Final Presentation

This summer research experience has been eye opening since day one. I found myself eager to investigate the links associated between cancer and pesticide exposure here in the central valley. At first I thought it would be simple to find data bases that would provide me with data specific to our counties in the San Joaquin Valley and I could correlate these to the pesticide usage per country. However, I learned that it was not as simple to work with this population and I could only imagine how difficult it is to work with farmworkers, specially migrant farmworkers who are constantly migrating in our state. Interesting findings I found stated a higher incidence of prostate cancer by 14% among licensed restricted use pesticide applicators than for other men in North Carolina and Iowa in specific those being exposed to methyl bromide. The Agriculture Health Study, also identified pesticides that presented a positive relationship with cancer. These studies all suggested further investigation due to many limitations in the study. I then looked at the residential proximity and the incidence of breast cancer but the studies I encountered found no evidence that women living in area of recent high agriculture pesticide presented higher breast cancer incidence rates. Limitations to these studies stated that pre-existing historical data on agricultural pesticide use in conjunction with data on residential histories for those with or at risk of cancer were not available or easy to collect.

Not being able to directly find a link between pesticide exposure and cancer due to the limitations when looking at this population of farmworkers and not having the data to work with sparked a greater interest in me in this area of research. I came across a literature search which focused on the acute pesticide illnesses associated with off target pesticide drift from agricultural applications and I could easily relate to the study because I come from a migrant farmworking family and my parents themselves have presented acute pesticide illnesses due to the pesticide exposure through their job occupation. Headaches, rashes, dizziness are some of the symptoms my parents have complained about after coming home from a long day of work out in the fields; this literature search identified children at higher risk for non-occupational exposure which lead me to my last research study, the C.H.A.M.A.C.O.S. study.

This longitudinal birth cohort study examines pesticide chemicals and other environmental factors that affect children's growth and developmental health. Although it is a recent and small cohort study which began enrolling children in 1999-2000 I find it a potential future population study that can grow and provide cancer incidence rates and data on other health complications among these children who have been exposed to pesticides since before they were born. The study also shows a disparity observed among farmworkers and their family which are at higher exposure to pesticides which results in various health complications.

All in all, this experience has reassured my passion for research in specific to research among the latino farmworkers population. I hope to continue to be involved in research that focuses on the pesticide exposure among farmworkers and the disparities among this group of individuals. I admire and respect the work of researchers because even though I did not find any great discovery through my work I was able to observe the team work among all research studies which contribute in their own way to the bigger picture of identifying potential carcinogens and health disparities. There are so many factors to consider and take into account before making any correlation between data that is acquired and that is something I have profoundly learned and still need further guidance with. I am thankful for this opportunity to be a part of this years Cancer Research Scholars which has exposed me to a possible future career in research available after my undergraduate education.

Week 7

It's crazy how quickly the time passed. I feel like it was just yesterday that we moved in and got our lab assignments.

This past week was pretty productive. We completed a couple western blots with which I feel pretty comfortable. Dieter has also taught me a couple of new techniques and procedures. We did a DNA extraction from the yeast cells and were able to run a pcr (comfortable with that too) from it. He also showed me how to run digests for different things. The first was a DNA digest where we verified that certain plasmids were correct. Second was the protein digest. He had some GFP and wanted to verify that it was in each sample.

On Friday, we went to Blue Water Seafood Market & Grill. I had eaten there with Alex last year, and the food was equally good this time. I definitely recommend it for the group next year.

The end and final presentations are coming up quickly. School is also just around the corner. We'll see how I deal with the return to the Fresno heat.

Week 7

This week, we were able to figure out an idea of why we were not seeing binding in PR3 :) in a Dot Blot. We went ahead and tested our idea and finally were able to get PR3 binding in a Dot Blot :) Aside from Dot Blots, this week we got to prepare for the Proximity Ligation Assay by doing cytochemistry with mouse neutrophils. Next week we will be continuing with this and hopefully have a PLA done in time for our final presentation. Aside from lab work, this week the Salvesen lab had their annual beach party (very fun and relaxing). I had a delicious California burrito made of carne asada with french fries and sour cream :)

Week 6

This was a very busy week, we repeated many Dot Blots. We troubleshoot by changing the protein and probe concentrations and we still were not happy with our results. We had a spotty background, or fluorescence where we did not want to have a signal. Finally we left for the weekend with a good Dot Blot that had the signal where there needed to be one for HNE. However we still saw no binding of probe in PR3 :( in a Dot Blot, but there was PR3 and probe binding in a Western Blot.

week 6

We spent the 6 week performing mostly dot blots in order to determine the correct concentration of probe to use in the Pla assay. We also spent part of week trouble shooting because we were getting mixed results from our dot blots when using different concentrations of enzyme. We ran two Dot Blots in order to test if our concentrations were correct and to see if washing the nitrocellulose membrane in the Dot Blot apparatus had an effect on fluorescence. After developing our membrane we determine that washing the membrane in the Dot Blot apparatus was decreasing the intensity of the fluorescence. Once we knew that our dilutions were correct, we needed to come up with an explanation as to why we were seeing different results for our Dot Blots and Western Blot when using the same concentration of enzyme. This problem will be tested next week, and we will also get started on our Pla assays.

My Experience as an Intern Week 6

     Yay! The NMR was finally fixed, Jose and I had the opportunity to shadow Elisa during both the sample prep and the NMR screening. The only downside was that the sample changer was still not working and Elisa had to go and manually change the sample every 30 min.
     It was an incredible experience to be inside an NMR facility. These machines are huge. It is not a great scenery but the excitement comes from knowing how powerful this piece of equipment is. It has the capability of giving you information bits of the chemical components to build the map of protein and identify what shifts the peptide has generated by binding to the protein.
      Most of our week was centered in protein expression and purification and NMR specrtra analysis. Jose and I scanned all of the 76 spectras in four days. More detail about this and the steps to follow will be provided in the presentation this week. At the end of week 6 we had the fantastic news that the sample changer was fixed and is know working beautifully.

Week 6

     This week, we returned to a sense of normalcy. Judith helped us immensely, and we ran western blots, a couple PCRs, and polysomes. Since we didnt get any results from our western blots last week (we now realize it was due to technique error), we carefully reran the ssa2 (24hr on, 1 hr recover) blot. the images we developed were good and conclusive. Unfortunately, we flubbed the transfer for the sks2 membranes since no one set a timer. We will rerun the blot on Monday.
     The polysomes were not conclusive. We used the 24hr on +5hr recovery ( switching from EMM to YES media) samples. The profiles did not reveal a rescue effect, so we will run western blots to see if there was enough of the protein expressed.

This Friday, we went out for dinner. Pizza on Pearl is an Italian restaurant that I had previously visited. We split a pizza which was a welcome break from cooking. On Saturday, I went exploring in the area surrounding the campus. We had some old bread, so I was looking for some seagulls (and birds really) to feed. I must have walked about 4 miles looking for some birds. I went all the way out to the glider port but decided that the 2 mile hike down to the beach was a bit too far just to feed birds. When I came back, I walked around the Eleanor Roosevelt College (ERC)  campus and found a bird by a dumpster. After feeding it a piece, it decided to fly off. Instead of chasing after the bird, I left the remaining bread on the ground by a dumpster, so the bird could return and eat it.

This weekend has been particularly windy, and there have been numerous people flying in gliders and hot air balloons. There is a great view of both from the apartment.


That's all for now. Im looking forward to the presentations this Friday. I will check-in in a week's time.

Week 5

     In week 5 I enjoyed learning how to do Dot Blots, especially how we were able to adapt the protocol to use the technique with the probes of interests. Although we had some setbacks with some of our Dot Blots not obtaining what we expected, I was able to learn a new tool and how to adapt a protocol and get the expected result. This week we also did kinetics with PR3 and substrate four. It was observed that this enzyme is not soluble. It was interesting to see the difference between a non-soluble enzyme and a soluble one. In addition I was very glad we were able to get results for the presentation and I agree with Philip, this round of presentations went smother. I was able to apply some presentation tips Dr. Salvesen gave to Luis and me, which was very helpful. 

Week 5

 First off, I would like to apologize for not posting earlier and for not posting last week. I had a little issue locating the blog. I have two Google accounts so I would sign in with my other account onto blogger and the blog would not appear. Now that I had some time to think about and solve the issue, I have located the blog in my other account as you guys probably figured out if your reading this. Anyways now for the science...

      In week five we have finally acquired enough Bid protein to run the NMR! Like, anything else we have done in Pellecchia's Lab, they want us to acquire the necessary background and knowledge to be successful in an experiment and to give us an idea of why and how things happen. Saying thus, we were given a number of articles on NMR, which included how it works, what region to look at in our experiment, the advantages, disadvantages, etc. After going through the articles we briefly helped Elisa (our post-doc) preparing the NMR tubes to get ready for the screening. It was delayed because both of the NMR machines were down.  She also explained to us the project much more in-depth and what exactly are we looking for. In the mean time while the delay we started to express EphA3, once again.

    The second presentation was also held in week 5. I believe everyone has encountered their share of successes and failure, which is nice to sit down and talk about the failures as much as the successes. I felt everyone more relaxed, during the presentations because we knew what to expect. Overall, I believe everyone did a good job and just need to continue implementing  everyone's advice and continue working hard and with a purpose.

 

My Experience as an Intern week 5

     This was a great week and a not so great week. Elisa was able to use the protein we purified to run a 1D HSQC NMR experiment of our protein. From the spectra we can tell that there is nothing wrong with our protein it is well folded. Elisa one of our lab mentors, has a sample of very precious protein that she needed to screen, and was just sitting in 4℃. Jose and I were going to learn how to set up the sample for NMR analysis, unfortunately, one of the NMR machines was not working. The second machine was working there were some issues with the sample changer but Elisa said we could do this manually.  Then, sadly there were some issues with the sample changer and Elisa could not start the experiments over the weekend.

     In regards to protein expression, Jose and I started to express the second protein of interest. Unfortunately, we did not get good purification or yield. We are going to give it a second attempt.  Along with the laboratory work, we have also been learning background information necessary for NMR use, and understanding. Elisa is great mentor and does a great job simplifying the concepts for us.

     I really enjoyed learning about all of your advancements and struggles in your respective experiments. It is great to hear about what we all do. I wish you all great luck in your experiments and I am excited to hear more about what your findings are. Wish you all have a great week  J .

week 5

Last week was a busy week, one of my priorities was to obtain data from our Dot Blots so that Claudia and I could have something to present on Friday. The main focus of the week was understanding Dot Blots, learning how to performed a Dot Blot, and determining the right concentration of antibodies use for the Pla Assay. Although we didn't get to scan our Dot Blot with HNE we still got good data which we presented on our Friday.

Week 5

During the week I met with Chuck in order to go over some of my data and my approach to analysis. After talking with Chuck and determining what type of approach I would take in data analysis, I quickly saw that there was not enough data available for the specific regions I had in mind. Thus, as I stated in the presentation this presented itself as a limitation for my project.

After presenting on Friday I received quite a bit of helpful questions and suggestions. As suggested, I will now try to look at obesity over 5 year increments (of the data is available) for all California counties instead of just San Joaquin valley. Thus, I will be attempting to do a comparison of the specified variables between different regions or groups of counties. In doing this I will be able to see if there is a trend and better establish whether or not there is a relationship between obesity and prostate cancer.

Another insightful suggestion I received was to look at whether there was more than just a linear relationship between the two variables. Obesity is a complex disease and it is likely that the relationship with cancer (if it exist) is more complicated than thought to be. I will continue to meet with my mentors and see if I can establish a better plan of analysis and hopefully depict clearer and more in depth results.


Overall, it was interesting to see how everyone's projects are going along. It was also a relief to hear that others were experiencing some difficulties as there projects progressed as well.

Week 5

      This week was particularly interesting. We spent the week without Judith or Dieter in the lab all the time. We performed a couple western blots. It was different working independently. Since we didnt get any definitive results, I question whether I did each part properly. I appreciate the suggestion to use the control to see if there were any error in the procedure.

  This weeks presentations also went by smoothly. It seemed like everyone was much more relaxed since they knew what exactly to expect. The updates on the projects were informative.

Finally, today, Jose, Luis and I went to Rock Bottom to watch the final of the Gold Cup. It was a fun and good time. We dont have espn so it was fun to watch sports on the big screen.

That's all for this week.

Week 4

Hello everyone, on week4, we were not able to commence our PLA due to time constraints. My thoughts for week four were, it would be a very busy week, lab wise, but as you have read it was not the case, because we only had two full work days. This does not mean we were not busy, because we were, but doing other things. Here is what we did, we attended Dr. Salvesen’s talk that was given to the Summer Bridge students at UCSD on Monday July, 15. I really liked the way Dr. Salvesen presented on apoptosis. Specially how he gave names to the proteins depending on the role they have on the pathway. It was the first time I heard the proteins be called jury, judge and executioners but it reinforce his explanation of the apoptotic pathway. All of the six interns worked on a presentation we did for Journal club at UCSD for the Bridge program. In addition, we had the opportunity to attend the 2013 Cancer Center Post-doc/Graduate student retreat. I had a great time at the retreat. I enjoyed learning what other types of research is taking place at Sanford Burnham’s Cancer Center. In addition, it was very interesting to see the graduate students presenting styles. Some of the presentations were added to some of the best presentations I have seen in my life. I really enjoyed the presenters that made their talks into a story. They had very good transitions from one slide to the next or from one experiment to the other. They made it clear that you need to have many experiments to test your hypothesis. Finally but not least, Luis and I got to take a look at protocols of the techniques we will be using for Week 5.

week 4

Last week was a very slow week because we did not get to do much lab work due to events that took place outside the lab. On Monday we attended a seminar on programmed cell death given by Dr. Guy Salvesen which helped me better understand the Neutrophil project. Then on Wednesday we had to review an article on cell death for the students in Bridge program. On Thursday we attended postdoctoral retreat in which graduates students and research professionals gave presentations on the projects that they were working on. It was a great learning experience watching them present their data and I plan to use what I learned on my future presentations.

Week 4

This week was very different from the weeks prior.

First, we presented an article by Dr. Salveson et al that discusses the activation of the apical caspases. We were able to split the presentation between the 6 of us. I think it went really well. A few people asked questions, and more were baffled that we found some problems with the science (more so the presentation of) in the paper. Afterward, a couple of the Bridge program organizers commended us on a job well done.

Secondly, we attended a retreat/ symposium on Thursday. We saw many presentations by grad students and post-docs. I found it a bit hard to follow at time since they used advanced terminology. Overall, I thought it was an in depth look at the lab experience of PhD/post-doc. During lunch, a couple of us met Dr. Ze'ev and Bill. With Dieter (Dr. Wolf wants us to address him as Dieter), they discussed the perils and problems of acquiring funding and maintaining a lab. The sandwiches served at lunch had interesting combinations of flavors; roast beef with a weird horseradish and turkey with a cranberry jelly.

This was our first full week with Dieter in lab. He helped us perfect our PCR technique and troubleshoot it. On Friday, we ran a gel to examine our PCR from Wednesday, and IT WORKED! This next wekk will be interesting since both Dieter and Judith will be out of lab. We will be running western blots and PCRs to look for different things.

Lastly, I went exploring on Saturday. I grew weary of hanging out in my room, so I walked around the village east. There are some cool terraces on the 12th floor ( or on top of one of the ecoflats building) where you can relax. I spent a couple hours reading my book. On Saturday, I also adventured to Serra Mesa where I got a haircut at one of the oldest barbershops in the area.

This is all for now. I will check in again soon!

July 19

Jose and I just met with Dr. Kwon yesterday afternoon and we discussed once again our data research. We had been looking through SEER at the various data sets available in regards to breast cancer and prostate cancer. Looking at county level and the hispanic population in particular in comparison to other groups showed that the white race presents both higher incidence and mortality rates. Dr. Kwon then suggested we take a different approach and focus on the risk factors of different groups. Another interesting observation was that there was a clear decrease of incidence and mortality rates over time which is great! But it is also interesting to look into the possible diagnoses or treatment that have made this possible. There is also disparity on genetics that could be approached in our study and further research will be conducted to find studies that are focused on this particular area.

Week 3 Experience

My week three experience in the lab was definitely a new and exciting learning process. I can say the researching and preparation, before the actual protein expression was definitely helpful. It gave me a great insight on the whole process and the science of why things are done and happen in the expression. Since our post-doc mentor was on vacation, we were paired with John Stebbins, a fellow scientist in the lab. He was definitely helpful and showed and explained each step of the protein expression. Our results were not what we expected, as we did not obtain a high protein yield. We will re-try the expression next week on our own. I definitely feel prepared and excited to re-do the expression without any major assistance besides some questions we may have during the expression.

Week 3 also consisted of our first Fresno-Sanford Burnham journal conference. I felt that the presentations were good, overall. A lot of great suggestions were said, that I believe should be inputted into future presentations. I definatley felt prepared and comfortable for the presentation, as we had practice runs and advice from Dr.Pellecchia and John. I look forward to starting the protein expression next week on our own. 

My experience as an intern week 4

          Jose and I were left on our own. We were to start the protein expression protocol on our own with out major guidance from the scientist. If we had any questions we could freely ask and were given a response. We were bothy really enthusiastic about running the autoclave and setting up our media to start cultures to work with today. To our dismay, the autoclave was not working :( Jose and I had our day all planned. The scenario reminded me that things especially in biology do not always go as expected. The nonfunctional autoclave would move us a bit behind of our planned out schedule. Luckily, after attending Dr. Salvesen's talk and then meeting with the rest of the cohort (to dissect the journal article we will be presenting for journal club at UCSD) we went to the autoclave and a kind person had already placed our flask in the autoclave. Our day was saved by this act of kindness and we successfully started the cultures.

My experience as an intern during week 3

          My third week working in the lab was great. I was happy to start working and getting my hands on the pipetters. We were introduced to the technique optimized for the expression of the protein in E. coli BL21 starr cells to grow batches of bacteria. I enjoyed seeing how the equipment at the institute has facilitated the smooth progress of experiments. Personally, I was thrilled to learn a new technique that assist in lysing cells open. There is a pressure homogenizer to lyse cells open, never before had I seen one, since I am most familiar with the use of the sonicator. We also worked on our first presentation related to the project. Dr. Pellecchia even gave us feed back via e-mail. It was great to get suggestions from abroad. As soon as we completed the expression of the protein of interest we ran the sample on an SDS PAGE. Unfortunately, our protein expression did not go s planned, we did not get the results we expected.

          Presentations went well. Personally, both Jose and I identified some areas of improvement and got some ideas from the other presenters. In respect to the other presenters, I just have some comments that I think will help the audience understand the information. Some of the explanations should be somewhat simpler and please label graphs, charts and diagrams. Some slides did not contain titles on their figures or axis and this was somewhat confusing. Including this sort of information would really come handy, because the audience will have more time to focus on what you are delivering instead of attempting to decipher what the graphs are representing.

Week 3

Hi everyone, I really enjoyed learning about what you all were working on for the past three weeks. I look forward on learning more on everyones research and see what their outcome is. So this past week, Luis and I continue to do Kinetics with the assistance of Dr. Salvesen and Scott. The process we went through to obtain good results was interesting and a great learning opportunity. Luis and I found out that data obtained from kinetics can be misleading because not all data obtained is what it appears to be. We got data that looked like it was good but in reality it did not graph a nice Michaelis Menten or a linear graph. Eventually, after Scott’s and Dr. Salvesen’s troubleshooting we were able to get good results by lowering the substrate concentration. So as all of you have learned, this week (week four) we will be  working on NETs and PLA and I am super excited.  

Week 3

This week went by fast and the presentation on Friday only added more pressure for Claudia and I to complete our Enzyme kinetics so that we could have data to present on Friday. I was not happy with the presentation we gave on Friday and I know that it could have been better. I have learned a lot from my experience this week and I will prepare myself better for the next presentation.

Week 3

     This week went by really quickly. In lab I learned a few more techniques. We ran polysome profiles, and made the gradients that go with them. On the profile, each peak corresponds to part of the lysate of the cells. The first big peak is the lysate which is full of extra protein and light cell parts. After that, we have peaks for the 40s and 60s subunits of the ribosome. The 80s comes next. Following the 80s, we come to the polysomes ( strands of mRNA with multiple ribosomes actively elongating). The higher the peak the more of the respective substance is in that layer. It has been observed that when eIF3e is deleted we see fewer high number polysomes ( polysomes of 3 and higher).

     This week I finally got to meet Dr. Wolf. He had been out of the country for the past few weeks. He helped us optimize our PCR. We ran our DNA again and still have to interpret the images from the gel.

     On Tuesday, we had dinner downtown for Jose's birthday. Trying to find parking was awful. Luckily, I found a garage that wasn't too expensive nor was it too far away. For dinner, we ate at Yardhouse which was an interesting restaurant. Since we don't ESPN in our apartment, it was nice to be able to watch some sports again.

    Lastly, we had our first presentation this week. I think it went really well for everyone. It was interesting hearing about the projects and hearing the PIs' various questions. It was particularly entertaining to see Dr. Wolf and Dr. Salveson go back and forth discussing the details of the Salveson project.

Week 2

As everyone probably mentioned, this week was a short one due to the holiday. Although it was a short week, Luis and I were as busy as last week. We got to run several SDS-Page gels. In addition we were able to learn and shadow the rest of the steps needed for a western blot. We also learned more about our project and did some enzyme kinetics, which we will continue to do on week three.

My experience as an intern during week 2

As a result of the July 4 holiday, our time spent in lab during week #2 was only three days, during which Jose and I continued to learn about the project we will be tackling for the remainder of our time here at the institute. Most of our time was spent working on our power point presentation. We also had two meetings with Dr. Pellecchia. He introduced the new protein EphA3, that he and his lab members are interested in studying further. He gave us a brief overview of the overall aim of the project and indicated what direction the project is headed to. I am thrilled to start actual experiments on Monday. I will definitely keep you all posted on our experience in the bench. A postdoc will be assisting us with protein expression of Bid. Jose and I will be busy bees for the duration of this third week :). I am filled with excitement to start working and I can't wait to see how the project progresses as the weeks go by, especially since I will be learning about NMR. The application of this technique is new to me and I am really excited to add it to my tool box at the end of the summer :)

Week 2

          Another week has past us by at Sanford Burnham and I have to say I am really becoming comfortable with our project, which deals with the protein Bid and EphA3. Our goal is to identify and possibly synthesize peptide(s) that bind to Bid. We plan to do this by first purifying and expressing the protein, screening the library of compounds by NMR, synthesizing the individual peptides, and finally characterizing the peptides. Through this point, we have been detailing our course of action, mapping out our deadlines for our eight weeks here,  intensively researching and gaining more background knowledge for our project and formulating our presentation for this upcoming week. Since our post-doc mentor,  Elisa is on vacation, we have been able to interact with Dr. Pellechia more on a daily basis. He has clearly mapped out and explained his expectations and has also been a big help in regards to our presentation by giving us pointers and constructive criticism. I am actually pretty excited to present! This upcoming week is when the real fun starts as we will be commencing our protein expression of Bid!

Week 2

     Since there are holidays for the 4th and 5th, my second week in lab has come to a close.

     This week we mainly ran PCRs for ssa2 and sks2. Unfortunately, none of the gels have given us results. Subsequently, we have spent time trying to troubleshoot our methods. We have tried a rerunning the samples (while being more meticulous), running the samples on a temperature gradient, trying samples with new forward and reverse primers, and finally trying the sample on a different machine. Since none of those improved the images we got, Judith recommended that we try using different concentrations of the parts of the PCR (eg less concentrated genomic DNA).

     Fortunately, I have become much more comfortable with making the gels, performing the electrophoresis, and imaging the gels. Judith is an excellent teacher and is always there to help me improve my techniques, expand my knowledge, and answer all of my questions.

   Finally, we ran another part of our western blot. We added rabbit antibodies to get a darker result. Judith explained that the rabbit antibodies are not as specific as the ones we used previously (the rat), and it showed on the picture. There was a significant increase in the unspecific binding, and the image was "dirtier" (the image was darker and there were many sections with a dark haze).

   This week I started commuting by bike to Sanford-Burnham. It is much faster than walking. That is unless you get a flat tire which happened when I tried to return today. It was a lovely walk with my bike on my back!

    I'm looking forward to next week and learning more. So far, it has been very educational and a lot of fun. Judith is a patient and great teacher! I am starting to feel much more comfortable with the pipetting, gel electrophoresis, and the other procedures that we performed.

Hard at work in the Salvesen lab

Kinetics

Claudia and Luis hard at work on enzyme kinetics, with Scott Snipas.  Everyone is still smiling!

Naturally the first experiments conducted by Scott and Guy Salvesen went a bit wrong, but a swift change of buffers, and the capable hands and minds of Claudia and Luis saved the day, just in time for the holiday!

Salvesen Lab Week 1 06/24/13-06/28/13

The first day at Sanford Burnham was the day I found out the lab I was placed in, it was Dr. Salvesen’s lab. I was very glad and excited when I received this news because his lab is an Apoptosis lab. This day also included completing HR paperwork, a tour of the facilities, and receiving our access and id cards (id cards could not print at first but by the end of the day the problem was solved). Finally each of the students were left at their respective labs and the first thing Luis and I did, was safety training in the computer. We then did over night stocks and cell cultures for a mini prep the lab manager (Scott) then completed on tuesday.

On the second day, all the interns headed to UCSD for an orientation. Firstly, we heard a talk on group study and journal club. Believe it or not, I actually got good pointers on what to tell my future students how to benefit from group study, because not only do I have my self perspective, but those from fellow students and faculty. Secondly, we went to lunch and then tour the West campus (includes the Medical School and Biomedical Sciences). Lastly, but not least, we heard a talk on goal setting, speaking, and presenting.

On the third day, we had orientation with Dr. Salvesen. We went over the Bridges schedule (UCSD program for accepted and prospective students) and establish we will be attending the first two journal clubs and Dr. Salvesen’s talk. This will allow us to get an idea of how we are suppose to present our Journal club on July 17 in the Bridges program. In addition the dates for the video conference were decided. Afterwards Luis and I met with Dr. Salvesen and Scott to talk about our project. Our project is on NETosis and elastase. We will look at enzyme kinetics and western blots. Then we went to hear a talk by a colleague of Dr. Salvesen’s, Dr. Zhen Jiang on the “Imbalance between neutrophil elastase and its inhibitor alpha1-antitrypsin regulates metabolic function in obesity”. In addition we also stacked an SDS-Page gel and loaded various proteins to be use in the test of a new transfer method.

Thursday involved looking for research articles and reviews on NETosis. Luis and I also attended Dr. Salvesen’s Journal club. This was an interesting experience, because we were not given the paper, thus we did not read it. At first I was clueless but then I was able to understand some of what they were talking about. The good thing is we will be added to the e-mail list. Finally, we went to biosafety for about two in a half hours and then called it a day. On Friday, Luis and I stacked two SDS-Page gels, and made buffers required for the protocol we shadow Scott on the enzyme activity of proteinase 3 and elastase. This was going to be a short project Luis and I were going to work on but since the results are needed ASAP we shadow Scott. For next week we will be loading the proteinase 3 and elastase samples into SDS-Page gels and work on getting the enzyme kinetics.

My first week was a busy week and I am looking forward to the following weeks. I am very excited in completing our project and seeing the outcome of our hard work (Luis and mine).

My experience during week #1

My week mainly consisted of orientations, tours, safety training, and employment paperwork. Most of my time out of lab was spent getting familiar with the routes to the institute and auditorium where the UCSD seminars will be held at. In lab we were introduced to the research project that a post-doctoral fellow will be training Jose and I. Unfortunately for us, she happened to started her two week vacation. Next week we will be meeting with Dr. Pellecchia. We will be showing our presentation and getting more details on the specific project we will be working on. I did not want to give too many details on the project itself since I don’t know what is shareable and what is not. Let me say that I am very excited for the project that I will be working on. I love the lab space, it is huge compared to what we have in Fresno. There are several rows of bench spaces. Everyone seems very professional and dedicated to the research in the institute. I personally felt in love with the laboratory lay out and the library. Like all the buildings in the institute the library is accessible with a key card and you can go any time you like, which I consider very convenientJ. Oh and printing is free (which is a bonus) I spent a great time this past week researching information on the protein and protocols important for my project.  Over all in my first week I have discovered that this top institute has many great things to offer in addition to the great science. If you are interested in learning more details of my experience this week, below is a more extensive report. Hope you all have a great second week and I am really excited to learn more about all of the work the other interns will be doing. 

My first day as an intern at Sanford Burnham Medical Research Institute was an exciting, busy, and tiring day. Well at least the morning was busy, the afternoon not that much. On my way to the institute I got lost, my GPS decided to loose signal during the time when I most needed its service. Luckily I had remembered the name of the street and other institutes that were nearby. After the panic of being lost and almost being late on the first day I arrived to the institutes’ headquarters. I had no idea what building I needed to be in. I was glad to have had one of the other interns phone number, so I texted her asking for building information. Upon my arrival I was greeted by a lovely lady named Vivian. She quickly asked for my ID and then took all of us interns (six) to fill out a bunch of paperwork that all newly hired personnel fills. After this we were escorted to get our picture taken for our ID cards. We were also given a parking pass. I was really happy that parking is free at the institute. Another lovely lady named America escorted me and another intern to meet the principal investigator of the lab in which we would be working. He was surprised to see us, he knew we were coming but was not sure when to expect us. We were introduced to current lab members and assigned a workspace of our own. I even get to have a computer of my own to work at during my stay in the lab. The postdoctoral associate in the lab that will be training us assisted with setting up the computers to take a safety orientation for new employees. After this we had nothing to do since the post doc was in a meeting we left to lunch. After lunch we had a mini meeting where she let us know that we will be working on protein expression and possibly purification. She will provide us with reading material.

On day two, we had orientation at UCSD. All of us in the internship cohort decided to walk together to the auditorium located in the Biomedical Sciences Building. Unfortunately we did not know our way through the campus. The place where we are staying is located in the north side of campus and the Biomedical Sciences Building is located in the School of Medicine which is situated on the south western side of UCSD. Once we finally made it to the orientation we heard a talk by Dr. Lawrence Alfred on working in study groups and journal club presentations. Our cohort is known as the “Fresno people” by Dr. Alfred. We will be doing a journal club presentation on July 17, 2013 from 1pm to 2pm. Afterwards, we went for lunch and explored the campus. We had lunch at the Price center and then visited the library. We then had a west campus tour that was mostly geared toward incoming transfer students. Our final event of the day was a talk by Dr. Georgia Robins Sadler. The talk consisted of good pointers for time management and goal setting. In addition she gave some insight on public speaking. She really emphasized on the importance of speaking from the tip of your tongue and throwing your voice at the last person on the row of the auditorium.

On Wednesday the 26, we had an orientation at 9am. Dr. Salveson and we interns decided which seminars from the Bridges program were best for us to attend. We decided to attend the health disparities seminar, journal club #1 and #2, since we will be presenting during journal club #3 it is best if we see how these presentations should be carried out. If time permits we should also attend the rest of Dr. Sadler's seminars on personal leadership, research ethics and managing your image. For the remainder of the morning Jose and I spent our time adding some finishing touches to a presentation on protein expression previously assigned to us. Then the postdoctoral associate that will be training us explained our project further, basically they are interested in isolating and purifying their protein of interest and applying the technique of protein NMR spectroscopy along with high-throughput screening of combinatorial libraries. We were assigned a journal article to read and learn more about the procedures and techniques. The information we learn will be added to our power point.

Thursday and Friday morning were spent on researching information on our protein, its pathway and role in apoptosis.  We were given a 2 ½ hour safety training class. The class was geared towards those who are doing biological research. Further on they will be giving a chemical safety class sometime in the end of July. We will also be attending this safety course.  

 

WEEK ONE - Summer 2013

How did everything go this week?