Today, June 4, 2007, was interesting for the most part. First off, the ToxStart training at 8:50 a.m. was very informative and fun. I gained so much knowledge about toxicology that really benefitted me later in the day as I began my lab work. I totally understood almost everything that my mentor, Shawn, was talking about! This really gave me a boost in my confidence knowing that I understand the scientific "lingo."
After lunch at about 1:15 pm, I went to the lab I am working in at the College of Pharmacy. I met with my mentor and learned of all the lab equipment used. I also discovered what I am going to be doing. I am working with arsenic, which is a carcinogen found in the bladder cells. After discovering all of the equipment and background information, we went up to a lab to create cell cultures. When Shawn told me I was actually making my own cultures, I was surprised. I always had the idea that I would be the clean up crew. I observed how to create cultures and how to work in vitro. I experienced how it feels to work in a lab and creating cell cultures. I also looked under a microscope to observe the bladder cells.
By the time that was all done with, the time was about 3:30 pm. I received a few more research papers that had basic background knowledge of arsenic and the use of the bladder cells. It is really neat to learn that the bladder cell is vital because it is known as a detoxifier. After having some of my questions answered, I was about to leave and go home. I am so exhausted but I had such good times being in the lab and working as a researcher. Hopefully I feel much more confident in my knowledge and my lab skills in order to reach my peak and do the best possible job I can. That will come soon.
Yet again, ToxStart training amazes me again. It is just so fascinating to learn about environmental health because there is so much information involved! Environmental health is defined to be the welfare of people in the environment. We did so many activities that I found to be interesting today. Katy let us test our breathing and see how it feels to be a person with asthma. That was sad because I couldn't breathe at all!! Another thing I remembered was the presentation from Georg Wondrak who presented his work on skin cancer. It was pretty amazing. I had no idea that there were three different types of skin cancer! Now the most memorable part of the training. The group (consisting of Shiana, Alex and Tiffany) and Katy were discussing Hanta virus and I was so curious about knowing what caused it. Me and my big mouth now have scarred me. I discovered that it was caused by mice!! If you all didn't know, my phobia of rodents really kicked in. To put this in simpler terms, I suffered a spaz attack.
After lunch at about 1:00 pm, I walked into my lab down in the basement (AKA floor one) of the College of Pharmacy. Today was practically the most amazing day of my internship so far! I definitely experienced lab work to the max! I watched Shawn, my mentor, work on performing a Trypan Blue Exclusion Assay, which allows the bladder cells to be counted individually. Then after observing, he told me I was doing this...from scratch. I guess in these lab situations, as an intern, you are expected to do whatever it is you may not be expecting to do. I copied whatever Shawn did and was successful in doing it! In a few days, I will have to feed my cells again. That was exciting because I feel like my lab skills are definitely improving one hundred percent. Apparently my counting skills are still a bit rusty because I miscounted cells many times. That was a LAUGH OUT LOUD moment during the day.
After completing the assay, we went back down to the lab and I read research papers for about 15 minutes and then checked out at 4:45 pm. All in all, this day was entertaining, yet educational. This is the balance of fun and work that I am looking forward to everyday. Definitely, with each and every day, my skills in the lab are improving exceptionally and my best has yet to come.
I have only been in the lab two days this week, but Aysen, the grad student I am shadowing, has already taught me so much. I've helped her run Western blots, DNA amplification and purification, and protein purifications so far. We are working on one of her projects with flagella, the part of E. coli which allows it to be motile. Presently, we are trying to isolate and amplify a specific protein in the flagella with our procedures.
The first day I started Aysen was running three different procedures at the same time, one of which I had never heard of and the other two with which I was only vaguely familiar. It was intimidating at first, trying to jot down everything and make sense of it, but the thick stack of papers I was assigned to read is helping with that. I just read a research paper describing the traits and behavior of different pathogenic strains of E. coli and am on to another stack of papers of how pathogens in general invade hosts.
Today I gave my presentation on my research paper and had some technical difficulties, but it worked out in the end. When I first started annotating this paper, I was really just pushing myself through the sentences, word by word - looking each term up in the dictionary; it was tedious and frustrating. Finally, I mustered some courage and asked Aysen for some advice on how to get through my first big reference paper(although I was sure it was pretty basic material) and she really lessened my work load while helping me understand the content more. Referencing multiple sources (wikipedia!google!mentors!) and focusing on sections of the paper Aysen suggested helped so much!
Next week, I hope to be able to run amplifications and purifications on my own and get a little more responsibility. I'm having a great time in the lab and with the other interns and am really looking forward to our weeks together!
Well, in a three-day span, I haven't been able to cover as much ground as some interns because I was involved with the ToxStart training. We discussed environmental hazards and various other ideas, such as research ethics. It was pretty interesting, and it was easy to understand because I was trained for this in an earlier internship.
Anyway, Mark and I briefly discussed and agreed that the plan would either be a branch off or a continuation of their current research. The plan is to discuss how MEKK4 and Filamin-1 interactions are important for heart valve development. It's been previously shown to interact in other systems and could explain a cause for congenital heart defects. It was shown that MEKK4 is necessary for phosphorylation of proteins.
Currently, we are perfecting the MEKK4 and Filamin-1 immunostaining procedure that is to be performed either Monday or Wednesday, because it is possibly a two-day procedure and we're trying to perfect it as much as we can under the time constraints.
i think this is where my blog is suppose to go!!!!
Hello Fellow Interns Shiana, Tiffany, Kim, Mon-Ning, Logan, Greg, Alex, and Andrew!!!
Oh yeah Hi Marti, Travis, and all other staff that read this post!!!
Okay here it goes everybody-->
I am conducting extensive research in the Wildlife and Fisheries Sciences Laboratory under the direction of Mrs. Melanie Culver (Really great lady by the way!!!). A graduate student by the name of Tony Dee is my mentor; another graduate student who works in the same laboratory is Demetre “I don’t know his last name” (Greg’s Mentor). Furthermore, there are roughly ten other researchers working in the same laboratory researching a variety of different venues ranging from Bob Cats to Rattle snakes I am not sure of the “official” terminology of there research though. This is nice because I am able to see how well others function in the lab setting.
The first day in the laboratory was an AWESOME experience. The mentors were eager to work hand and hand with Greg and myself. The mentors first dove right in, showing us the rules and regulations of the laboratory so there would be NO “cross contamination” while we handled very delicate Deoxyribonucleic Acid (DNA). In the laboratory we proceeded to get familiar with the instrumentation as well as got to know who these people are that we will be working side by side with for the next six weeks OF OUR LIVES!!! We cracked a couple of jokes with one another, found out what types of music each other liked, and also favorite types of movies. I recommend that each intern get to know their mentor on a personal level so it makes for a more enjoyable experience (Not to personal though).
So far in the laboratory we have done trials of PCR (Polymerase Chain Reaction) and have run gel electrophoresis many times. I believe the purpose of the last few days working has been entirely focused on reiterating the protocol and procedures in the lab setting because it is crucial to do everything precisely. Recently, (today) I had the “DISTINCT” PLEASURE of being able to take samples, pieces of ears with hair and blood, which other researchers extracted DNA from living creatures and cut them up into smaller pieces and divide them into specific test tubes. This gave me a sense of self satisfaction because I knew I was contributing in a positive way to the overall mission of the laboratory. As I was doing this task Greg and I conserved with Greg stating: “Hey dude, some undergraduates don’t even get to do what we are doing in the lab…” This made me realize that this internship is a great opportunity for success and will open doors for those who take advantage of the knowledge they acquire.
I would like to conclude my first blog entry by saying “never squander such a valuable resource, understand the investment which your mentors are putting into you.”
This last week and couple of days have been more than I knew to expect. I was surprised at how comfortable I felt with the group of students I was with within the first day of our internship, and then again pleasantly surprised when the comment I made voicing as much was agreed with. Training in a classroom together with Nadja that first day for some four hours did the trick, all right. Despite my existing background in laboratory techniques, Nadja, Jeff, Rachel, and the other students all helped make the review of knowledge fun for me. Much of our days were spent smiling or laughing in between our mini-labs and lectures, both at each other and at side jokes. The presenters that we had the chance to listen to this week were so enthused and animated about their own work that it was hard for me to not be drawn into their projects.
Having been assigned to a lab in the College of Pharmacy, I was required to take an extra toxicology course this second week. I readily appreciated the chance for this additional background before I was fully immersed in my lab work; for a surety, it helped me to better understand the research papers that I had to read for my lab. The teachers and presenters during this segment of learning, which this week included again Marti and Katy, were very willing and patient about teaching us what they thought we could benefit from. Their support and the friendliness of the BIO5 staff I have met so far has definitely made it easier to ask for help and interact with them.
Onward ho to lab life--the exciting part! My mentor's name is Ruiyu Xie (but I call her Rae, for short) and she has been working at the College of Pharmacy for at least three years. She is very easy to approach with questions and explains concepts to me I have not learned yet patiently. Through the past four days we've talked about everything from our backgrounds, families, and friends to even troublesome laptop problems. Dr. Monks was a delight to conversate with when I met with him on Tuesday, as well. He first came from the UK, hence his accent, and came to the U.S. to continue his studies. I also met Rae's best friend who works under Dr. Lau, Chi Lin, who I discovered knew my parents! I had no idea. Not only that, but a former student of my high school and a friend of my older sister's, is also volunteering in Dr. Lau's lab this summer. Evidently, it's a small world. I have also made friends with so many other undergraduate and graduate students that I look forward to seeing them every day around the lab.
Research-wise, I will be working with a mitochondrion-specific peroxidase called peroxiredoxin III (Prx III). Past research suggests that the enzyme Prx III is a critical regulator in the redox stage of a cell. Reactive oxygen species (ROS) must be reduced ultimately to compounds that consist of mainly water so that they do not harm the cell. Catalase, glutathione peroxidase (GPx), and Prx can all reduce a ROS called hydrogen peroxide, but the mitochondrion lacks catalase and must import glutathione (GSH). The only enzyme that it inherently has to perform this job is Prx; however, specifically Prx III in mitochondria. Past research has discovered that there is about 30 times more Prx III than GPx1 in the mitochondria. This seems to indicate that Prx III may have more roles than the regulation of apoptosis in the mitochondria.
In order to further determine the function of Prx III, I will render Prx III unable to function in a live cell and observe what cell processes no longer proceed normally because of its 'absence.' To disable Prx III, I will mutate it by replacing two specific amino acids in it called cysteine (Cys) 108 and Cys 229 with another amino acid called serine (Ser). These two particlar Cys amino acids were chosen because they have been found in past studies to form the disulfide bond necessary for Prx III to function. Ser was chosen to replace Cys because it is the most similar in structure to Cys and it will not change the three dimensional structure of Prx III.
So far, Rae and I have sent in a viral plasmid to be sequenced (for which reasons will be saved for another entry) and must wait until the results are returned in order for us to proceed with the next step of our experiment. Though our plasmid was sent in two days ago and were expected to be finished sequenced before today, we should receive them for sure tomorrow. Then, the real lab work begins. Meanwhile, we have designed two mutagenesis primers that we ordered today--a process that included locating and then translating the Prx III's nucleotides into amino acids, locating the specific amino acids of interest in terms of nucleotides, figuring calculations, and comparing primer possibilities to find the optimal ones. The completion of this project will be beneficial to the research of a great many people working in the same field, and I am more than ready to put my eager energy and time into it.
What a week it has been! The only thing more exciting is the promise of more to come!
This week me and Daniel finally got into our lab and met our mentors and we have had a blast. Our mentors got us acquainted with the lab and the projects that we will be working on for the next couple of weeks. (I will be working with Matt and Demetre on Matt's Tiger Rattlesnake project and Daniel will be working mainly on Tony's Flat-tailed Horned Lizard project.)Once acquainted Daniel and I jumped right into the fray running PCR and Gel Electrophoresis on countless samples with countless more to come. (Matt's project has samples from over 10 generations of Tiger Rattlesnakes.)
Even though it might seem a menial task it never gets dull and I know that my work is a big contribution to the group. I know that soon enough these samples will be complete and we will more onto eventually get to move on to more complex things. Tony has even sent samples out to be sequenced and once they get back he will begin teaching us how to find (and what to do with) microsatellites.
I look forward to this and much more in the up coming weeks! --Adios
This first week in my lab with Gladys has been an intense experience! I really appreciate the fact that Gladys wants me to feel comfortable with the lab assignments, so she invites me to ask her any questions that I might have. So far I have been learning about the way that ecstasy (MDMA) causes neurotoxic effects in rats. This research will one day contribute to identification of the causes and effects of neurotoxicity of ecstasy in humans. I believe that my next few weeks with Gladys is going to be such a valuable opportunity. I am beginning to have my own responsibilities in the lab; Gladys has given me the job of running the Protein Determination procedures, which utilizes a spectrophotometer to identify the concentrations of proteins in solutions. When this has been discovered, we can then use the information to determine protein content of cell fractions and use the previously ascertained protein concentrations to run gel electrophoresis. I will also be working on the next steps in Gladys' experiment. She has already injected the metabolites of ecstasy into the rats' striatums (in the brain) and shown that they decrease the level of neurotransmitters in the brain. Next week I will be helping her do a Western blot analysis of the proteins (SERT, DAT, VMAT2, TPH, and TH) from the dissected brain to determine the extent of the neurotoxicity experienced by the rats. Gladys is going to lead me through all of the following procedures so that I understand her methods. I am definitely looking forward to the rest of my internship!
Sorry this is late Marti, I've been out of town at the conference like I told you. I had posted it on the blog earlier, just not here. Sorry again, and I hope things are well with you.
The past two days in my lab have been pleasantly intense. I'm working directly with an undergrad student named Brianna who has been totally understanding of my lack of scientific vocabulary (We end up using the term "stuff" to describe things like cell debris or various reagants in transfections all the time) and has already taught me (nearly) unfathomable amounts of information. I also spend a good amount of time with Jun, a post-doc who gets published about twice a year. He teaches by writing all over absolutely everything, including the walls of the lab, and quizzes me at various times during the day.
I began my internship by meeting the various other workers in the lab, and discovering that I will have my own research project, overseen by myself that will actually be contributing to the research of the lab. I will be identifying the location of the promoter region on the elongation factor 1 alpha-encoding gene. To do this I'll have to synthesize 3 pAaEF-1 alphaGL3 luciferase reporter plasmids. I even understoo that and how I was going to accomplish it after only 30 minutes in the lab! Since I began I have: performed a modified version of the miniprep, ran a basic electrophoresis and analyzed and photographed the gel (thanks for teaching me how Nadja!), ordered enzymes that we will use to induce a double digestion of a plasmid to test whether we can use RNAi (RNA interference) to suppress the experession of various proteins, done transfection with some S2 cells, dissected mosquitoes, isolated genomic DNA of an Ae. Aegypti, and ran a luciferase assay. My days have been cram-packed full of activities that allow me to learn more quickly than I could have imagined. Amazingly I now understand and use most of the terminology heard in the lab that seemed like a foreign language when I started. I'm also able to run my own experiements with Brianna bascially watching over my shoulder to make sure I don't do anything stupid (Luckily, I haven't yet!).
I walked into my lab knowing nearly nothing about the field I would be working in. After only two days I could work by myself in that very same lab and actually know what I was doing! (That's what I get to start next week...) Everyone is totally helpful and always willing to field my numerous questions about what we are doing, why we're doing it, and how that will lead into what we're doing next. I'm so confident walking into the lab now and getting started on any protocl Brianna gives me. I am also having loads of fun. Brianna and I laugh constantly about the randomest things in the lab, like pulling out the guts of a skeeter (that's a mosquito for those of you that don't speak my language :-) ). It is also great fun to run an experiment and obtain results that will actually aid in research. I'm loving everything about the experience and hope everyone else is ahving just as much fun!
It seems like this whole week has just blown by us, well it did for me at least. I'm working with Dr. Orbach in the Marley Building on the Third floor in the labs directly on the opposite side of the elevators on the right hand side (if you are facing south). The first day in Dr Orbach’s lab was pretty much background information, which I found most helpful with the oncoming days. From his discussions, I have concluded that I will be working with a mysterious fungus that has caused the death of a dog here in Tucson. My job, this summer, is to identify what kind of fungus it is by looking at it genetically and morphologically. He gave me a lot of material to read, which helped me comprehend the delicate world of Fungi. Dr Orbach also showed me the lab and some of the people I would be working in the same room with for the next couple of weeks.
I’m working along side a teacher intern, who has two years of lab experience behind her. Her name is Vicky and she has been keeping the lab from becoming too boring and overwhelming. On the second day, Vicky and I did some PCR and Electrophoresis. The graduate student and lab technician Natalia has been showing me and Vicky the ropes. She provided us with instruction on where all the chemicals, tubes, centrifuges, plates, and what not are. Dr. Orbach’s lab is super organized and super neat.
On Wednesday and Thursday, Natalia let us loose on certain tasks that Dr. Orbach wanted us to do. Wednesday, Vicky and I worked with genomic DNA that was collected from sample soils where pets or animals were known to have been affected by Valley Fever and run gels to see if each sample actually had DNA. Today, Thursday, we both took two specified solutions of DNA and made dilutions from it to produce PCR. Our results were pretty much the same. Both of our PCR reactions produced no DNA product. Also, today I went down to the veterinary diagnostics lab to pick up the samples of fungus that I will be working with for the rest of this summer. The fungus actually looks pretty gross and weird and down right dirty. Everyone in the lab is pretty excited about it and I am too, but the fact that it killed a dog worries me.
Hopefully I will be able to start my actual exploration of the unknown fungus soon, but until then I will continue to run tests on a buddy project with Teacher Intern Vicky.
PS. Everyone in Dr. Orbach's lab is really nice and definately eager to help you if you have questions. It's pretty much do your own thing there and try not to bother everyone else too much. The lab has a very chill environment, but I do have to comment on the fact that one of the rooms smells a lot like a fish tank gone south.
14 comments:
Today, June 4, 2007, was interesting for the most part. First off, the ToxStart training at 8:50 a.m. was very informative and fun. I gained so much knowledge about toxicology that really benefitted me later in the day as I began my lab work. I totally understood almost everything that my mentor, Shawn, was talking about! This really gave me a boost in my confidence knowing that I understand the scientific "lingo."
After lunch at about 1:15 pm, I went to the lab I am working in at the College of Pharmacy. I met with my mentor and learned of all the lab equipment used. I also discovered what I am going to be doing. I am working with arsenic, which is a carcinogen found in the bladder cells. After discovering all of the equipment and background information, we went up to a lab to create cell cultures. When Shawn told me I was actually making my own cultures, I was surprised. I always had the idea that I would be the clean up crew. I observed how to create cultures and how to work in vitro. I experienced how it feels to work in a lab and creating cell cultures. I also looked under a microscope to observe the bladder cells.
By the time that was all done with, the time was about 3:30 pm. I received a few more research papers that had basic background knowledge of arsenic and the use of the bladder cells. It is really neat to learn that the bladder cell is vital because it is known as a detoxifier. After having some of my questions answered, I was about to leave and go home. I am so exhausted but I had such good times being in the lab and working as a researcher. Hopefully I feel much more confident in my knowledge and my lab skills in order to reach my peak and do the best possible job I can. That will come soon.
~A. Vo
(To be continued...)
June 5, 2007
Yet again, ToxStart training amazes me again. It is just so fascinating to learn about environmental health because there is so much information involved! Environmental health is defined to be the welfare of people in the environment. We did so many activities that I found to be interesting today. Katy let us test our breathing and see how it feels to be a person with asthma. That was sad because I couldn't breathe at all!! Another thing I remembered was the presentation from Georg Wondrak who presented his work on skin cancer. It was pretty amazing. I had no idea that there were three different types of skin cancer! Now the most memorable part of the training. The group (consisting of Shiana, Alex and Tiffany) and Katy were discussing Hanta virus and I was so curious about knowing what caused it. Me and my big mouth now have scarred me. I discovered that it was caused by mice!! If you all didn't know, my phobia of rodents really kicked in. To put this in simpler terms, I suffered a spaz attack.
After lunch at about 1:00 pm, I walked into my lab down in the basement (AKA floor one) of the College of Pharmacy. Today was practically the most amazing day of my internship so far! I definitely experienced lab work to the max! I watched Shawn, my mentor, work on performing a Trypan Blue Exclusion Assay, which allows the bladder cells to be counted individually. Then after observing, he told me I was doing this...from scratch. I guess in these lab situations, as an intern, you are expected to do whatever it is you may not be expecting to do. I copied whatever Shawn did and was successful in doing it! In a few days, I will have to feed my cells again. That was exciting because I feel like my lab skills are definitely improving one hundred percent. Apparently my counting skills are still a bit rusty because I miscounted cells many times. That was a LAUGH OUT LOUD moment during the day.
After completing the assay, we went back down to the lab and I read research papers for about 15 minutes and then checked out at 4:45 pm. All in all, this day was entertaining, yet educational. This is the balance of fun and work that I am looking forward to everyday. Definitely, with each and every day, my skills in the lab are improving exceptionally and my best has yet to come.
Later everyone-
~A. Vo
(To be continued...)
I have only been in the lab two days this week, but Aysen, the grad student I am shadowing, has already taught me so much. I've helped her run Western blots, DNA amplification and purification, and protein purifications so far. We are working on one of her projects with flagella, the part of E. coli which allows it to be motile. Presently, we are trying to isolate and amplify a specific protein in the flagella with our procedures.
The first day I started Aysen was running three different procedures at the same time, one of which I had never heard of and the other two with which I was only vaguely familiar. It was intimidating at first, trying to jot down everything and make sense of it, but the thick stack of papers I was assigned to read is helping with that. I just read a research paper describing the traits and behavior of different pathogenic strains of E. coli and am on to another stack of papers of how pathogens in general invade hosts.
Today I gave my presentation on my research paper and had some technical difficulties, but it worked out in the end. When I first started annotating this paper, I was really just pushing myself through the sentences, word by word - looking each term up in the dictionary; it was tedious and frustrating. Finally, I mustered some courage and asked Aysen for some advice on how to get through my first big reference paper(although I was sure it was pretty basic material) and she really lessened my work load while helping me understand the content more. Referencing multiple sources (wikipedia!google!mentors!) and focusing on sections of the paper Aysen suggested helped so much!
Next week, I hope to be able to run amplifications and purifications on my own and get a little more responsibility. I'm having a great time in the lab and with the other interns and am really looking forward to our weeks together!
Well, in a three-day span, I haven't been able to cover as much ground as some interns because I was involved with the ToxStart training. We discussed environmental hazards and various other ideas, such as research ethics. It was pretty interesting, and it was easy to understand because I was trained for this in an earlier internship.
Anyway, Mark and I briefly discussed and agreed that the plan would either be a branch off or a continuation of their current research. The plan is to discuss how MEKK4 and Filamin-1 interactions are important for heart valve development. It's been previously shown to interact in other systems and could explain a cause for congenital heart defects. It was shown that MEKK4 is necessary for phosphorylation of proteins.
Currently, we are perfecting the MEKK4 and Filamin-1 immunostaining procedure that is to be performed either Monday or Wednesday, because it is possibly a two-day procedure and we're trying to perfect it as much as we can under the time constraints.
i think this is where my blog is suppose to go!!!!
Hello Fellow Interns Shiana, Tiffany, Kim, Mon-Ning, Logan, Greg, Alex, and Andrew!!!
Oh yeah Hi Marti, Travis, and all other staff that read this post!!!
Okay here it goes everybody-->
I am conducting extensive research in the Wildlife and Fisheries Sciences Laboratory under the direction of Mrs. Melanie Culver (Really great lady by the way!!!). A graduate student by the name of Tony Dee is my mentor; another graduate student who works in the same laboratory is Demetre “I don’t know his last name” (Greg’s Mentor). Furthermore, there are roughly ten other researchers working in the same laboratory researching a variety of different venues ranging from Bob Cats to Rattle snakes I am not sure of the “official” terminology of there research though. This is nice because I am able to see how well others function in the lab setting.
The first day in the laboratory was an AWESOME experience. The mentors were eager to work hand and hand with Greg and myself. The mentors first dove right in, showing us the rules and regulations of the laboratory so there would be NO “cross contamination” while we handled very delicate Deoxyribonucleic Acid (DNA). In the laboratory we proceeded to get familiar with the instrumentation as well as got to know who these people are that we will be working side by side with for the next six weeks OF OUR LIVES!!! We cracked a couple of jokes with one another, found out what types of music each other liked, and also favorite types of movies. I recommend that each intern get to know their mentor on a personal level so it makes for a more enjoyable experience (Not to personal though).
So far in the laboratory we have done trials of PCR (Polymerase Chain Reaction) and have run gel electrophoresis many times. I believe the purpose of the last few days working has been entirely focused on reiterating the protocol and procedures in the lab setting because it is crucial to do everything precisely. Recently, (today) I had the “DISTINCT” PLEASURE of being able to take samples, pieces of ears with hair and blood, which other researchers extracted DNA from living creatures and cut them up into smaller pieces and divide them into specific test tubes. This gave me a sense of self satisfaction because I knew I was contributing in a positive way to the overall mission of the laboratory. As I was doing this task Greg and I conserved with Greg stating: “Hey dude, some undergraduates don’t even get to do what we are doing in the lab…” This made me realize that this internship is a great opportunity for success and will open doors for those who take advantage of the knowledge they acquire.
I would like to conclude my first blog entry by saying “never squander such a valuable resource, understand the investment which your mentors are putting into you.”
-Daniel
Promising Beginnings
This last week and couple of days have been more than I knew to expect. I was surprised at how comfortable I felt with the group of students I was with within the first day of our internship, and then again pleasantly surprised when the comment I made voicing as much was agreed with. Training in a classroom together with Nadja that first day for some four hours did the trick, all right. Despite my existing background in laboratory techniques, Nadja, Jeff, Rachel, and the other students all helped make the review of knowledge fun for me. Much of our days were spent smiling or laughing in between our mini-labs and lectures, both at each other and at side jokes. The presenters that we had the chance to listen to this week were so enthused and animated about their own work that it was hard for me to not be drawn into their projects.
Having been assigned to a lab in the College of Pharmacy, I was required to take an extra toxicology course this second week. I readily appreciated the chance for this additional background before I was fully immersed in my lab work; for a surety, it helped me to better understand the research papers that I had to read for my lab. The teachers and presenters during this segment of learning, which this week included again Marti and Katy, were very willing and patient about teaching us what they thought we could benefit from. Their support and the friendliness of the BIO5 staff I have met so far has definitely made it easier to ask for help and interact with them.
Onward ho to lab life--the exciting part! My mentor's name is Ruiyu Xie (but I call her Rae, for short) and she has been working at the College of Pharmacy for at least three years. She is very easy to approach with questions and explains concepts to me I have not learned yet patiently. Through the past four days we've talked about everything from our backgrounds, families, and friends to even troublesome laptop problems. Dr. Monks was a delight to conversate with when I met with him on Tuesday, as well. He first came from the UK, hence his accent, and came to the U.S. to continue his studies. I also met Rae's best friend who works under Dr. Lau, Chi Lin, who I discovered knew my parents! I had no idea. Not only that, but a former student of my high school and a friend of my older sister's, is also volunteering in Dr. Lau's lab this summer. Evidently, it's a small world. I have also made friends with so many other undergraduate and graduate students that I look forward to seeing them every day around the lab.
Research-wise, I will be working with a mitochondrion-specific peroxidase called peroxiredoxin III (Prx III). Past research suggests that the enzyme Prx III is a critical regulator in the redox stage of a cell. Reactive oxygen species (ROS) must be reduced ultimately to compounds that consist of mainly water so that they do not harm the cell. Catalase, glutathione peroxidase (GPx), and Prx can all reduce a ROS called hydrogen peroxide, but the mitochondrion lacks catalase and must import glutathione (GSH). The only enzyme that it inherently has to perform this job is Prx; however, specifically Prx III in mitochondria. Past research has discovered that there is about 30 times more Prx III than GPx1 in the mitochondria. This seems to indicate that Prx III may have more roles than the regulation of apoptosis in the mitochondria.
In order to further determine the function of Prx III, I will render Prx III unable to function in a live cell and observe what cell processes no longer proceed normally because of its 'absence.' To disable Prx III, I will mutate it by replacing two specific amino acids in it called cysteine (Cys) 108 and Cys 229 with another amino acid called serine (Ser). These two particlar Cys amino acids were chosen because they have been found in past studies to form the disulfide bond necessary for Prx III to function. Ser was chosen to replace Cys because it is the most similar in structure to Cys and it will not change the three dimensional structure of Prx III.
So far, Rae and I have sent in a viral plasmid to be sequenced (for which reasons will be saved for another entry) and must wait until the results are returned in order for us to proceed with the next step of our experiment. Though our plasmid was sent in two days ago and were expected to be finished sequenced before today, we should receive them for sure tomorrow. Then, the real lab work begins. Meanwhile, we have designed two mutagenesis primers that we ordered today--a process that included locating and then translating the Prx III's nucleotides into amino acids, locating the specific amino acids of interest in terms of nucleotides, figuring calculations, and comparing primer possibilities to find the optimal ones. The completion of this project will be beneficial to the research of a great many people working in the same field, and I am more than ready to put my eager energy and time into it.
What a week it has been! The only thing more exciting is the promise of more to come!
This week me and Daniel finally got into our lab and met our mentors and we have had a blast. Our mentors got us acquainted with the lab and the projects that we will be working on for the next couple of weeks. (I will be working with Matt and Demetre on Matt's Tiger Rattlesnake project and Daniel will be working mainly on Tony's Flat-tailed Horned Lizard project.)Once acquainted Daniel and I jumped right into the fray running PCR and Gel Electrophoresis on countless samples with countless more to come. (Matt's project has samples from over 10 generations of Tiger Rattlesnakes.)
Even though it might seem a menial task it never gets dull and I know that my work is a big contribution to the group. I know that soon enough these samples will be complete and we will more onto eventually get to move on to more complex things. Tony has even sent samples out to be sequenced and once they get back he will begin teaching us how to find (and what to do with) microsatellites.
I look forward to this and much more in the up coming weeks! --Adios
This first week in my lab with Gladys has been an intense experience! I really appreciate the fact that Gladys wants me to feel comfortable with the lab assignments, so she invites me to ask her any questions that I might have. So far I have been learning about the way that ecstasy (MDMA) causes neurotoxic effects in rats. This research will one day contribute to identification of the causes and effects of neurotoxicity of ecstasy in humans.
I believe that my next few weeks with Gladys is going to be such a valuable opportunity. I am beginning to have my own responsibilities in the lab; Gladys has given me the job of running the Protein Determination procedures, which utilizes a spectrophotometer to identify the concentrations of proteins in solutions. When this has been discovered, we can then use the information to determine protein content of cell fractions and use the previously ascertained protein concentrations to run gel electrophoresis.
I will also be working on the next steps in Gladys' experiment. She has already injected the metabolites of ecstasy into the rats' striatums (in the brain) and shown that they decrease the level of neurotransmitters in the brain. Next week I will be helping her do a Western blot analysis of the proteins (SERT, DAT, VMAT2, TPH, and TH) from the dissected brain to determine the extent of the neurotoxicity experienced by the rats.
Gladys is going to lead me through all of the following procedures so that I understand her methods. I am definitely looking forward to the rest of my internship!
Sorry this is late Marti, I've been out of town at the conference like I told you. I had posted it on the blog earlier, just not here. Sorry again, and I hope things are well with you.
The past two days in my lab have been pleasantly intense. I'm working directly with an undergrad student named Brianna who has been totally understanding of my lack of scientific vocabulary (We end up using the term "stuff" to describe things like cell debris or various reagants in transfections all the time) and has already taught me (nearly) unfathomable amounts of information. I also spend a good amount of time with Jun, a post-doc who gets published about twice a year. He teaches by writing all over absolutely everything, including the walls of the lab, and quizzes me at various times during the day.
I began my internship by meeting the various other workers in the lab, and discovering that I will have my own research project, overseen by myself that will actually be contributing to the research of the lab. I will be identifying the location of the promoter region on the elongation factor 1 alpha-encoding gene. To do this I'll have to synthesize 3 pAaEF-1 alphaGL3 luciferase reporter plasmids. I even understoo that and how I was going to accomplish it after only 30 minutes in the lab! Since I began I have: performed a modified version of the miniprep, ran a basic electrophoresis and analyzed and photographed the gel (thanks for teaching me how Nadja!), ordered enzymes that we will use to induce a double digestion of a plasmid to test whether we can use RNAi (RNA interference) to suppress the experession of various proteins, done transfection with some S2 cells, dissected mosquitoes, isolated genomic DNA of an Ae. Aegypti, and ran a luciferase assay. My days have been cram-packed full of activities that allow me to learn more quickly than I could have imagined. Amazingly I now understand and use most of the terminology heard in the lab that seemed like a foreign language when I started. I'm also able to run my own experiements with Brianna bascially watching over my shoulder to make sure I don't do anything stupid (Luckily, I haven't yet!).
I walked into my lab knowing nearly nothing about the field I would be working in. After only two days I could work by myself in that very same lab and actually know what I was doing! (That's what I get to start next week...) Everyone is totally helpful and always willing to field my numerous questions about what we are doing, why we're doing it, and how that will lead into what we're doing next. I'm so confident walking into the lab now and getting started on any protocl Brianna gives me. I am also having loads of fun. Brianna and I laugh constantly about the randomest things in the lab, like pulling out the guts of a skeeter (that's a mosquito for those of you that don't speak my language :-) ). It is also great fun to run an experiment and obtain results that will actually aid in research. I'm loving everything about the experience and hope everyone else is ahving just as much fun!
Hey Guys,
It seems like this whole week has just blown by us, well it did for me at least. I'm working with Dr. Orbach in the Marley Building on the Third floor in the labs directly on the opposite side of the elevators on the right hand side (if you are facing south). The first day in Dr Orbach’s lab was pretty much background information, which I found most helpful with the oncoming days. From his discussions, I have concluded that I will be working with a mysterious fungus that has caused the death of a dog here in Tucson. My job, this summer, is to identify what kind of fungus it is by looking at it genetically and morphologically. He gave me a lot of material to read, which helped me comprehend the delicate world of Fungi. Dr Orbach also showed me the lab and some of the people I would be working in the same room with for the next couple of weeks.
I’m working along side a teacher intern, who has two years of lab experience behind her. Her name is Vicky and she has been keeping the lab from becoming too boring and overwhelming. On the second day, Vicky and I did some PCR and Electrophoresis. The graduate student and lab technician Natalia has been showing me and Vicky the ropes. She provided us with instruction on where all the chemicals, tubes, centrifuges, plates, and what not are. Dr. Orbach’s lab is super organized and super neat.
On Wednesday and Thursday, Natalia let us loose on certain tasks that Dr. Orbach wanted us to do. Wednesday, Vicky and I worked with genomic DNA that was collected from sample soils where pets or animals were known to have been affected by Valley Fever and run gels to see if each sample actually had DNA. Today, Thursday, we both took two specified solutions of DNA and made dilutions from it to produce PCR. Our results were pretty much the same. Both of our PCR reactions produced no DNA product. Also, today I went down to the veterinary diagnostics lab to pick up the samples of fungus that I will be working with for the rest of this summer. The fungus actually looks pretty gross and weird and down right dirty. Everyone in the lab is pretty excited about it and I am too, but the fact that it killed a dog worries me.
Hopefully I will be able to start my actual exploration of the unknown fungus soon, but until then I will continue to run tests on a buddy project with Teacher Intern Vicky.
PS. Everyone in Dr. Orbach's lab is really nice and definately eager to help you if you have questions. It's pretty much do your own thing there and try not to bother everyone else too much. The lab has a very chill environment, but I do have to comment on the fact that one of the rooms smells a lot like a fish tank gone south.
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