Hi this is Harry Zhang, and I just finished my 5-week lab work with Dr. Ballatore at UPenn. I participated in Dr. Ballatore's current project of making and categorizing carboxylic acid isosteres.
Methylation and LDA alkylation both failed to get rid of the CPD dimer, so Dr. Ballatore suggested another possible factor: the concentration of the starting material. If the starting CPD is too concentrated, it would be easier for it to attach to itself and form dimers. Using the rest of the new batch of CPD, I ran the same alkylation, again with LDA, but this time added more solvent so the starting CPD was ten times more dilute. Since this was the last week, I really hoped that this would work because we have been tackling this problem for almost the full duration of my stay and I would not have really contributed to the making of model compounds if this method did not work. Thankfully, after a work up and column, the LC-MS graph showed only our desired product's mass, and no dimers. That basically concluded my work with Dr. Ballatore and he said that he would send me more data once he finishes the whole project.
Although I have really only made one new model compound (the unmethylated CPD isostere was already made before and I only did it as a practice), I got a taste of what it is like to work with a scientific problem in real labs. By working at the issue in different angles, accompanied with constant testing, we were able to solve the persistent dimerization problem.
Overall, I think the 5 weeks at UPenn showed me what it is like to work in the field of scientific research. It consists of both logical and creative thinking, a lot of cool technology, but also a lot of repetitive work that sometimes even drives Dr. Ballatore crazy.
Showing posts with label University of Pennsylvania. Show all posts
Showing posts with label University of Pennsylvania. Show all posts
Wednesday, September 4, 2013
Week 4 - In the process of solving the dimerization issue
Hi this is Harry Zhang, I'm working at the Ballatore lab at UPenn and this is the 4th week that I've been working with Dr.Ballatore on making carboxylic isosteres (model compounds).
Towards the end of last week, I made another batch of protected CPD for the new LDA alkylation. Making the LDA was also a tedious process, and that was why Dr. Ballatore preferred using KHMDS. The making of LDA was mostly done by him and I was responsible for the alkylation. Since I've already done at least three alkylations, the process was familiar and I didn't make any mistakes so the color of the product was more "right", according to Dr. Ballatore. After working up the product and doing an HPLC, we still found the existence of the dimer. Dr. Ballatore collected samples for NMR to further analyze it while I made more methylated CPD.
I think after three weeks of practice, this week's lab work felt a lot more manageable and I actually had confidence that I wouldn't make a mistake like spilling dichloryl methane or making a cloud of silica powder. I felt that I was able to get a lot more done without the help of either Dr. Ballatore or the post-doc Bryant.
This was also the last week of the stay at Peddie. Over the weekend I moved to a hotel 2 blocks away from the lab to make life a lot easier (no more 3 hour commutes every day).
Towards the end of last week, I made another batch of protected CPD for the new LDA alkylation. Making the LDA was also a tedious process, and that was why Dr. Ballatore preferred using KHMDS. The making of LDA was mostly done by him and I was responsible for the alkylation. Since I've already done at least three alkylations, the process was familiar and I didn't make any mistakes so the color of the product was more "right", according to Dr. Ballatore. After working up the product and doing an HPLC, we still found the existence of the dimer. Dr. Ballatore collected samples for NMR to further analyze it while I made more methylated CPD.
I think after three weeks of practice, this week's lab work felt a lot more manageable and I actually had confidence that I wouldn't make a mistake like spilling dichloryl methane or making a cloud of silica powder. I felt that I was able to get a lot more done without the help of either Dr. Ballatore or the post-doc Bryant.
This was also the last week of the stay at Peddie. Over the weekend I moved to a hotel 2 blocks away from the lab to make life a lot easier (no more 3 hour commutes every day).
Monday, July 22, 2013
Linksvayer Lab week 6- Gels and why I don't like them
Hi my name is Ben Wagner and I've been working in the Linksvayer Lab at
Penn. We work on evolutionary biology and collective decision making in
ants.
Although I still have 2 weeks left in the lab, I feel like I've already learned what will be my most important lesson from this summer. This lesson is simple: Science takes forever. I'm not saying this is a negative way (necessarily) but more of an important lesson all future exp-ers and scientists should know. I have had multiple hour long incubation and waiting periods, ant feeding periods that took up most of my day, and my project expand until it is 10 times the original size, with 20 times as much work.
But regardless, week 6 was an excellent week, although it started off very badly. The week was a week of PCR and Gel electrophoresis, which shouldn't be bad. PCR is easy, gels are fine, just a lot of waiting time, but that's okay! PCR appeared to be running correctly We had already run a number of gels, and the creation of these gels lead to spills, leaks, and a small TAE buffer explosion in the microwave. But that's okay, nothing serious and its all in the name of science! Probably half our samples had been tested in at least one marker in the gel (so 1/8th what the final sample amount will be).
Then, A talk with an old lab Post-Doc, Luigi, resulted in my learning that all the PCR i had run so far, and tested on the gels, was completely wrong. It pretty much came down to my strands had been coming out at somewhere around 50 bp, which Riley and I thought was correct. Nope! They should be around 250-300. So we decided to find the issue. We started single-plexing (one marker instead of multiple), fiddled with the marker amount, changed temperatures in the thermocycler. Then, Dr. Linksvayer gave us the advice to use use 4uL DNA, instead of the 1uL that multiple protocols told us to use. Now we have have successful results on the gel!!! The next step is to see if this will work with multiplexing, because otherwise this project will not be finished anytime soon.
With only 2 weeks left, I'm not so sure this project will be finished, especially because Dr. Linksvayer wants me to help with behavioral things in those weeks. And because we haven't actually submitted anything to sequencing yet, which normally takes about a month, and then after that statistical tests need to be run to make a photogenic tree.... So it won't be done by the time I am. But maybe data collection will be. We'll just have to see. Hope all my fellow exp-ers have had a good summer in their labs, I'll keep you guys posted.
Although I still have 2 weeks left in the lab, I feel like I've already learned what will be my most important lesson from this summer. This lesson is simple: Science takes forever. I'm not saying this is a negative way (necessarily) but more of an important lesson all future exp-ers and scientists should know. I have had multiple hour long incubation and waiting periods, ant feeding periods that took up most of my day, and my project expand until it is 10 times the original size, with 20 times as much work.
But regardless, week 6 was an excellent week, although it started off very badly. The week was a week of PCR and Gel electrophoresis, which shouldn't be bad. PCR is easy, gels are fine, just a lot of waiting time, but that's okay! PCR appeared to be running correctly We had already run a number of gels, and the creation of these gels lead to spills, leaks, and a small TAE buffer explosion in the microwave. But that's okay, nothing serious and its all in the name of science! Probably half our samples had been tested in at least one marker in the gel (so 1/8th what the final sample amount will be).
Then, A talk with an old lab Post-Doc, Luigi, resulted in my learning that all the PCR i had run so far, and tested on the gels, was completely wrong. It pretty much came down to my strands had been coming out at somewhere around 50 bp, which Riley and I thought was correct. Nope! They should be around 250-300. So we decided to find the issue. We started single-plexing (one marker instead of multiple), fiddled with the marker amount, changed temperatures in the thermocycler. Then, Dr. Linksvayer gave us the advice to use use 4uL DNA, instead of the 1uL that multiple protocols told us to use. Now we have have successful results on the gel!!! The next step is to see if this will work with multiplexing, because otherwise this project will not be finished anytime soon.
With only 2 weeks left, I'm not so sure this project will be finished, especially because Dr. Linksvayer wants me to help with behavioral things in those weeks. And because we haven't actually submitted anything to sequencing yet, which normally takes about a month, and then after that statistical tests need to be run to make a photogenic tree.... So it won't be done by the time I am. But maybe data collection will be. We'll just have to see. Hope all my fellow exp-ers have had a good summer in their labs, I'll keep you guys posted.
Tuesday, July 16, 2013
More Dimers - Week 3
Hi I'm Harry and I'm working in the Ballatore lab at UPenn, I'm joining in the lab's project to create a set of carboxylic acid isosteres.
After finding the dimerization issue, we tried two different things: 1. Do the same alkylation with the left-over CPD but with a 1:1:1 CPD base and benzyl bromide ratio, we did this because the dimerization might have been caused by excess CPD and not enough base and benzyl bromide to react with. 2. Do the same alkylation but this time with a methylated version of CPD. My PI predicts that the methyl group should prevent the formation of CPD dimers. The LC-MS of the product of both methods showed significantly greater yield of the product we want but unfortunately we still see the dimers. We deprotected the products and using high-performance liquid chromatography (HPLC), which accurately separates our desired product and the impurities, we collected our products.
To deal with the persisting dimerization issue, my PI suggested we change the base from KHMDS to LDA, a stronger base because he had done an akylation with LDA without encountering any dimers. To do this I had to make more protected CPD. Meanwhile we set up a separate reaction with a completely different starting material. However, the reaction did not produce any of our desired product and was considered a failed reaction.
This is the general outline of the week's lab work but also a lot of time was used in regular column chromatography, extraction, and the most annoying part: waiting for the extracted product to dry. I'm starting to repeat the same procedures for each reaction: reaction setup, monitoring using TLC and LC-MS, then quenching/extracting with water and ethyl acetate, chromatography (HPLC or regular chromatography), and finally an NMR analysis. It's great that I'm finally starting to do these steps by myself without my PI or post-doc.
After finding the dimerization issue, we tried two different things: 1. Do the same alkylation with the left-over CPD but with a 1:1:1 CPD base and benzyl bromide ratio, we did this because the dimerization might have been caused by excess CPD and not enough base and benzyl bromide to react with. 2. Do the same alkylation but this time with a methylated version of CPD. My PI predicts that the methyl group should prevent the formation of CPD dimers. The LC-MS of the product of both methods showed significantly greater yield of the product we want but unfortunately we still see the dimers. We deprotected the products and using high-performance liquid chromatography (HPLC), which accurately separates our desired product and the impurities, we collected our products.
To deal with the persisting dimerization issue, my PI suggested we change the base from KHMDS to LDA, a stronger base because he had done an akylation with LDA without encountering any dimers. To do this I had to make more protected CPD. Meanwhile we set up a separate reaction with a completely different starting material. However, the reaction did not produce any of our desired product and was considered a failed reaction.
This is the general outline of the week's lab work but also a lot of time was used in regular column chromatography, extraction, and the most annoying part: waiting for the extracted product to dry. I'm starting to repeat the same procedures for each reaction: reaction setup, monitoring using TLC and LC-MS, then quenching/extracting with water and ethyl acetate, chromatography (HPLC or regular chromatography), and finally an NMR analysis. It's great that I'm finally starting to do these steps by myself without my PI or post-doc.
Wednesday, July 10, 2013
Linksvayer Lab: mid Week 5
Hi my name is Ben Wagner and I've been working in the Linksvayer Lab at
Penn. We work on evolutionary biology and collective decision making in
ants.
At the middle of week 5 I am still working on the microsatellites project, still with hope that I'll be able to get onto an animal behavior in the coming weeks. To remind you what my current project is... I have been taking 15 ants from a large number of colonies, and individually crushing, adding buffers, centrifuging, letting incubate, and finally perform PCR on these samples. There are also steps of Nano Dropping, where I use a Nano Drop machine to test light refraction at certain wave lengths, telling me how much DNA in is the sample, and running gel electrophoresis after PCR, in order to see the size of my samples. We are looking for microsatellites, also known as Short Tandem Repeats (STRs), in order to tell the difference between the genetic codes of the different colonies. Due to the caste systems Pharaoh (and other) ants use, the genetic code of a single colony is very identical, and two sister worker ants are more related than any human is to another human on average, except for identical twins. We are not trying to sequence the entire genome because that takes a long time and is very expensive. Instead we are looking fro Micro Satellites, which we expect could be different between colonies. As an example,we might be looking for a code that says to make a little extra of a certain protein in one colony when compared to another, as opposed to the code that says grow legs, or something all ants do.
Unfortunately I am currently in an awkward spot in time, as we have run out of the Taq MasterMix Polymerase needed to run PCR, as well as multiple of the markers needed to do multiplexing, which is marking the genetic sequence. So for the next few days I am starting up on new colonies, and preparing them for PCR. This means the project is likely to continue even longer, since we had not originally planned on doing more colonies (past the amount from my last post), and because we need to wait for delivery.
Hopefully things will become more exciting here in the near future, but for now its back to crushing ants!
At the middle of week 5 I am still working on the microsatellites project, still with hope that I'll be able to get onto an animal behavior in the coming weeks. To remind you what my current project is... I have been taking 15 ants from a large number of colonies, and individually crushing, adding buffers, centrifuging, letting incubate, and finally perform PCR on these samples. There are also steps of Nano Dropping, where I use a Nano Drop machine to test light refraction at certain wave lengths, telling me how much DNA in is the sample, and running gel electrophoresis after PCR, in order to see the size of my samples. We are looking for microsatellites, also known as Short Tandem Repeats (STRs), in order to tell the difference between the genetic codes of the different colonies. Due to the caste systems Pharaoh (and other) ants use, the genetic code of a single colony is very identical, and two sister worker ants are more related than any human is to another human on average, except for identical twins. We are not trying to sequence the entire genome because that takes a long time and is very expensive. Instead we are looking fro Micro Satellites, which we expect could be different between colonies. As an example,we might be looking for a code that says to make a little extra of a certain protein in one colony when compared to another, as opposed to the code that says grow legs, or something all ants do.
Unfortunately I am currently in an awkward spot in time, as we have run out of the Taq MasterMix Polymerase needed to run PCR, as well as multiple of the markers needed to do multiplexing, which is marking the genetic sequence. So for the next few days I am starting up on new colonies, and preparing them for PCR. This means the project is likely to continue even longer, since we had not originally planned on doing more colonies (past the amount from my last post), and because we need to wait for delivery.
Hopefully things will become more exciting here in the near future, but for now its back to crushing ants!
Monday, July 1, 2013
Product Characterization - Week 2
Hi I'm Harry and I'm currently working with Dr. Ballatore in a chemistry lab at UPenn focusing on chemical synthesis of isosteres.
At the end of the previous week we were trying to figure out the content of a product that was not what we expected. To further characterize the compound, in addition to LC-MS, the post-doc Brian took me down to the nuclear magnetic resonance (NMR) machine. Apparently the magnetic field around the machine is so strong that if you had a credit card in your pocket it would be deactivated. Brian tried to explain to me how the NMR works in simple terms because the actual theory requires chemistry and physics knowledge that are well beyond my level. So basically the NMR creates a magnetic field that can change the direction an electron spins (it can only spin in two possible directions), and the machine can measure the amount of energy required to make that change. The energy required is presented on the resulting graph as a chemical shift, which is essentially the position of a peak on the graph. In a proton NMR, the integration of each peak shows the number of protons at that location; in a carbon NMR, each peak represents one carbon atom. Because the energy required to make the change in spin direction is related to the chemical environment that the atom is in (which simply means the other atoms around it in the chemical structure), each proton or carbon in a specific location will have a specific range of chemical shift. So if you know that a carbon atom in a carbonyl group will always show up on the left end of the graph, a peak on the left end will indicate that you have a carbonyl carbon. The NMR essentially gives us more information on the structure of the compound that we have made.
The NMR result certainly did not represent the compound we wanted, so while Dr. Ballatore and Brian were trying to figure out what was going on with the NMR (I can't interpret a NMR graph), he had me set up another reaction to deprotect the compound. The isobutane that was attached in the first step of the reaction was a "protection" of the reactive carbonyl oxygen. Once deprotected, we ran another LC-MS to see what was in the compound. As expected, the largest peak showed the same molecular weight as before minus an isobutane. After some guessing around, Dr. Ballatore figured it out. What happened was that the reaction produced a large amount of dimers, compounds that had two cyclopentanediones. It was pretty amazing how he just guessed the right one.
While all this was happening, we had set up a separate reaction which was a lot simpler than the one we were working on, it only had one step and didn't require reflux or deprotection. The reaction sill uses cyclopentanedione, and it basically adds the benzyl ring on the other side of the structure. Changing the location of the benzyl group can affect the compound's acidity and ability to penetrate membranes.
After figuring out what went wrong, we redid the reaction and this time modified the run-time to minimize dimerization.
Sunday, June 30, 2013
Linksvayer Lab: end of Week 3
Hi my name is Ben Wagner and I've been working in the Linksvayer Lab at Penn. We work on evolutionary biology and collective decision making in ants.
My second and third weeks in the lab turned out to be very similar to the first. I'm still working on the genetics project, where we are finding differences in micro-satellites in the Pharaoh Ant colonies in the lab. This information is important for the future of the lab, because it will allow us to compare colonies genetically as well as behaviorally, and determine if certain actions/activities, such as one colony having twice as many queens although still being the same size as another (Pharaoh Ants are polygynous which means they have multiple queens); we then compare this to the genetic difference between the two or more colonies. My P.I. left this week to go to some conferences in Europe, where he'll be learning ant stinger dissection techniques, and talking with the top ant experts on the continent! But before he left he gave me new directions with my project, by which I mean he expanded it. I'm now doing about a dozen more colonies than my previously reported amount, as well as running gel electrophoresis in multiple samples from each colony to test if the PCR worked before submitting them for sequencing.
In total the lab week has been pretty slow. Most of the projects in the lab are coming to a close, so most of my fellow researchers are anxious to finish and start new projects. Although I know my project will not be finished anytime soon, I'll hopefully begin working on more behavioral based work, just to mix things up. Because of many projects almost being finished, everyone has had a little more time to hang out, so I got to know everyone in the lab a lot better, and we even went out for fro-yo after work one day. Unfortunately, we had to say good-bye to our lab tech Katie, who is leaving to go to grad school. But we're excited for our new lab tech Michael to be in charge because he's a really fun guy.
I haven't gotten a chance to return to the Berger lab yet, mainly because every time Riley's been there its been rather serious business. To remind you, Riley, my grad student, works in both Dr. Linksvayer evolutionary biology ant lab and Dr. Berger's epigentics in ants lab. So he's been over there trying to talk to Dr. Berger about his next steps not only in his project but in his future at the lab. This means I've had a lot more unsupervised lab work, to the point of Riley calling me "99%, if not completly, autonomous". I've also taken it upon myself to sign up for ant feeding, which as a temporary volunteer I'm not required to do, but I wanted to do my part. Its a rather long process, due to the hundred or so colonies of Pharaoh Ants and another 300-400 colonies of another type (which I can't remember because I don't use them). For both we need to give them new food and water, which is always interesting because they usually start making nests and climbing all over the test tubes they get water from.
I'm not expecting too much of a change this week, this Riley's going to be at an "ant meeting" all Monday and Tuesday, and with July being off... there will be mostly more of the same. But I am excited for the Penn/CHOP exp lunch Tuesday!
My second and third weeks in the lab turned out to be very similar to the first. I'm still working on the genetics project, where we are finding differences in micro-satellites in the Pharaoh Ant colonies in the lab. This information is important for the future of the lab, because it will allow us to compare colonies genetically as well as behaviorally, and determine if certain actions/activities, such as one colony having twice as many queens although still being the same size as another (Pharaoh Ants are polygynous which means they have multiple queens); we then compare this to the genetic difference between the two or more colonies. My P.I. left this week to go to some conferences in Europe, where he'll be learning ant stinger dissection techniques, and talking with the top ant experts on the continent! But before he left he gave me new directions with my project, by which I mean he expanded it. I'm now doing about a dozen more colonies than my previously reported amount, as well as running gel electrophoresis in multiple samples from each colony to test if the PCR worked before submitting them for sequencing.
In total the lab week has been pretty slow. Most of the projects in the lab are coming to a close, so most of my fellow researchers are anxious to finish and start new projects. Although I know my project will not be finished anytime soon, I'll hopefully begin working on more behavioral based work, just to mix things up. Because of many projects almost being finished, everyone has had a little more time to hang out, so I got to know everyone in the lab a lot better, and we even went out for fro-yo after work one day. Unfortunately, we had to say good-bye to our lab tech Katie, who is leaving to go to grad school. But we're excited for our new lab tech Michael to be in charge because he's a really fun guy.
I haven't gotten a chance to return to the Berger lab yet, mainly because every time Riley's been there its been rather serious business. To remind you, Riley, my grad student, works in both Dr. Linksvayer evolutionary biology ant lab and Dr. Berger's epigentics in ants lab. So he's been over there trying to talk to Dr. Berger about his next steps not only in his project but in his future at the lab. This means I've had a lot more unsupervised lab work, to the point of Riley calling me "99%, if not completly, autonomous". I've also taken it upon myself to sign up for ant feeding, which as a temporary volunteer I'm not required to do, but I wanted to do my part. Its a rather long process, due to the hundred or so colonies of Pharaoh Ants and another 300-400 colonies of another type (which I can't remember because I don't use them). For both we need to give them new food and water, which is always interesting because they usually start making nests and climbing all over the test tubes they get water from.
I'm not expecting too much of a change this week, this Riley's going to be at an "ant meeting" all Monday and Tuesday, and with July being off... there will be mostly more of the same. But I am excited for the Penn/CHOP exp lunch Tuesday!
Monday, June 24, 2013
Making Isosteres - Week 1
The first week at the lab was really interesting and fun except for the fact that I almost broke a finger (which had nothing to do with the lab but I had to take a day off for it). Overall I was happy that I wasn't burdened with piles of articles but instead got to do a lot of hands-on work. The lab is pretty messy, my PI said that they don't do a very good job making things neat and orderly unless there's an inspection. There are only two other people besides my PI and me in the room, a grad student and an undergrad. They were pretty busy with their own projects (which were similar to what I'm doing) so I mainly worked with my PI directly and a post-doc who's working next door. Unlike some of the other labs, I didn't have to go through hours of training sessions. On the first day, basically as soon as I arrived, my PI started writing chemical structures on a blackboard and told me that this is the reaction that I'm doing. Then I followed the instructions to weigh out the solids and get the correct volume of liquids and put them in a round-bottom flask. Although I've used all the instruments before (analytical balance, weighing paper, syringes, pipettes) and the task wasn't particularly hard, I was still a little scared because I was handling all these glassware and chemicals on my first day. The reaction I set up was a reflux reaction in which the flask is placed in a hot wax bath with a condenser on top so any solvent that evaporates will go into the condenser instead of falling back into the reaction solution.The purpose of the reaction was to replace a proton with an isobutane, the first step in a three-step process that would result in an isostere of 1,3-cyclopentanedione, the chemical I'm currently working with.
On the second day, I worked with the post-doc the whole time. He demonstrated some of the more complicated (but actually really basic) processes like thin layer chromatography (determines the solvent condition suitable for the compound and checks if there are products made), column chromatography (a tedious process that may take over an hour, separates the product solution into fractions, the fractions are then tested using TLC to see which ones contain the desired product), and purification methods including using water to quench the reaction, using ethyl acetate to separate the organic and inorganic layers, and using sodium sulfate to eliminate any left-over water. These are the standard procedures for almost every reaction that I will do.
Next day morning I got a black fingernail and went to the lab in pain. My PI showed me the Liquid Chromatography-Mass Spectrocoply (LC-MS) machine and tested the solution I collected the day before. The LC-MS basically runs a mini-column and presents a graph on the computer that contains peaks. These peaks represent the compounds in the product solution; the machine gives the molecular weight of every compound and we are trying to find the peak with the molecular weight that corresponds to the product we want. If it is a big peak then that means the reaction is successful and we got the right product. There are other peaks on the graph that corresponds to the left-over reactants and some side-products. Unfortunately we could not find the right peak and even my PI couldn't figure out what happened. After lunch I went to the ER because the finger was starting to bother me a lot. Since I couldn't use my right hand, I stayed in the dorm the next day.
After the weekend, I still couldn't use the bruised finger but my PI said it's fine and he'll help me do anything that required my right hand index finger. I still got to set up the next reaction, this time in a cold bath made of dry ice and acetone. Meanwhile we did more LC-MS tests on the product of the previous reaction and found that our desired product exists but in a very small amount compared to the main peak that had a different molecular weight. So the week ended with an unknown product.
On the second day, I worked with the post-doc the whole time. He demonstrated some of the more complicated (but actually really basic) processes like thin layer chromatography (determines the solvent condition suitable for the compound and checks if there are products made), column chromatography (a tedious process that may take over an hour, separates the product solution into fractions, the fractions are then tested using TLC to see which ones contain the desired product), and purification methods including using water to quench the reaction, using ethyl acetate to separate the organic and inorganic layers, and using sodium sulfate to eliminate any left-over water. These are the standard procedures for almost every reaction that I will do.
Next day morning I got a black fingernail and went to the lab in pain. My PI showed me the Liquid Chromatography-Mass Spectrocoply (LC-MS) machine and tested the solution I collected the day before. The LC-MS basically runs a mini-column and presents a graph on the computer that contains peaks. These peaks represent the compounds in the product solution; the machine gives the molecular weight of every compound and we are trying to find the peak with the molecular weight that corresponds to the product we want. If it is a big peak then that means the reaction is successful and we got the right product. There are other peaks on the graph that corresponds to the left-over reactants and some side-products. Unfortunately we could not find the right peak and even my PI couldn't figure out what happened. After lunch I went to the ER because the finger was starting to bother me a lot. Since I couldn't use my right hand, I stayed in the dorm the next day.
After the weekend, I still couldn't use the bruised finger but my PI said it's fine and he'll help me do anything that required my right hand index finger. I still got to set up the next reaction, this time in a cold bath made of dry ice and acetone. Meanwhile we did more LC-MS tests on the product of the previous reaction and found that our desired product exists but in a very small amount compared to the main peak that had a different molecular weight. So the week ended with an unknown product.
Friday, June 21, 2013
Week 1 (and a half): The Art of Crushing Ants
This summer I'm working at Penn in the Linksvayer Lab, which is focused on evolutionary biology through animal behavior and genetics in ants. At first my work was set back a week by a full safety class. But on June 10th I took the safety class, and after long commute by car, then train, then walking, (about 100 minutes in total, half train, and split evenly between car and walking) I started Tuesday June 11th. Although the lab focuses on animal behavior, because of my past experience in performing PCR (thank you Dr. Peretz and BioTech class!), I am starting off by comparing micro-satellites (points on the genome which we expect to change) in the different colonies of Monomorium pharaonis, called Pharaoh Ants. To do this, we (Me and Riley, the grad-student working with me), are taking 15 ants per colony, for about 15 total colonies, and going through the process of separating each ant, crushing them using a pestle and liquid nitrogen, applying many buffers and Elution, and going through tons of centrifuging. This is what I have been doing for the past week. Starting this afternoon I will begin applying 4 different marker sets to identify the ants, performing PCR, and getting each ant sequenced. For those of you doing the math: its 15 ants x 15 colonies x 4 marker sets = about 900 ants micro-satellite sequences!!!
The most amazing thing about the my experience so far is that this project is MY project! Riley has some of his own stuff, and works with me often, but the project is mine to do and complete, and the info is going to be used for future projects. I should be done this by the end of next week, and then I really start working with everyone on a BIG animal behavior project (which I'll keep a secret for now!). But once that project is finished, I'll be able to compare my results from the micro-satellite to make a final determination about the results from that project, tying in most of the work I'll be doing during my 8 weeks.
There is one more EXTREMELY awesome thing about my experience here. While Dr. Linksvayer's lab is amazing, and I'm becoming friends with the other 8 or so people working here, I have the added bonus of working with another lab! Riley has until the end of the summer to decide between Dr. Linksvayer's and Dr. Berger's lab, so in the mean time we work in both. Dr. Shelley Berger focuses still on ants, but specifically epigenetics. Dr. Berger has a lab of about 35 people, and works in the very high tech Smilow research center, still at Penn. Riley is working on completely different projects at Dr. Berger's lab, and I've gotten to help him over there when we have some time in the afternoon. There I've been able to use really high tech machines, like a Sonic Crusher, which they use to crush ant samples WITH SOUND instead of using a pestle. I've also been able to attend lab meetings, talks by visiting experts, and hopefully next week I'll be doing an ant brain dissection, which has absolutely nothing to do with my work, but everything to do with Riley's.
Not only am I getting great lab experience through my work, but I'm getting to see the work of dozens of other researchers, who are glad to tell me (and brag) about their research. I also get to compare the feeling of a huge and older high tech with a small and newer lab. I can't wait to continue my work and eventually move onto animal behavior, and I'll keep everyone posted with how it goes!
The most amazing thing about the my experience so far is that this project is MY project! Riley has some of his own stuff, and works with me often, but the project is mine to do and complete, and the info is going to be used for future projects. I should be done this by the end of next week, and then I really start working with everyone on a BIG animal behavior project (which I'll keep a secret for now!). But once that project is finished, I'll be able to compare my results from the micro-satellite to make a final determination about the results from that project, tying in most of the work I'll be doing during my 8 weeks.
There is one more EXTREMELY awesome thing about my experience here. While Dr. Linksvayer's lab is amazing, and I'm becoming friends with the other 8 or so people working here, I have the added bonus of working with another lab! Riley has until the end of the summer to decide between Dr. Linksvayer's and Dr. Berger's lab, so in the mean time we work in both. Dr. Shelley Berger focuses still on ants, but specifically epigenetics. Dr. Berger has a lab of about 35 people, and works in the very high tech Smilow research center, still at Penn. Riley is working on completely different projects at Dr. Berger's lab, and I've gotten to help him over there when we have some time in the afternoon. There I've been able to use really high tech machines, like a Sonic Crusher, which they use to crush ant samples WITH SOUND instead of using a pestle. I've also been able to attend lab meetings, talks by visiting experts, and hopefully next week I'll be doing an ant brain dissection, which has absolutely nothing to do with my work, but everything to do with Riley's.
Not only am I getting great lab experience through my work, but I'm getting to see the work of dozens of other researchers, who are glad to tell me (and brag) about their research. I also get to compare the feeling of a huge and older high tech with a small and newer lab. I can't wait to continue my work and eventually move onto animal behavior, and I'll keep everyone posted with how it goes!
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