was able to go to the lab and start practicing using the pipet with my mentor Chris. He gave me a tour of the lab and I was very fascinated by the various gadgets that they use. I have never seen such things in my life. He explained to me how the TaqMan works. It is very similar to a PCR except it involves probes that emit light waves. He explained how I would be looking at various DNA’s from patients with AD/HD, attempting to look for a single nucleotide polymorphism mutation that is common with most/ if not all of them. So, I am highly invigorated to start my research. I cannot wait to see what more will come from the next several weeks!
My first week in the program was extremely interesting. There was so much to learn and I have never been exposed to so many lab instruments/ technologies in the past. On Monday, my Principal Investigator, Dr. Allison Ashley-Koch, cordially greeted me. We then walked to the Center of Human Genetics, the area wherein I will be primarily doing my research. During my first day, I had to sign a Confidentiality form, and then Dr. Allison began introducing me to my project. It involves trying to find out if environmental factors such as smoking, lead exposure, alcohol use, and so forth, heightens the risk or is related to Attention- Deficit/ Hyperactivity Disorder (AD/HD). I read about the basics of Genetics in medicine to gain a better understanding of the subject. In addition, I read more about assessing AD/HD. I learned that AD/HD involves hyperactive-impulsive or inattentive symptoms that caused impairment and were present before seven years of age. Overall, it was a day of trying to understand the concept of the main subject I was trying to research.
Tuesday was another exciting day! It mostly dealt with the clinical side of research. After meeting with Dr. Allison, I was introduced to Linda Exelbierd, who is the AD/HD study coordinator. She is in-charge with consenting the patients and informing them of the benefits/ risks of their study participation. The proband is usually a child under the age of twelve who has AD/HD. She tries to consent as many of the proband’s family member to see the history of AD/HD within that family. To participate in the study, the family often has to go through many steps. They have to answer many questionnaires, developmental histories, and general information. In addition, they have to be checked for their attention span as well as have their blood samples are drawn. The process then repeats after two years. Linda actually showed me several pedigrees of patients she inputted in the computer. It was interesting to see the various generations affected with AD/HD. After meeting with Linda, I was introduced to Shelley Keats, another clinical employee. She inputs questionnaire data into the computer and she is also present during family meetings. As a matter of fact, I may be able to observe a family meeting when they have one! One very striking thing that we talked about was a disorder known as Trichotillomania, wherein people pull their hairs or pick their skin excessively to the point of baldness. According to Shelley, patients whom she has spoken to in the past told her that they do not feel any pain when they pull their hairs or pick their skin. Tuesday was very intriguing.
Next came Wednesday. The highlight of that day was surely getting an I.D. badge. It made me feel “Official” !! After that, Melanie Kail and a fellow personnel showed me how they put patient data into the computer. Melanie will help me organize my data after working in the lab. We looked through the data and queried the factors that might affect AD/HD. We analyzed the results and placed it in a spreadsheet. Unfortunately, we didn’t see much correlation but it might have just been due to the fact that we did not have that big of a population size. One significant thing though is that all the children whose mothers drank while pregnant were affected. I was asked to observe a clinical meeting as well. They were mostly talking about regulations dealing with accessing patient files. Then, for the rest of the day, I completed several IRB modules as well as Online Safety Training Sessions.
On Thursday, I met with Dr. Allison again in the morning and she and I talked about my first week as well as the activities that I participated in during the morning with the Howard Hughes Program. We read about the role of dopamine transporter (DAT) genotype and maternal prenatal smoking on children with AD/HD. Dopamine transporter is the system that helps neurons with transporting messages/ impulses. The journal stated that children with two copies of the DAT allele and had prenatal smoke exposure had greater hyperactive-impulsive scores compared to its contrary. For the rest of the day, I completed some more safety training and I read more excerpts from journals.
Lastly, Friday was perhaps the best part of my week. Dr. Allison was teaching me about the structure of a DNA. I then attended a session with Julie Rochelle as well as other new personnel in the Center for Human Genetics. She discussed lab safety rules, the dress code, and other ethics rules. Next, I was able to go to the lab and start practicing using the pipet with my mentor Chris. He gave me a tour of the lab and I was very fascinated by the various gadgets that they use. I have never seen such things in my life. He explained to me how the TaqMan works. It is very similar to a PCR except it involves probes that emit light waves. He explained how I would be looking at various DNA’s from patients with AD/HD, attempting to look for a single nucleotide polymorphism mutation that is common with most/ if not all of them. So, I am highly invigorated to start my research. I cannot wait to see what more will come from the next several weeks!
Toxic fumes and E-coli
Hey,
My name is Annie Chen, and I'm working in Dr. Gunsch's Civil and Environmental Engineering lab this summer. My project is the study of plasmid transfer rates between different bacteria. Plasmids are DNA molecules that can move from one bacterium to another freely. I'm going to be building a bioreactor to manipulate the conditions under which Pseudomonas putida (P. putida) transfers its plasmids to E-coli. The plasmid in P. putida has the code for the degradation of toluene, which is an anthropogenic compound that smells like nail polish remover. Toluene (C7H8 *organic chemistry!* :-D) is released into the atmosphere by the volatilization of petroleum fuels and paint thinners and it also leaches into water during the disposal of fuels. The liquid can cause irreversible brain damage if a person breathes its fumes for extended periods of time. So if you ever see me forgetting where I am and what I’m doing, or fainting, you know what happened. ;-) Hopefully, the results of the experiment will be used in other bioreactors to help degrade toluene more efficiently. Exciting stuff, isn’t it?
This week, I’ve been mostly working in the lab, measuring the concentrations of toluene to see its rate of degradation. Figuring out how often I need to respike the solutions of toluene is very important because the P. putida needs to eat the toluene to obtain nutrients, or else the bacteria will starve! My mentor Ruoting taught me how to use the Gas Chromatograph machine, the autoclave, and the spectrophotometer, inoculate bacteria and make Basal media for the P. putida. Yup, that’s about it. I can’t wait for next week!
À demain, mes amis!
Annie
My name is Annie Chen, and I'm working in Dr. Gunsch's Civil and Environmental Engineering lab this summer. My project is the study of plasmid transfer rates between different bacteria. Plasmids are DNA molecules that can move from one bacterium to another freely. I'm going to be building a bioreactor to manipulate the conditions under which Pseudomonas putida (P. putida) transfers its plasmids to E-coli. The plasmid in P. putida has the code for the degradation of toluene, which is an anthropogenic compound that smells like nail polish remover. Toluene (C7H8 *organic chemistry!* :-D) is released into the atmosphere by the volatilization of petroleum fuels and paint thinners and it also leaches into water during the disposal of fuels. The liquid can cause irreversible brain damage if a person breathes its fumes for extended periods of time. So if you ever see me forgetting where I am and what I’m doing, or fainting, you know what happened. ;-) Hopefully, the results of the experiment will be used in other bioreactors to help degrade toluene more efficiently. Exciting stuff, isn’t it?
This week, I’ve been mostly working in the lab, measuring the concentrations of toluene to see its rate of degradation. Figuring out how often I need to respike the solutions of toluene is very important because the P. putida needs to eat the toluene to obtain nutrients, or else the bacteria will starve! My mentor Ruoting taught me how to use the Gas Chromatograph machine, the autoclave, and the spectrophotometer, inoculate bacteria and make Basal media for the P. putida. Yup, that’s about it. I can’t wait for next week!
À demain, mes amis!
Annie
Drug Addiction
One step for Howard Hughes kind as I finally begin to get to decode the mice behavior of some of the tapes where they have been injected with illegal substances.
Saturday, June 16, 2007
Ecology
Hello everyone,
I'm Baninder Baidwan from Southern High School and I will be a senior coming this fall. My PI is Dr. Justin Wright in the Biology Department, however the majority of the time I will be working with my mentor, Jenny, in the French Family Science Center. My lab is working on finding the effects of plants on soil microbial communities. My project will focus on two methods that sterilize soil, autoclaving and gamma irradiation. Autoclaving in simple terms is just baking the soil and gamma irradiation is putting soil in the microwave, but with different wavelengths. So, I will try to determine which method is more effective in sterilizing soil.
This first week has been really exciting. Before starting the program I imagined myself just sitting in a lab doing boring stuff, but I was proven wrong. I took part in a variety of interesting and fun things. The first day I started with helping an undergrad measure the surface area of plants and the mass of plant roots. It was pretty neat because all the technology we used made me feel like a scientist. On Tuesday I helped Eileen, another grad student, make containers that she designed that will collect/store the gases given off by the plants. Making those containers involved a lot of physical work, but it was fun, because it was the first time I got to work with big cutting machines and other equipment I never saw myself using. Later on in the week I went to a stream with two grad students and one undergrad, to help them collect sediments that they needed for their research. It just so happened that when we got about half way through our process it started raining. We couldn't leave, because the students needed the sediments that day. Luckily, I was standing under a big tree that saved me from getting drenched. Although, we all got wet, the positive side to it was that we finished our task and had a great amount of fun while doing it. On Thursday, I helped out some undergrads do their job. I evacuated the atmospheric air out off these really small, cute bottles and put in Nitrogen gas. What made that exciting was that it involved needles and I had to use a timer so each bottle had the same amount of gas. Friday I had to make this solution using agar to make agar plates for my project. Agar plates provide the environment in which bacteria form, so using agar plates in my project will allow me to see if bacteria still form even after sterilizing the soil. While making the solution I tried not to breathe, because the agar was malodorous. I ended up having to make the solution twice because the first time my mentor and I added to much water. I had a great amount of fun during this first week and I can't wait to start another week of my internship.
I'm Baninder Baidwan from Southern High School and I will be a senior coming this fall. My PI is Dr. Justin Wright in the Biology Department, however the majority of the time I will be working with my mentor, Jenny, in the French Family Science Center. My lab is working on finding the effects of plants on soil microbial communities. My project will focus on two methods that sterilize soil, autoclaving and gamma irradiation. Autoclaving in simple terms is just baking the soil and gamma irradiation is putting soil in the microwave, but with different wavelengths. So, I will try to determine which method is more effective in sterilizing soil.
This first week has been really exciting. Before starting the program I imagined myself just sitting in a lab doing boring stuff, but I was proven wrong. I took part in a variety of interesting and fun things. The first day I started with helping an undergrad measure the surface area of plants and the mass of plant roots. It was pretty neat because all the technology we used made me feel like a scientist. On Tuesday I helped Eileen, another grad student, make containers that she designed that will collect/store the gases given off by the plants. Making those containers involved a lot of physical work, but it was fun, because it was the first time I got to work with big cutting machines and other equipment I never saw myself using. Later on in the week I went to a stream with two grad students and one undergrad, to help them collect sediments that they needed for their research. It just so happened that when we got about half way through our process it started raining. We couldn't leave, because the students needed the sediments that day. Luckily, I was standing under a big tree that saved me from getting drenched. Although, we all got wet, the positive side to it was that we finished our task and had a great amount of fun while doing it. On Thursday, I helped out some undergrads do their job. I evacuated the atmospheric air out off these really small, cute bottles and put in Nitrogen gas. What made that exciting was that it involved needles and I had to use a timer so each bottle had the same amount of gas. Friday I had to make this solution using agar to make agar plates for my project. Agar plates provide the environment in which bacteria form, so using agar plates in my project will allow me to see if bacteria still form even after sterilizing the soil. While making the solution I tried not to breathe, because the agar was malodorous. I ended up having to make the solution twice because the first time my mentor and I added to much water. I had a great amount of fun during this first week and I can't wait to start another week of my internship.
modules, cell counts, and TRPC6
Hey Everyone!
I'm Maya, and I'm working in the lab of the nephrologist Dr. Winn with Dr. T.V. Damodaran which is researching the effects of the gene TRPC6 in focal segmental glomerulosclorosis, er, rather, FSGS. FSGS causes a failure in the glomeruli on the kidneys which then leads to an increase in calcium and waste in the blood and an increase of red blood cells and protein in the urine. It is suspected that TRPC6 may affect and add to the increase of calcium, and it is my lab's job to find out if and how this can be true. For the next 6 weeks, I am going to be measuring the calcium levels in the blood and bone marrow of mice to check for traces of TRPC6, and to be honest, I'm a little scared about the bone extraction surgery!
This past week has been as eventful as it has the opposite. Monday, I had a mini orientation. I met everyone around the lab and got comfortable with the space. I was also given my Duke unique ID and several other ID's I will need around the lab. Tuesday, I spent most of my time doing my safety modules and completeing my IRBs. They didn't have much else planned for me, so I went home early these two days. Wednesday, I started some bench work. When I first arrived at the lab, I finished another handful of unexptected modules then went with my mentor T.V. to count the number of living cells in human blood samples affected by FSGS. After I was done doing all that, I went to, what is referred to as 'the building next to teh coal pile' to get my Duke ID badge, which makes me feel quite spiffy. Thursday, I was supposed to help the lab move gain more space, but I ate a bad peach at lunch and was forced to go home around 2 in the afternoon. Yesterday, I read mostly about TRPC6, went to another full orientation with all of the interns in the entire building, then went to the library with T. V. to check out books about procedures to extract bones, the spleen, and the thymus in mice. On Monday, I have a lab meeting at 2:30, and I can't wait to go!
As for me on a more personal level, I'm just a nerd who happens to really love music, harry potter (by the way, 24 more days till the movie and 34 till the book!!!), and rocking out. As a matter of fact, for the people that don't know already, I will be bringing my guitar on Wednesday of next week to play some songs i wrote and some you guys may know during our group lunch! I am very excited, and I hope not to sound too terrible. That's all for now I suppose, and I'll write again some time next week!
Cheers!
I'm Maya, and I'm working in the lab of the nephrologist Dr. Winn with Dr. T.V. Damodaran which is researching the effects of the gene TRPC6 in focal segmental glomerulosclorosis, er, rather, FSGS. FSGS causes a failure in the glomeruli on the kidneys which then leads to an increase in calcium and waste in the blood and an increase of red blood cells and protein in the urine. It is suspected that TRPC6 may affect and add to the increase of calcium, and it is my lab's job to find out if and how this can be true. For the next 6 weeks, I am going to be measuring the calcium levels in the blood and bone marrow of mice to check for traces of TRPC6, and to be honest, I'm a little scared about the bone extraction surgery!
This past week has been as eventful as it has the opposite. Monday, I had a mini orientation. I met everyone around the lab and got comfortable with the space. I was also given my Duke unique ID and several other ID's I will need around the lab. Tuesday, I spent most of my time doing my safety modules and completeing my IRBs. They didn't have much else planned for me, so I went home early these two days. Wednesday, I started some bench work. When I first arrived at the lab, I finished another handful of unexptected modules then went with my mentor T.V. to count the number of living cells in human blood samples affected by FSGS. After I was done doing all that, I went to, what is referred to as 'the building next to teh coal pile' to get my Duke ID badge, which makes me feel quite spiffy. Thursday, I was supposed to help the lab move gain more space, but I ate a bad peach at lunch and was forced to go home around 2 in the afternoon. Yesterday, I read mostly about TRPC6, went to another full orientation with all of the interns in the entire building, then went to the library with T. V. to check out books about procedures to extract bones, the spleen, and the thymus in mice. On Monday, I have a lab meeting at 2:30, and I can't wait to go!
As for me on a more personal level, I'm just a nerd who happens to really love music, harry potter (by the way, 24 more days till the movie and 34 till the book!!!), and rocking out. As a matter of fact, for the people that don't know already, I will be bringing my guitar on Wednesday of next week to play some songs i wrote and some you guys may know during our group lunch! I am very excited, and I hope not to sound too terrible. That's all for now I suppose, and I'll write again some time next week!
Cheers!
parasitic insight
I thought since we ran out of time this week for my research talk, I'd give a short synopsis of my thesis project.
My project concerns how biological communities respond to climate change. As the climate changes, the habitable areas of a species will shift, and in many cases species distributions will have to move 100's of kilometers to avoid extinction. For instance, American beech, Fagus grandifolia, (a large component of eastern hardwood forests, a common tree here in the Triangle) is predicted to be almost completely extirpated from its range in the U.S. and will find hospitable habitat mostly in Canada. But will this tree species be able to migrate fast enough to its new habitat? We're interested not only in this one tree species' survival but also with other components of this forest community. How will the entire community respond to global warming? As a clue to the migration capacity of different forest components, we look at how a host tree and an understory parasitic plant responded to a past era of global warming that occurred following the last ice age. We're working on tracing the post-glacial colonization routes of the parasitic plant, Epifagus virginiana, and comparing it with the migration history of its host tree, the American beech.
The photo shows an Epifagus virginiana infection. Epifagus are the brown stick like things poking up from the ground. They have no chlorophyll or leaves and get all their food and nutrients from the beech tree they're connected to. Notice how they appear to be in a line; this colony happens to be connected to a large beech root near the soil surface.
My project concerns how biological communities respond to climate change. As the climate changes, the habitable areas of a species will shift, and in many cases species distributions will have to move 100's of kilometers to avoid extinction. For instance, American beech, Fagus grandifolia, (a large component of eastern hardwood forests, a common tree here in the Triangle) is predicted to be almost completely extirpated from its range in the U.S. and will find hospitable habitat mostly in Canada. But will this tree species be able to migrate fast enough to its new habitat? We're interested not only in this one tree species' survival but also with other components of this forest community. How will the entire community respond to global warming? As a clue to the migration capacity of different forest components, we look at how a host tree and an understory parasitic plant responded to a past era of global warming that occurred following the last ice age. We're working on tracing the post-glacial colonization routes of the parasitic plant, Epifagus virginiana, and comparing it with the migration history of its host tree, the American beech.
The photo shows an Epifagus virginiana infection. Epifagus are the brown stick like things poking up from the ground. They have no chlorophyll or leaves and get all their food and nutrients from the beech tree they're connected to. Notice how they appear to be in a line; this colony happens to be connected to a large beech root near the soil surface.
Friday, June 15, 2007
First week with the monkey flowers
My name is Mai Nakamura, and I'm a rising senior at East Chapel Hill High School. My PI for the program is Dr. John Willis, and I'll mostly be working with Carrie Wu and David Lowry. My project will be to figure out whether the Mimulus tilingii is more similar, in terms of its DNA and its morphology, to the geographically neighboring Mimulus guttatus or more similar to other Mimulus tilingii that are farther away. I think this method of working on two projects at the same time is wonderful for me because I not only have the opportunity to work with the molecular component of Mimulus but I also don't lose track of the "big picture" by actually doing physical gardening-type experimental work and getting soil in my fingernails which allows me to keep in touch with the underlying goals of the molecular work in the lab. I don't know about the rest of you but for me in biology lab last year, I would often know to stir this enzyme into this test tube or to pour a dye into that cocktail, but I didn't have a strong grasp of what I was supposed to be trying to accomplish. There would always be a big, gaping question - "Why am I doing this, and what is this for?". So I really like this method of two ongoing projects because it answers this question and doesn't leave me in a state of uncertainty =].
Monday: I had already met most of the people in the Willis lab last week, so Carrie and David immediately started me working on relocating various pre-planted Mimulus seeds that had been going through "winter" to the greenhouse where they will hopefully start germinating in the next week or so. With a clipboard, I wrote down the population names and the individual's number on a sheet of paper, and I later put that information on an Excel document so that the recording of the germination/flowering dates will be easier later on. Then, David and I went back down to the greenhouse and started "selfing" or self-fertilizing some Mimulus guttatus. (I found out that it's a lot harder than it looks/sounds...) Then, we went up to the lab conference room, and David and Carrie began to explain to me the concept of QTL mapping. I'm really lucky to have two mentors that are both really good at explaining hard concepts!
Tuesday: After this morning's gel electrophoresis, I went to the lab and did gel electrophoresis again with Carrie! It was great because I actually felt a lot more comfortable the second time with having this process still fresh in my mind. Hopefully, it'll be drilled into me by the time I have to do it for actual experimental data. So for the gel electrophoresis, we used some PCR results from another lab member and a hyperIV ladder...And it worked out well! We used the machine with the ultraviolet light (I don't really know its name or how it works) and printed out a picture of the gel.
Wednesday: Amazingly, some of the seeds began to germinate after only two days! However, seeds from some populations, probably those that have a long growing season that can afford to germinate later, remained dormant. The other major event of the day was "PCRing" with Carrie. It was a lot harder than I thought it would be, with all the different programs depending on the microsatellites used or whether ESTs markers are used. At the end, thankfully, all the tubes seemed as though they had about the same volume of liquid in it, so hopefully the gel that we will be making tomorrow will show good results.
Thursday: Today, Carrie and I used gel electrophoresis to test to see whether we had good PCR results from yesterday. Carrie pretty much let me make the gel by myself, always standing right next to me and pointing a few things out once in a while. While we let the gel dry, we went into the conference room again, and Carrie went over in detail what she would like for me to accomplish this summer. Since Mimulus tilingii are high-altitude plants that live all the way up in the alpines, researchers don't yet know whether they evolved independently from convergent evolution or whether there had been a widespread area characterized by cold weather way-back-when that eventually diminished to create these now isolated Mimulus tilingii populations that can only survive at high altitudes. So, what I'm going to be doing this summer is comparing, phenotypically and genotypically, the Mimulus tilingii populations among each other and between Mimulus guttatus . If we find that the Mimulus tilingii are more similar to each other, this probably means that the wide-spread colder region did exist and that there was more recent gene flow among the tilingii . On the other hand, if we find that the Mimulus tilingii populations are more similar to the various Mimulus guttatus populations, then that suggests that there has been more recent gene flow between the two separate species populations. After that, we went back to the lab for the running of the gel after which we discovered that the PCR had gone well! Once again, using that UV light machine, we printed out a picture of the gel.
Friday: Today, we did another PCR but with two different markers - EST641 and EST332. While the PCR was going, I made various dilutions of all the markers that I will be using along with some dNTP. After, I made another gel with the PCR results, and I saw that I hadn't done as well as the previous time...but it wasn't bad. That pretty much took up most of the afternoon.
I hope everyone else is enjoying themselves as much as I am! I am absolutely exhausted...
Monday: I had already met most of the people in the Willis lab last week, so Carrie and David immediately started me working on relocating various pre-planted Mimulus seeds that had been going through "winter" to the greenhouse where they will hopefully start germinating in the next week or so. With a clipboard, I wrote down the population names and the individual's number on a sheet of paper, and I later put that information on an Excel document so that the recording of the germination/flowering dates will be easier later on. Then, David and I went back down to the greenhouse and started "selfing" or self-fertilizing some Mimulus guttatus. (I found out that it's a lot harder than it looks/sounds...) Then, we went up to the lab conference room, and David and Carrie began to explain to me the concept of QTL mapping. I'm really lucky to have two mentors that are both really good at explaining hard concepts!
Tuesday: After this morning's gel electrophoresis, I went to the lab and did gel electrophoresis again with Carrie! It was great because I actually felt a lot more comfortable the second time with having this process still fresh in my mind. Hopefully, it'll be drilled into me by the time I have to do it for actual experimental data. So for the gel electrophoresis, we used some PCR results from another lab member and a hyperIV ladder...And it worked out well! We used the machine with the ultraviolet light (I don't really know its name or how it works) and printed out a picture of the gel.
Wednesday: Amazingly, some of the seeds began to germinate after only two days! However, seeds from some populations, probably those that have a long growing season that can afford to germinate later, remained dormant. The other major event of the day was "PCRing" with Carrie. It was a lot harder than I thought it would be, with all the different programs depending on the microsatellites used or whether ESTs markers are used. At the end, thankfully, all the tubes seemed as though they had about the same volume of liquid in it, so hopefully the gel that we will be making tomorrow will show good results.
Thursday: Today, Carrie and I used gel electrophoresis to test to see whether we had good PCR results from yesterday. Carrie pretty much let me make the gel by myself, always standing right next to me and pointing a few things out once in a while. While we let the gel dry, we went into the conference room again, and Carrie went over in detail what she would like for me to accomplish this summer. Since Mimulus tilingii are high-altitude plants that live all the way up in the alpines, researchers don't yet know whether they evolved independently from convergent evolution or whether there had been a widespread area characterized by cold weather way-back-when that eventually diminished to create these now isolated Mimulus tilingii populations that can only survive at high altitudes. So, what I'm going to be doing this summer is comparing, phenotypically and genotypically, the Mimulus tilingii populations among each other and between Mimulus guttatus . If we find that the Mimulus tilingii are more similar to each other, this probably means that the wide-spread colder region did exist and that there was more recent gene flow among the tilingii . On the other hand, if we find that the Mimulus tilingii populations are more similar to the various Mimulus guttatus populations, then that suggests that there has been more recent gene flow between the two separate species populations. After that, we went back to the lab for the running of the gel after which we discovered that the PCR had gone well! Once again, using that UV light machine, we printed out a picture of the gel.
Friday: Today, we did another PCR but with two different markers - EST641 and EST332. While the PCR was going, I made various dilutions of all the markers that I will be using along with some dNTP. After, I made another gel with the PCR results, and I saw that I hadn't done as well as the previous time...but it wasn't bad. That pretty much took up most of the afternoon.
I hope everyone else is enjoying themselves as much as I am! I am absolutely exhausted...
aphids and duct tape
Hey guys, this is Zoe. First and foremost... some of you guys heard today when I said that I made top 10 for the Stuck at Prom contest (in which participants make their prom attire out of duct tape). So I would really appreciate it if you could vote for me - there's one vote per e-mail PER DAY, so you could vote everyday if you felt so inclined, and you could tell your friends/family too... /hint. Anyway, my entry is number 3981. It doesn't take long. Here's the address:
http://www.stuckatprom.com/contests/prom/entries_finalist.asp
So, I guess that's enough promoting myself... I guess as a bit of an introduction, since people like to talk about themselves, outside of biology I'm really into painting, drawing, sewing, and artistic stuff like that. I also practice kendo, which is Japanese sword fighting, and I watch a lot of anime. I also really like DDR and katamari damacy and some other games, but I'm not really that much of a hardcore gamer. I guess that's enough.
My first week in the lab was pretty interesting. Every other day was kind of better or worse in some ways, but that's probably more because of my mood than anything else. I'm in the mycology lab of the Bio Sci building, but I'm not really working with fungi. I'm studying the endosymbiotic bacteria of aphids - there are primary symbionts called Buchnera that live in the guts of the aphids and provide some essential amino acids for them, and secondary symbionts that not much is known about. Anyway, my lab has a hammock and chili pepper lights, which is the first thing I noticed about it and thought was kind of cool... there are also a lot of nifty mushroom pictures everywhere. I've been doing a lot of PCR and gel electrophoresis and I've had some reading assignments. Other than that there's not really that much else to say, I guess, since we all probably have somewhat similar feelings about this first week, and other people have written quite a bit about it.
http://www.stuckatprom.com/contests/prom/entries_finalist.asp
So, I guess that's enough promoting myself... I guess as a bit of an introduction, since people like to talk about themselves, outside of biology I'm really into painting, drawing, sewing, and artistic stuff like that. I also practice kendo, which is Japanese sword fighting, and I watch a lot of anime. I also really like DDR and katamari damacy and some other games, but I'm not really that much of a hardcore gamer. I guess that's enough.
My first week in the lab was pretty interesting. Every other day was kind of better or worse in some ways, but that's probably more because of my mood than anything else. I'm in the mycology lab of the Bio Sci building, but I'm not really working with fungi. I'm studying the endosymbiotic bacteria of aphids - there are primary symbionts called Buchnera that live in the guts of the aphids and provide some essential amino acids for them, and secondary symbionts that not much is known about. Anyway, my lab has a hammock and chili pepper lights, which is the first thing I noticed about it and thought was kind of cool... there are also a lot of nifty mushroom pictures everywhere. I've been doing a lot of PCR and gel electrophoresis and I've had some reading assignments. Other than that there's not really that much else to say, I guess, since we all probably have somewhat similar feelings about this first week, and other people have written quite a bit about it.
Thursday, June 14, 2007
Week One in Dr. Markert's Lab
Hello everyone! My name's Allie Stashko and I'll be a senior next year at Chapel Hill High. This summer I'm working with Dr. Markert in the Thymus Transplantation Lab. The thymus is where your T-cells in your blood come from. Babies with complete DiGeorge Syndrome are born with no thymus, and thus have no way to fight off infection. This is the only lab that does this transplant surgery, so the patients come from all across the world. Patients who have had a successful transplant continue to send back blood samples periodically to make sure everything is in check and for research.
Most of the procedures in the lab involve human blood and tissue, so I'm not allowed to handle any of it. Instead this summer I'll be doing a lot of data analysis and going back through old patient records for studies. For the first couple of days Dr. Markert spent time teaching an undergrad in the lab and me how to read and interpret flow charts. Flow cytometry is basically a way of finding out and quantifying the different types of cells in a sample. I learned some of the different assays they use to check on the levels of lymphocites and the surface proteins and antibodies that go with each type of cell. At first it was a lot to keep track of and I was constantly going back to my notes but it's getting easier and easier to recognize the types of cells by the antibodies they go with.
Today was the first day that I was able to start my project. The project involves going through old patients' flow charts to see if CD56+hi (a type of NK cell) exist pre transplant in patients and how the levels compare to post transplant and in control blood samples. Although this involves a lot of excel and photocopying, it's still very interesting and helps me to get a better understanding of what all the tiny little dots on a flow chart really mean.
Most of the procedures in the lab involve human blood and tissue, so I'm not allowed to handle any of it. Instead this summer I'll be doing a lot of data analysis and going back through old patient records for studies. For the first couple of days Dr. Markert spent time teaching an undergrad in the lab and me how to read and interpret flow charts. Flow cytometry is basically a way of finding out and quantifying the different types of cells in a sample. I learned some of the different assays they use to check on the levels of lymphocites and the surface proteins and antibodies that go with each type of cell. At first it was a lot to keep track of and I was constantly going back to my notes but it's getting easier and easier to recognize the types of cells by the antibodies they go with.
Today was the first day that I was able to start my project. The project involves going through old patients' flow charts to see if CD56+hi (a type of NK cell) exist pre transplant in patients and how the levels compare to post transplant and in control blood samples. Although this involves a lot of excel and photocopying, it's still very interesting and helps me to get a better understanding of what all the tiny little dots on a flow chart really mean.
first week in the lab
Hi, my name is Elizabeth Deerhake and I'm working in Dr. Arepally's lab this summer. The lab is rather small compared to others on campus - it consists of an undergraduate, lab tech, research assistant, and Dr. Arepally. She often makes rounds in the hospital as well. Hannah, a student in Howard Hughes last year, was asked to come back and work in the lab this summer. She and I both go to NCSSM so it's nice to have someone I'm familiar with. The lab is researching HITT, an immune response to the blood-thinner heparin which can cause severe clotting. The antigen is a complex of the heparin and the protein PF4. My project will be finding the concentration of PF4 in the general population. I will run ELISAs to find the amount of the protein in many many samples from the Blood Bank. This week, I've become oriented in the lab and have learned how to run an ELISA. I've got lots of pipetting to look forward to this summer! I've really enjoyed the team atmosphere of the lab and it's interesting to hear about different portions of the research. Today, some data came back showing the relation between charge density on the complex and clotting. Before, many hypothesized that size played the major role. It's really exciting to truly be on the cutting edge of scientific research, especially when the applications are so life-changing.
Lord of the Flies
Hi! My name is Caitlin Burk. I'm going to be a senior at Durham Academy next year, and I'm working with Drosophila (fruit fly) genetics in Dr. Dan Kiehart's lab in the French Family Science Center. My lab is interested in (among other things) myosin, a motor protein, and dorsal closure--when the fly embryo closes up on the dorsal side (time lapse video here, it's the one on the left).
The first few days in the lab have been pretty fun. Ruth Montague, one of the other people who works in the lab, has been showing me the ropes. I have learned to change fly cages (to collect embryos), quarantine flies (to prevent mites), to collect virgins (females that have already mated can store sperm from multiple males, and this can result in undesired offspring), and make slides for the imaging microscope. When you make a slide, the embryos, which look like clearish-white hot dogs, have to all be oriented dorsal side up in nice little lines. This can be hard because a) it's hard for me to tell which side is the dorsal one and b) the wet embryos are slippery, on agar, very small (2 lines of 6 embryos is less than 1/4 square cm), and I'm using a probe with an unsteady hand. I'm getting better though. One thing I think is interesting is that on the slides, the embryos are in halocarbon oil. They can still breathe in the oil, and are alive when you look at them under (over?) the confocal microscope. On the scope, you can view your slides in two ways: 1) normally. 2) you can turn on the laser attatched to the microscope and look at the embryos on a computer linked to a camera on the scope. Some embryos have transgenes, or genes that have been inserted by a scientist, that tag myosin with GFP (green fluorescent protein). The laser excites these proteins, and the camera has a lens that can show the fluorescence (if you looked through the microscope yourself, the laser would zap your eyes). One other thing I learned: When scientists discover a fly gene, they can name it whatever they want. There are genes called armadillo, spaghetti squash, hedgehog, etc.
Today I went to my first lab meeting, where Vinay, a grad student, presented the work he's been doing on the formation of fly hair. It was a little over my head, but I was able to actually understand most of what he was saying for about 45 minutes and then asked questions later. I also finally got to meet Dr. Kiehart, who got stuck coming back from Montreal yesterday. We planned out my project, which will deal with the brightness of the fluorescence of different GFP-flies. Fluorescence differs between different flies because of the position of the transgene. In one line of flies, the gene may have inserted itself in a very thick and crowded part of the DNA. Transcription enzymes will have a hard time getting to this section, and the gene won't be expressed very much (dim fluorescence). If in another line of flies, the gene inserts itself in a more spread out and accessible part of the genome, it will be more expressed (bright fluorescence) because the RNA polymerase can more readily transcribe the gene.
Anyway, I have to go read a paper to get ready for my project. More information my project--and why it's helpful for my lab--later (and hopefully pictures too!).
The first few days in the lab have been pretty fun. Ruth Montague, one of the other people who works in the lab, has been showing me the ropes. I have learned to change fly cages (to collect embryos), quarantine flies (to prevent mites), to collect virgins (females that have already mated can store sperm from multiple males, and this can result in undesired offspring), and make slides for the imaging microscope. When you make a slide, the embryos, which look like clearish-white hot dogs, have to all be oriented dorsal side up in nice little lines. This can be hard because a) it's hard for me to tell which side is the dorsal one and b) the wet embryos are slippery, on agar, very small (2 lines of 6 embryos is less than 1/4 square cm), and I'm using a probe with an unsteady hand. I'm getting better though. One thing I think is interesting is that on the slides, the embryos are in halocarbon oil. They can still breathe in the oil, and are alive when you look at them under (over?) the confocal microscope. On the scope, you can view your slides in two ways: 1) normally. 2) you can turn on the laser attatched to the microscope and look at the embryos on a computer linked to a camera on the scope. Some embryos have transgenes, or genes that have been inserted by a scientist, that tag myosin with GFP (green fluorescent protein). The laser excites these proteins, and the camera has a lens that can show the fluorescence (if you looked through the microscope yourself, the laser would zap your eyes). One other thing I learned: When scientists discover a fly gene, they can name it whatever they want. There are genes called armadillo, spaghetti squash, hedgehog, etc.
Today I went to my first lab meeting, where Vinay, a grad student, presented the work he's been doing on the formation of fly hair. It was a little over my head, but I was able to actually understand most of what he was saying for about 45 minutes and then asked questions later. I also finally got to meet Dr. Kiehart, who got stuck coming back from Montreal yesterday. We planned out my project, which will deal with the brightness of the fluorescence of different GFP-flies. Fluorescence differs between different flies because of the position of the transgene. In one line of flies, the gene may have inserted itself in a very thick and crowded part of the DNA. Transcription enzymes will have a hard time getting to this section, and the gene won't be expressed very much (dim fluorescence). If in another line of flies, the gene inserts itself in a more spread out and accessible part of the genome, it will be more expressed (bright fluorescence) because the RNA polymerase can more readily transcribe the gene.
Anyway, I have to go read a paper to get ready for my project. More information my project--and why it's helpful for my lab--later (and hopefully pictures too!).
Photos-DLC
I took some photos at the DLC yesterday and today- so now you can match the lemurs' faces with personalities!!
Teres-working on ascending number pairs and getting it right!
Miguel using his hands at the computer
PEDRO! Everyone's favorite little mongoose lemur...
Teres, a shy ringtailed lemur
Paiute aka "John Travolta"
Red Rover-the old man was born in 1982!
Teres-working on ascending number pairs and getting it right!
Miguel using his hands at the computer
PEDRO! Everyone's favorite little mongoose lemur...
Teres, a shy ringtailed lemur
Paiute aka "John Travolta"
Red Rover-the old man was born in 1982!
Wednesday, June 13, 2007
Sea Urchin Gene Networks
Hi! My name is Eden Rouse and I am working in Greg Wray's lab, though he is currently on a trip to Africa. This lab's primary organism is the purple sea urchin (Strongylocentrotus purpuratus). A room near the lab houses a collection of live sea urchins from all along California's coast. Right now, the lab is working on an 8 by 8 cross with the purple sea urchin and one other species of sea urchin. They sequence the genomes of each parent, then select individual offspring to analyze. They hope to gain valuable insight into the evolutionary history of the purple sea urchin's genome as well as observe differences in populations by analyzing SNPs, which are specific point mutations in an individual's DNA. Common techniques used in the lab are gel electrophoresis, PCR, DNA purification, and gel extraction. I'm sure I will learn many more techniques as I continue working in the lab. The sea urchins are kept in artificial seawater tanks where they are fed and attended to. On my first day, I got to touch a sea urchin for the first time. I was afraid that the spines of the urchin would hurt, but I was able to hold the urchin in my hand. I also learned that sea urchins can actually move. To extract DNA from the urchin, you must pull out a spine and collect the clump of meat on the end. The lab works with the sea urchin's genome because it is a model organism and much genetic research has already been done on it, so for example, PCRs are easy to do because you already know the primer sequence to be used if you want to amplify a specific gene or bp sequence. This lab is interested in the evolutionary history of specifically the DNA of s. purpuratus as well as gene networks (these are groups of genes that work together to create a certain biological organ or limb or structure. One gene's expression affects the transcription of another.). So far this week, I have witnessed a gel electrophoresis, a gel extraction, and I started doing PCR today. It was my first time, so I learned a lot. I got to use a fancy micropipette that automatically dispences and extracts liquid, and also allows the user to dispense in repetitions. All the technology and new protocols in the lab are exciting; I can't wait to start my project.
Tuesday, June 12, 2007
1st Blog Assignment
Please post two things by the end of this week:
1. Introduce yourself to the group! Let us know who you're working with this summer and a little about your project. If possible, include some photos of yourself, your lab mates, etc. in the lab. We'd love to see you in action.
2. Reflect on this first week in the lab. Describe a new experience you had, or tell us about something you've learned, or write about anything you found interesting in the lab this week. Stuck for ideas? Check out our sister program's blog.
1. Introduce yourself to the group! Let us know who you're working with this summer and a little about your project. If possible, include some photos of yourself, your lab mates, etc. in the lab. We'd love to see you in action.
2. Reflect on this first week in the lab. Describe a new experience you had, or tell us about something you've learned, or write about anything you found interesting in the lab this week. Stuck for ideas? Check out our sister program's blog.
Babies and Lemurs
My name is Anna Jaffe, I am a rising senior at Carolina Friends School, and I am working in Dr. Elizabeth Brannon's lab at Duke (http://www.duke.edu/web/mind/level2/faculty/liz/cdlab.htm). I am going to be working there for seven weeks, and by the end will have a project to present. I am working in the baby lab most of the time (except for from 3-5, when I am with the lemurs), which is where I will do my project. Right now we are working on ordinal numerical knowledge in infants, which looks at the way infants can understand numbers. Can they tell which of two numbers is greater? Can they see when that changes?
Although Dr. Brannon is my P.I., I am working with lots of different people in the lab. In the baby lab, I am working with Umay Suanda and Emily Hopkins, as well as others in the lab. I am also running tests in the Duke Lemur Center every day with Jennifer, Rosa, and Peter.
Today was my second day in my lab, but I have jumped in right away. I left lunch early so that I could meet the baby who was coming at 12:30. He was a cutle little guy, and was wide-eyed at the big shiny buildings and equipment. We sat him in the chair, and then Umay, Emily and I ran the test. The baby looked at a screen, where different images showed up. He was shown similar images (i.e. more green dots than red dots) for a habituation period. Then, he was given test trials, where he was shown either a familiar (more green than red) or a novel (more red than green) image. We recorded looking time to see whether the baby looked more at the new images than at the ones to which he had been habituated. For his hard wrk, the baby was given an infant scientist award and a t-shirt!
At the DLC, Rosa, Jennifer and I ran the tests on six monkeys. The lemurs work with a machine with a touch screen. Each lemur does either Match to Sample, Risk, or Lesser Numbers. In Match to Sample, the lemurs have to match an image to one of two options; in Risk, lemurs are first habituated to two images-one image gives them two sugar pellets every time, and the other either gives them one or three-then they must pick-will they take the risk or stay with the familiar two pellets; and lesser numbers-the lemur must pick the square with the smaller number to get the pellet.
The lemurs are all so fun, and they all have personalities! Pedro is sweet and very friendly; he is a mongoose lemur. Today for some reason he was curled up into a tiny little ball on the edge of a branch (perhaps he was cold from the fan?). However, he was as excited as ever to run the experiment and would always come over to see us when we walked past. Red Rover, who we don't run tests on, is an old lemur. He was born in 1982 (older than I am-lemurs are middle aged/old at around 15-20) and is now pretty demented. He sits around in his cage with his tongue out-it doesn't go back in! Another lemur, whom I have nicknamed John Travolta, has overactive scent glands (what a smell!). I have nicknamed him thus because he reminds me of a young John Travolta in "Grease"-his hair looks the same as the boys hair in the movie, as if he did it that way on purpose (it's actually his scent...). He is a sweety, albeit that he smells absolutely terrible-like nothing else I've ever seen. And then there's the baby sifaka we walk past on our way back to the lab....but "don't get too close or the mother will pee on you," says Jennifer.
All together I love my lab, and can't wait to keep working with such adorable subjects! Even entering data isn't too bad when every once in a while you get to hang out with two of the cutest things: babies and lemurs!
Although Dr. Brannon is my P.I., I am working with lots of different people in the lab. In the baby lab, I am working with Umay Suanda and Emily Hopkins, as well as others in the lab. I am also running tests in the Duke Lemur Center every day with Jennifer, Rosa, and Peter.
Today was my second day in my lab, but I have jumped in right away. I left lunch early so that I could meet the baby who was coming at 12:30. He was a cutle little guy, and was wide-eyed at the big shiny buildings and equipment. We sat him in the chair, and then Umay, Emily and I ran the test. The baby looked at a screen, where different images showed up. He was shown similar images (i.e. more green dots than red dots) for a habituation period. Then, he was given test trials, where he was shown either a familiar (more green than red) or a novel (more red than green) image. We recorded looking time to see whether the baby looked more at the new images than at the ones to which he had been habituated. For his hard wrk, the baby was given an infant scientist award and a t-shirt!
At the DLC, Rosa, Jennifer and I ran the tests on six monkeys. The lemurs work with a machine with a touch screen. Each lemur does either Match to Sample, Risk, or Lesser Numbers. In Match to Sample, the lemurs have to match an image to one of two options; in Risk, lemurs are first habituated to two images-one image gives them two sugar pellets every time, and the other either gives them one or three-then they must pick-will they take the risk or stay with the familiar two pellets; and lesser numbers-the lemur must pick the square with the smaller number to get the pellet.
The lemurs are all so fun, and they all have personalities! Pedro is sweet and very friendly; he is a mongoose lemur. Today for some reason he was curled up into a tiny little ball on the edge of a branch (perhaps he was cold from the fan?). However, he was as excited as ever to run the experiment and would always come over to see us when we walked past. Red Rover, who we don't run tests on, is an old lemur. He was born in 1982 (older than I am-lemurs are middle aged/old at around 15-20) and is now pretty demented. He sits around in his cage with his tongue out-it doesn't go back in! Another lemur, whom I have nicknamed John Travolta, has overactive scent glands (what a smell!). I have nicknamed him thus because he reminds me of a young John Travolta in "Grease"-his hair looks the same as the boys hair in the movie, as if he did it that way on purpose (it's actually his scent...). He is a sweety, albeit that he smells absolutely terrible-like nothing else I've ever seen. And then there's the baby sifaka we walk past on our way back to the lab....but "don't get too close or the mother will pee on you," says Jennifer.
All together I love my lab, and can't wait to keep working with such adorable subjects! Even entering data isn't too bad when every once in a while you get to hang out with two of the cutest things: babies and lemurs!
Blogging guidelines
Have fun with the blog! We genuinely want to hear about your adventures (and misadventures) in the lab this summer. Please post regularly about the things you're learning, any new experiences, and, especially, your reactions to those things. Also, be supportive of each other and comment on other people's posts.
General blog guidelines:
1. Please include labels in all of your posts. One of the labels must be your name (written the same way each time).
2. All students are welcome to play around with the template and style of the blog. Please do!
3. Remember this is a public blog. Please, no inappropriate content.
General blog guidelines:
1. Please include labels in all of your posts. One of the labels must be your name (written the same way each time).
2. All students are welcome to play around with the template and style of the blog. Please do!
3. Remember this is a public blog. Please, no inappropriate content.
Monday, June 11, 2007
How to post something on the blog!
1. Make sure you are logged in. You will need a google account to do so. Get one! It's free!
2. Make sure you have access to the blog. I need to give you permission to get access to posting. You should have received an email with a link to start posting. Follow the email's directions.
3. Once logged in and having access, you can now start posting! In the top right corner it should say 'New Post' click there. (If it doesn't say that, it probably says 'sign in', so do that first).
4. It will bring you to a screen where you fill in the Title and Body of your post. For newbies, stick to the 'compose screen'. If you know some html, click on 'edit html'. From the compose tab there are some basic formatting functions like bold, italics, etc.
5. Be sure to add a label to this post. Labels are just tags or keywords that describe what the post was generally about. Also, please always put your name as a label so that we can easily group all an individual's posts together. For instance, labels could be "Erica", "instructions", "introductions", "PCR", "Harry Potter". Just put something that could be useful in the label field. A post can have multiple labels, just separate them with commas.
6. You can preview your post, but when you're ready, click 'Publish Post', and you're done!
2. Make sure you have access to the blog. I need to give you permission to get access to posting. You should have received an email with a link to start posting. Follow the email's directions.
3. Once logged in and having access, you can now start posting! In the top right corner it should say 'New Post' click there. (If it doesn't say that, it probably says 'sign in', so do that first).
4. It will bring you to a screen where you fill in the Title and Body of your post. For newbies, stick to the 'compose screen'. If you know some html, click on 'edit html'. From the compose tab there are some basic formatting functions like bold, italics, etc.
5. Be sure to add a label to this post. Labels are just tags or keywords that describe what the post was generally about. Also, please always put your name as a label so that we can easily group all an individual's posts together. For instance, labels could be "Erica", "instructions", "introductions", "PCR", "Harry Potter". Just put something that could be useful in the label field. A post can have multiple labels, just separate them with commas.
6. You can preview your post, but when you're ready, click 'Publish Post', and you're done!
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