Adrian Hernandez Blog 3

Hello fellow MARC Trainees!

I can’t believe it is the last day of the MARC Summer program! 

I have now finished 10 secondary M.D.-Ph.D. applications and received two interview offers. This is definitely a bit slow, but I hope to finish the remaining 20 secondary applications within the next two weeks.

This past Wednesday we had our 10-week Summer Programs for Undergraduate Research (SPUR) poster session. I was really excited and glad to see all the work that my fellow researchers had done during the summer.

Here is a picture of me standing next to my poster :D

I turned in my summer research report earlier today and then went to hang out nearby in Culver City.

I am truly grateful for all the opportunities offered through the MARC summer program to network, learn about graduate studies, and further pursue my research on alternative pre-mRNA splicing. I can’t wait to see what the school year MARC program holds in store.

-Adrian Hernandez

Walter Hardesty Blog 3

     Hello everyone! The summer really has gone by so fast. I am so astounded by the amount of work that I’ve gotten done so far. There’s simply no way I could’ve done this during the quarter.

     I’ve spent the last few weeks trying to figure out why my carbonic anhydrase knockdown cell line is not exhibiting social motility at 5% CO2 during the SoMo assay. For a while, we all thought it was my technique. But now, we all think there’s something wrong with the cell line. After I showed the data to my P.I., he believes that I have kept these parasites in culture for too long.  Apparently, when you passage parasites (or any other microbe for that matter), in suspension culture for too long, they can acquire mutations or alter their gene expression levels in a way that can disturb normal knockdown levels upon RNAi (RNA Interference) induction with tetracycline. Wow, that was definitely a mouthful even for me! I guess the take-away lesson is that you want always want to be working with fresh aliquots of these parasites!

     Check them out! Notice the turbidity of the media in the flask. That’s a dense culture of parasites. Looks like it’s time to split (dilute) them into a new flask

 

     And also quickly, I wanted to introduce my good friend, Hoangkim Nguyen. She’s one of the graduate students who recently published a paper on CMF22, an axonemal protein that is required for propulsive motility in T. brucei. Kim is great! She has been a positive influence over my work here in the Hill Lab this summer. I come to her for advice on my projects, career plans, and life in general!

 

 



Walter Hardesty Blog 2

     Hey guys! I hope everyone is having an exhilarating summer both inside and outside of the lab. I’ve been working hard in the Hill Lab specifically with this social motility assay we like to call “SoMo.” I briefly explained it in my last blog and even showed a picture, but basically it’s a behavioral assay that tests the capacity for a trypanosomal cell line to engage in social motility. Because this is a new technique employed in the lab, we’re still working on optimizing the protocol. I’ve been the only researcher in our lab using this technique extensively as a way to answer my research question. For this reason, the graduate students, post-docs, and even my P.I. have oftentimes asked me for my input in terms of what I think works best. This is a great feeling because it underscores the importance of my contribution to the lab; it also reminds me that I am at the front lines of cutting-edge research. Other labs across the world including Switzerland are using this novel technique, so I assume it’s my responsibility to obtain robust and reproducible results!

     Anyway, enough of that. I’ve also been cloning in the carbonic anhydrase gene into a construct which contains an HA epitope. After my sequencing results improve (argh), I will soon be transfecting the parasites with the epitope-tagged construct and performing immunofluorescence to determine the localization of carbonic anhydrase.

Here’s me cloning.

 

So what you’re seeing here are a bunch of flasks containing different parasitic cell lines.

“IS THAT BLOOD?” one may ask

………

The answer is…….no! I wish, how cool would that be?

Actually, it’s just a pH indicator that turns red based on the pH range within the media inside.

 

 

 

Alyson Ramirez Blog 2

Hey guys!

So it’s been a while since I last checked in (sorry, I know you’re simply dying to hear about my latest experiences) and so many fun things have gone on in the past few weeks that it’ll be hard to keep things brief. I’ll do my best!

4^th of July: simply amazing. Photos below! We watched the best fireworks show I’ve ever seen in my life (timed perfectly to music) from behind MIT; the police presence was massive due to events earlier this year, and the show got pretty emotional. Boston Strong.

Research: things are going great! I’ve finished my first experiment, which was… completely inconclusive. But at least I know how to do in situs now, and I’ve been pretty self-directed the past two weeks while my mentor is in Spain- I know, I’m jealous of her too. I’m hoping to get more results from a second experiment next week, the fish have been reluctant to give me embryos (how selfish of them, right?) but I finally got things started this week. And I have to have a poster done in another two weeks. Where has this summer gone??

NYC: I travelled to the concrete jungle where dreams are made of last weekend. Wow. It was really hot and quite a change from the quiet, tree-lined streets of Cambridge. I ate some of the best food I’ve had all summer and ran around to all the places tourists flock to: Wall Street, the new World Trade Center, Staten Island, the Statue of Liberty, Central Park, Times Square, the Highline. And we did everything in one day! Needless to say my friend I was staying with was not amused with me dragging him around the city all day, but a few scoops of gelato made up for things. I also got to peek at a few of the schools I will be applying to in the fall for PhD programs, which has just made me more excited to continue my education.

Flour: I discovered this bakery down the street from where I’m living and any ideas of getting in shape/eating healthy this summer have officially been demolished. Just look at the picture of the sticky bun below and you’ll understand. I also woke up an hour early the other day to make sure I could get there for breakfast and still get to lab on time. Dedication.

Research seminars: Woah, people who work in this area are phenomenal scientists. We have weekly seminars where we get to meet the PI’s that everyone in my program is working with, and talk a little about their background. I’m completely awed by how everyone we have spoken with so far is so humble about their experiences, even though many of them have founded the institutions that they work in. Their dedication to translational research and finding solutions to the diseases that are so devastating to humans is really inspirational. It’s really made me consider why being involved in scientific research is important to me, and has made me more focused on my goals in the future.

There’s probably so much more that I could tell you about, but I won’t drag you through an unnecessarily long blog post. Until next time!

Adrian Hernandez Blog 2

Hi again fellow MARC trainees!

     I can’t believe the fifth week of the MARC-SPUR summer program is almost over! Currently busy studying for the GRE and taking the Princeton course offered by the SPUR program which has been a huge help. The latest workshops on how to apply for graduate level funding have been very insightful in showing other potential funding sources besides graduate level institutions. I have also started filling out secondary applications to several M.D.-Ph.D. programs and hope to send them out very soon.

     In terms of research, I have been busy studying the Rbfox proteins which are known tissue-specific splicing regulatory proteins. So far I have purified several Rbfox protein constructs which have deletions in the N- and C-termini to see if these mutations may affect RNA binding. I have also been trying to purify other proteins such as heterogeneous ribonucleoprotein F (hnRNP F) which is known to regulate splicing and mRNA stability and the KH type splicing regulatory protein (KSRP). I hope to simultaneously assay these proteins with an RNA substrate to see if there are possible protein-protein interactions that may affect protein-RNA binding.

Performing in vitro transcription to synthesize the radio-labeled RNA substrate.



Bacterial culture used for hnRNP F protein expression.

Adrian Hernandez Blog 1

Hello fellow MARC trainees!

      My name is Adrian Hernandez and I recently joined the MARC program this past spring quarter. That being said, the SPUR-MARC summer program highlights the beginning of my role as a MARC scholar. For the past two weeks I have attended and learned so much from the numerous workshops relating to research and graduate level studies. I especially found the workshop on personal statements to be insightful as I am in the middle of applying to several MD-PhD programs across the nation. I have also had the opportunity to meet other MARC trainees, as well as members of other summer programs who come from other states, like Tennessee.

     As part of my summer program I am continuing my research in alternative gene splicing in the lab of Dr. Douglas Black. Currently I am working on a side project dealing with the polypyrimidine tract binding protein (PTB) which is linked to the formation of the spliceosome complex for gene splicing. I am co-transfecting certain PTB constructs with reporter genes into N2A neuroblastoma cells to see how deletions in a specific linker region within PTB leads to altered splicing of the reporter gene during gene expression.

     I have been in Dr. Black’s lab for almost two years now and recently there have been some “changes” occurring as older post-docs pack up and head out to other colleges and universities to become principle investigators and run their own labs. Most notably I have been “asked” to move from my beloved bench and desk to foreign and not-to-distant lands.

On the left you will find my old, cleaned out desk. On the right is my new, cluttered and cramped space.

 

Here is a picture of my new lab bench. As you can see I have a lot more cleaning up to do.  

Taylor Brown Blog 4

Hello Everyone!

Sorry I’m late on my update haha; my labwork picks up and slows down, and now it’s slowed down, so I can write! Anyway, we got the sequencing results back! And I realized you may not know what colony PCR or a “miniprep” is…colony PCR is basically picking bacterial colonies and putting them, along with other reagents, into a machine that amplifies your DNA construct so that you can make sure it’s present by “running it on a gel” (gel electrophoresis). If you see bright bands around the size that your DNA should be, your DNA is there! A miniprep is basically a procedure you do after you have confirmed your DNA construct is present; you basically isolate the bacterial DNA from your colonies and purify it so that it can be sequenced. “Sequencing” is when you send your DNA off to a company so that they can provide you with the sequence of nucleotides (a long list of A,T,C, and G’s that code for your gene), and you compare your DNA results to the correct sequence that you were aiming for. Basically, the comparison looks like this:

 

except it’s much longer. The “subject” lines are part of the sequence for the gene that I want to study. The “query” lines are the sequencing results. You want a high Identity percentage, a low gaps percentage, and when you look at the long sequence you want to see lots of the vertical lines matching the letters in the subject and query lines (and no blanks where the vertical lines should be). So, my miniprep sequencing went well, and then it was on to a maxi prep! A “maxi prep” is basically like a miniprep, but growing up a LOT more bacteria. You start by taking a little bit of the bacteria that you used to do the colony PCR and the miniprep sequencing, placing it into LB broth (basically a liquid form of all of the nutrients the bacteria need to grow that looks like this:

(Photo credit to gbiosciences.com) and growing up a LOT of bacteria so that you can get a lot of DNA to work with (because as you know, bacteria replicate quickly). You know when you have enough a lot of bacteria because the flask gets really cloudy and smeeellllyyyyy! Haha I can’t describe the smell to you, really, but maxipreps aren’t my favorite thing to do; but they must be done! Anyway, then I purify the DNA again (with a procedure that I won’t go into detail about) and send it to sequencing one more time to confirm that I have the right DNA, and then comes the transfection! “Transfection” is when you take your DNA and viral components (the latter found in a liquid form in small tubes) and pipet them onto packaging cells in a dish. These cells then make the viruses for you with your DNA of interest, and then you put the virus onto the cells you really wish to study (called viral transduction), so that the virus can insert your DNA into your target cells. (My target cells are human breast epithelial cells called MCF 10As). But the whole process doesn’t just happen in a day, and it fails sometimes, so that’s what I’m working on now.

When you do virus work, you have to put on a space suit! Just kidding…but you have to put on a bunch of extra PPE (personal protective equipment) that includes: two pairs of gloves, a plastic gown with holes for your thumbs, and a face mask in addition to your labcoat (and long pants, socks, and close toed shoes). I modeled the process a bit for you below :) haha



And here's a picture of me in action :)



But anyway, looks like my cloning was a success guys! My mentor has another cloning project for me so that I can practice it some more, but looks like my first round of cloning went well! And I’m hoping my viral transfection and transduction worked so I can move on to my experiments! Thanks for reading; more info to come later!

Tay<3 br="" style="mso-special-character: line-break;"> p.s. …it’s my old man’s birthday today. Happy Birthday Papa! I love you(:

 

 



 

 

 

 

Ivan Flores Blog 2

Research has been going well so far. I am continuing to trouble shoot my cell culturing experiments by collecting cells on coverslips at different time points to be assayed for differentiation. At the same time, I have also begun to study the effect that IL-10 has on the transcription factor MyoD on quadricep muscle in vivo. This approach comes from qPCR data showing that MyoD is upregulated in IL-10 treated mice. Hopefully, everything goes well and the data I collect shows positive results. Other than research, I am still studying for the GRE and become more inspired to be accepted to graduate school. The mentoring on personal statement writing and advice that is given at the seminars greatly help with planning for graduate school early on. 

Brian Perez Blog 2

Just hanging out by one of the many
Stanford fountains

It is now the start of the fourth week of the Stanford Summer Research Program and I have now ordered everything I need in order to conduct quantitative PCR which will give my project on cardioprotection new data to analyze. I have also taught a high school student to conduct CPK assays which I think was a good teaching experience for me. I am still working on mastering the western blot techniques so that I can then obtain more data for my project. By the end of the week I will attend this year’s Amgen Scholars U.S. Symposium held at UCLA! I will be coming back home for the weekend, so I will have a chance to hello to some friends of mine.

This last weekend I also celebrated my birthday. I was fortunate enough that my family came to visit me all the way from Riverside. It was great to see my family again. We spent the day touring Stanford’s campus and then went to check out the Golden Gate Bridge at San Francisco.

  

At the Golden Gate Bridge!





On the 4th floor of Li Ka Shing Center for Learning and Knowledge Building (LKSC)





 



Brian Perez Blog 1

At the Oval, Stanford Univ.

My new summer research experience at Stanford looks promising. The first few days it rained all day, not what I expected for summer weather. The general climate here is much cooler that Los Angeles which I totally love.   Do not want to be too hot over the summer. The first week was very busy, so many orientations and ice-breakers, but it was worth it. I feel much closer to my new roommates who I am sharing a house with. During the end of the first week, the Stanford Summer Research Program took us on a scavenger hunt in San Francisco. It was great! The next day many of us from the program went to attend the Pride Parade held on Sunday which was also lots of fun. I finally got to see the amazing city.


I feel like I am going to learn a lot from this summer in the lab doing research and also about improving my professional skills. I am working in a lab that works with proteins and making peptides for pharmaceutical purposes. My project specifically focuses on new drug discovery aimed at protecting heart tissue during a heart attack. I am also going to be learning many new techniques that I am not familiar with that are essential in almost every lab like Western blots and cell culturing techniques. I have also been giving the opportunity to set up protocols for new experiments that the lab does not do, so the experience will be interesting since no one here really knows what to expect.

Some of my new friends on a tour of Stanford Univ.

Hanging out at San Francisco by the ocean!

 

Richard Flores Blog 2

Oh science....this week made me think of a quote I was told by my up and coming scientist buddy Jamie, it goes: “Science-if your experiment works the first time around, you’re not doing it right.” That sums up my week. I spend an entire week writing and testing the protocol for my experiment, Novel Object Recognition. It has never been done by anyone in my lab so I’m in charge of figuring it out. I was careful to make sure I had everything perfect.

Finally, after a week of preparations, I did my first ‘real’ test  in which I would actually collect data. Of course, it did not go as planned. The camera was having difficulty tracking the mice, the mice were running around as if they had never seen the arena (completely ignoring the objects), and the software was switching around parameters at random. Thus, I’ve spent this week reviewing my protocol with a fine toothed comb. Even though I was very distraught at my failed experiment, I remain optimistic that when I re-test it on Saturday, everything will go according to plan!

Ivan Flores Blog 1

My summer research has had a great start. This summer I am staying in my regular lab, working on getting more data for my research. Currently, I am in the middle of trouble shooting a few techniques that will be necessary for me to complete the in vitro portions of my project. The trouble shooting has been fun so far, since I have had to learn new techniques. These techniques include culturing cells on cover slips as well as collecting cells for creating kinase assays. Apart from doing research, I have also started taking GRE preparation classes. The classes add a new and fun challenge to balancing my time this summer. I have met new friends in the class, making it more enticing to attend each class. Hopefully the summer will continue being as great as it is now. Obtaining good results and doing well on the GRE exam will make the work thus far worth it.

Walter Hardesty Blog 1

Hey everybody!

 

My name is Walter Hardesty and I am beginning my fourth-year as an MIMG major. I’m one of the new MARCers, and am excited for a productive summer of research in Dr. Kent Hill’s Lab who works with Trypanosoma brucei. For those of you who are curious, T. brucei is a unicellular, eukaryotic parasite that causes a devastating disease in humans called African Sleeping Sickness. My work has been centered on a protein called carbonic anhydrase and its role in social motility. I am investigating its role by performing social motility assays on carbonic anhydrase knockdown lines at different levels of carbon dioxide, and seeing what happens!

 

Here’s what the assay looks like for a plate inoculated with cells and incubated at atmospheric levels of carbon dioxide:



 

How cool is that! Anyway, that’s just a taste of the work I will be doing this summer in the Hill Lab. Besides lab work, I’m also having a great time working with the other graduate students and post docs. My mentor, Edwin Saada, is great. He always pays close attention to my work in the lab in an effort to guide me on my path. I can’t wait until he teaches me a new technique in the lab called immunofluorescence!

 

Dr. Kent Hill is also terrific! He’s in his office in the lab nearly 3-4 times a week, which is a whopping amount of time (compared to what I’ve heard about other P.I.’s). We have meetings once in a while where he provides me with direction in my project. All in all, his help and support are excessive, and it feels great to know that I am at the forefront of science, alongside one of the leading scientists in trypanosome biology!

 

Until next time, later guys!

Here’s me at the lab! Keepin’ it reallllllll.

 



Julio Silva Blog 1

Hi everyone!
 
My name is Julio Silva. I’m a Biochemistry major and I’ll be starting my senior year and my second year of MARC this coming fall at UCLA. Like other MARC-ers, I am also in Cambridge/Boston, MA under the Howard Hughes Medical Institute (HHMI) Exceptional Research Opportunities Program (EXROP).

 
This week will mark the fifth week of my summer experience and I must say that it has so far been scientific heaven! I am doing HIV research at the Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard. The institute is a collaborative partnership between these three institutions and does cutting edge HIV research with the goal of effectively eradicating the AIDS epidemic. I’m doing my research in Dr. Bruce Walker’s lab, director of the Ragon Institute. My project is on the role of miRNAs during acute HIV infection, particularly their role in causing large bystander CD4T-cell (the target white blood cell of HIV) depletion.  I’m learning a lot of cool techniques, like flow cytometry and many miRNA-based techniques and I’m working with fresh human tissue that is sent to us straight from MGH! My results have so far been promising and my experience in general is amazing! The collaboration between these institutions and from the people that work here is one of the things that make this place so great. It’s like a giant team effort that comes from several arms to reach an ultimately unifying goal. The type of work that gets done here, even my own work, could not get done so efficiently if this type of collaboration did not exist.  My direct mentor, Dr. Juan Cubillos, too has taught me so much within these four weeks and has given me an enormous amount of his time. I am very grateful to have him.

 

I’ve also had the opportunity to go on rounds with Dr. Walker at MGH and I was able to see some amazing cases and even rare diseases like Gorham’s disease, a vanishing bone disease.  He treated me like a med student and he taught me some valuable, essential information about what it means to be a doctor. His patients love him because he profoundly cares about them. He goes on several trips to South Africa as well every year and I casually mentioned my interest in going there perhaps for next summer…. We’ll see how this turns out :)

Well, time to get back to figuring out why I suddenly got an increased amount of CD4 T-cells nine days after infection compared to day 3…. I think I must have gated wrong the first time… :(

I’ll share more soon!

Julio

Taylor Brown Blog 3

Hello Everyone,

 So I attempted cloning again to try and get an insert for 2 of my mutants and the wildtype RRM2, hoping that the third time was the charm. However after the letdown of Cloning attempts 1 and 2 (Cloning attempt 1= only 1 out of 3 of the inserts in bacteria; Cloning attempt 2= no inserts/bacteria!), I packed my bag for the beach this morning, with the intention of checking to see if I had bacterial colonies from my cloning and if there were none (which was the case the last time) I was going to do my labwork (work on assignments due for the MARC program as well as reading scientific papers) on the beach. Win-win situation, right? I thought so. So I walk into lab, and then to the common equipment room where I let my bacterial plates incubate overnight, telling myself that if I didn’t get colonies this time, it’s okay, I’ll get them next time and at least I get to enjoy the beach…and Wah-Lah!!! I had colonies on all of my plates, and none on the ligation control plate, which is EXACTLY what I was hoping for!!! (here is a very fuzzy picture of my plates haha…basically I got bacterial colonies and could proceed to the next step!....New phone with a better camera coming soon! lol)

 So I excitedly texted BJ, my mentor, (oh I didn’t show you a picture of us huh? Here you go haha)

 









Anyway, I excitedly texted him saying I got colonies, and he gave me the okay to go to the next step (he was on his way to lab). So today, I’ve been busy picking colonies, doing colony PCR, and I just finished loading my gel…We’ll see if the colonies I picked have an insert! I really hope so, because if they do it’s on to a miniprep and then sequencing to REALLY confirm that I did my cloning correctly; wish me luck! :D

 

P.S…after my gel is finished running, I’ll post the picture on here(:

 

That’s what I was looking for guys!!! ^ (not the circle; the bright bands). I’m so excited! Progress is being made! :DThanks for sharing my excitement :) I’ll write again soon!

-Tay

Taylor Brown Blog 2

Hello Readers! :)

Well, I’ve officially been in the MARC Research Summer Program for a week and a day! Boy has it been a ride (in a good way)….and it’s only just started! I’ve met so many cool people (and several of them are from out of state); that’ll be me next year! I’m excited! I should start thinking about where I want to go for the summer…hmmm….but anyway back to the program!
We had a “Considering Graduate School” Workshop with Dr. Simmons last week on Tuesday, and I found it very helpful! It’s nice to have a timeline of when everything should be completed, as well as the guidelines for the documents you have to submit with your graduate school application. I will definitely be using the handout as a reference!

When I’m not in a Workshop or eating lunch, most of the time I’m in…hah well where do you think? 40 hours a week baby! And boy do I need all the time I can get….I’m learning how to clone! And it is not easy hah! Bbbbuuuttttt, yesterday, I think I got 1 out of 3 of my constructs successfully cloned on my first try! (which may not sound like an accomplishment to you, but it is to me; cloning is no joke! Haha). Yesterday I ran a colony PCR on my bacteria, just to see if the DNA insert may be there before we send it to sequencing to confirm…and it looks like we have the insert we’re looking for! Hah I had to take a picture of it, even though it may not be my insert….but it’s still exciting stuff! :D

 (basically, the lanes with the letters are colonies from a plate that should have my construct. And the bands in the row with the two bright bands might be my insert! I’m sending colony A to sequencing to make sure)

I have to get the cloning finished before I can actually do experiments that will give me the data I want, and cloning doesn’t always work…so I’m working really hard to get through this step so I can start working with my cell lines (eventually…there are still lots of steps to do in between before I can get to that point…but progress is being made!). I’ve definitely learned that science requires PATIENCE haha.

When I’m not in lab (or rather, am waiting for a 2 hour digestion or PCR reaction to finish hah), I enjoy playing basketball (there’s a court in CHS! The court isn’t fabulous, but there’s a net, and that’s all I need! Haha).

Otherwise I am reading papers pertaining to my lab or project at one of my FAVORITE study spots on campus, Janss Steps!

(I’ve also recently discovered that the Bombshelter sells Crepes in the morning….I love Crepes!)

This past weekend, my parents also came to visit me! So I had lunch with them on Friday (sushi; yummm!) and then my Dad and I went to Santa Monica Beach on Saturday! I love our Daddy Daughter Days(:

Well, that’s all for now, folks [oh, and I promise the picture quality will be better once I get my new phone in August!]

Thanks for reading!(:

Taylor Brown Blog 1

Hello! (:

My name is Taylor Brown, and I am an incoming 3^rd year MIMG (Microbiology, Immunology, and Molecular Genetics) major and Biomedical Research minor at UCLA. I work in the laboratory of Dr. Heather R. Christofk, which studies novel genes and signaling events that contribute to metabolic transitions in human health and disease. I have been accepted into the MARC program, and am doing research on my own independent project this summer. My project is focused on viral ribonucleotide reductase small subunit (RRM2), an enzyme that catalyzes the reaction of ribonucleotides to deoxyribonucleotides. In a nutshell, the goal of my project is to better characterize how specific amino acid differences between human RRM2 and its viral homolog lead to potentially altered enzymatic function, and how these differences promote viral replication in the host cell.

After graduating from UCLA with a degree in MIMG, I will continue my education by pursuing a Ph.D in Cancer Biology or a related field. My goal is to continue working in cancer labs (and other labs with interesting topics as well) to gain more research experience, to better understand the scientific process, and to acquire background knowledge on cancer in general. I hope to become an effective cancer researcher, and to hopefully run my own lab one day, so I can apply the knowledge I have acquired through my research and schooling to develop therapeutic drugs and to help cancer patients worldwide.

I will be keeping you updated on my research progress this summer through this blog (as well as fun stuff too!). Hope you enjoy reading, and nice to meet you! :)

-Taylor

(p.s. don’t worry, my gloves were clean in this photo haha)