Wednesday, July 30, 2014

Completion

The day has finally come, the day my internship is completed.  It was a very bittersweet moment saying good-bye today (even though it is only for a month). I am glad that I had such a wonderful opportunity to work in lab over the summer and start my senior thesis.  I am ecstatic that I have the opportunity to return to the lab in a month.

Thank you for the ongoing support.  I am taking the GRE's next Friday, and am going into hard-core study mode.  At the moment, I am doing extremely well on the math sections and have some work to do on verbal.  Not to worry, you know my verbal skills are good just by reading this blog!

Until next time!  Have a wonderful rest of your week, and happy hump day. :)

Saturday, July 26, 2014

The Good and the Bad

Hello fellow readers,

This past week contained both triumphs and failures.  I finally recombined all of my DNA sequences onto a GFP tag.  In non-scientific terms, I took a circular piece of DNA that contains a fluorescent tag and inserted my DNA sequence into it.  I now have two mutant sequences, and one wild-type or unaltered DNA sequence.


The next step is to put my plasmid (the piece of DNA containing both my DNA sequence and the GFP tag) into Tetrahymena.  I am completing this step with a partner, and we are on our third try this week.  Tetrahymena have seven different mating types, or seven different sexes.  To insert the plasmid into Tetrahymena, you have to starve them and mix two different mating types together.  At this point, the cells are susceptible and they can take up the plasmid.  Unfortunately, the last two tries, it appears as though we had contamination and were trying to mate the same cell types.  

I have also been worried about the GRE's, which I am taking in 13 days.  It is difficult trying to balance everything.  I cannot wait to put this behind me.  While I want to remain at school and complete a few extra weeks of my internship, I am very excited to be at home.

When I got home yesterday, Cheryll was so unbelievably excited.  I haven't seen her this excited, and for a full 23 hours straight, in a very long time.  It appears as though she really missed me :).  I missed her too, along with the rest of my family.  T-6 days until I get to be home for a month.

"I cannot, I have lab"-- the story of my life

Saturday, July 19, 2014

That Hectic Life

Hello!

Life has been VERY hectic as of late.  Yesterday, I worked from 8:45 am to 10:00 pm.  Of course, working so late was unplanned so I did not pack dinner.  I crawled home like a zombie, and stopped for food on my way back to the apartment.  I think I actually fell asleep waiting for my food to be made at Legends Burgers.  The place was very iconic of Route 66 and the 70's.  I had a cheeseburger and a chocolate malt.  I thought it tasted good, but what do I know, I was half asleep.


As I said, I have been working crazy hours, and very hard.  I have gone through not one, not two, but five tip boxes.  





This week, I worked on amplifying the one plasmid that had the GFP tag (a fluorescence) with my desired DNA sequence.  Unfortunately, my other two plasmids that I mentioned on friday, were incorrect.  I have now created my own ultra competent cells, which are E.Coli cells that can take up my plasmid and amplify it, in the hopes that I can isolate my other two plasmids.  I am excited to have one plasmid that I can continue my experiments with.  I reran my experiment with the last of the histones (histones are proteins that the DNA wraps around to condense it from 2 meters to 6 micrometers) I had, which was looking at if one of the histones was shortened; my results were not as good as I expected, however I have results.  I do need some more information to finish my calculations and determine the actual amount of histones that I loaded before an accurate assessment of the experiment can be determined.  In the mean time, I have started to isolate more nuclei (which contain the DNA and therefore the histones) and then the histones so that I can rerun the experiment if desired.

My lab mate was mating Tetrahymena cells this week, and I have a really cool picture and video that I wanted to share with you.


video

I cannot believe how fast time has passed.  I just finished my 7th of 9 weeks for my internship this summer; I am sad that I cannot continue to work in the lab for the month of August.  I am loving it, and am really interested to see what the results of my experiments are!

We created lab shirts, and wore them today to show lab spirit at laser tag today with Keck Science!  They are so cool.  The picture portrays a Tetrahymena cell.  The quote is "If we knew what we were doing, it wouldn't be called research."--Einstein (spelled Einsten as an inside lab joke)


Of course, none of us pictured above would be nerdy if we didn't make and own a shirt like the one below.

After laser tag, a few of us went out for dinner at Bua Thai, and then ice cream at 21 choices.  I am currently in the process of eating the ice cream and may or may not have finished it by the time you read this.  By the way, the ice cream is a medium/ large.  It is oreo milkshake frozen yogurt with crushed oreos, cookie dough, and sprinkles, similar to Cold Stone.  




Of course, my life would not be complete without me making FOOD!  Most days, I enjoy being able to get creative with my dinners.  While I would love to not eat alone, it is nice because I do not have to worry about the food tasting bad.  Mainly, I eat chicken, zucchini, and sweet potatoes.  I am proud to say that everything I have made has tasted good.




I also picked up a lot of good, and healthy, food from Trader Joes this week.  I have been eating a salad everyday for lunch instead of a sandwich :)  I am very proud of myself for that.

If you have read some of my previous blog posts, then you know how much I love to make popsicles.  I have made a few lately, however I only have a picture of one of them.  I have tried oreos, wafers, pretzels, butterscotch chips. and chocolate sprinkles (shown below).  All have tasted pretty good; pretzels may have been my least favorite and chocolate sprinkles my favorite.

This weekend, I plan to finish writing my methods for my thesis for the experiments I have completed thus far, another draft of my introduction, and loads of GRE studying.  My motivation is going to be seeing Cheryll, my dog, next weekend.

Saturday, July 12, 2014

Success At Last

Good evening!  I am going to keep this blog post short tonight; I wanted to update you on the development of my experiments.  If you refer to my blog post a few weeks back, where I explain the GFP recombination that I was attempting to do, then you may understand the difficulties I was having on trying to get my reaction to work.  Well, I have gotten to the reaction to work and have successfully isolated the plasmid (contains the DNA sequence I desired with a fluorescent tag attached)!  I have conformed the isolation of one of my plasmids with my Professor, and I am waiting to here back on the other two.  After many unsuccessful reactions, and only becoming minimally frustrated, I felt elated!  The feeling of having accomplished the next step in my experiment, after SIX weeks, is equivalent to the feeling of a giddy five year old.

Thank you for all of the support; I cannot wait for next week and learning how to carry out the next experiment.

Tuesday, July 8, 2014

4th of July Fun

I just got back from an amazing weekend in the Bay Area.  I visited two of my friends from school, spending most of the weekend in the country side.  I went wine tasting for the first time, learning the difference between oaked and unoaked wine.  Afterwards, we took a walk in the countryside, feeding apples to the horses as we walked by.  I was so nervous that the horse was going to bite me!  You have to keep your fingers down, and the horse takes the whole apple in its mouth; it tickled.

Then, we went and saw fireworks at a Temple.  They were short, 15 minutes, and pretty good.  Keeping with the theme of Independence day, most of the firework were red, white, and blue.

After an exhausting day, the three of us decided to sleep in a full-sized bed.  What possessed us to do such a thing, I don't know, however it was the best I have slept in days!  We woke up and went to the beach for a few hours, where we fell asleep guarding our faces from the sun.

After such a tiresome experience at the beach, we stopped to refuel on the way back with some sugar: salt water taffy and Screamin mimi's amazing homemade ice cream.


For dinner, we made a squash lasagna, using vegetables straight from Hannah's Mother's garden.  Not only did we use fresh veggies, but we grated our own Swiss cheese and made two types of sauce from scratch.


The weather was beautiful, and we sat outside for the whole evening (~4 hours).  No bugs, no noise, just the light from the candles and some stars.

Sunday, Hannah and I spend the day in San Francisco.  We started at the Ferry building where we ate lunch.  We got a few different foods and shared them; this allowed for us to try a greater variety.  We tried an Italian doughnut (pictured), olive oils, a grilled cheese containing bread made there and cheese from the surrounding area (so good! pictured), and a famous soft-serve ice cream place.  


Of course, we couldn't stop there.  We went to China Town, where we got Boba (Milk Tea), a large pork bun, a sweet roll, egg tart, and egg roll for $4.75.  We were shocked at how inexpensive all of the food was.  We travelled pretty far down the main road, and then detoured a few shop fronts up to find this place.  It was well worth it!  Of course, ordering was a bit difficult as the people running the store-front did not speak english.


To end it all, we went to this huge Westfield mall.  There were five stories, winding stair cases and escalators, and lots of high-end food places.  Needless to say, it was VERY easy to get lost.  Hannah and I split a freshly-filled vanilla cream puff.  

Last, I went to Peet's Coffee for the first time this weekend.  I went to the original coffee house, and it was so good that I had to go back for seconds!  Before friday, I did not understand why everyone loved Peet's so much.  Now, I am a fan.

It was great to see my friends this weekend.  I have a lovely time with them, and cannot wait for the start of senior year!  

On a side note, I would like to update you on my thesis.  I have completed my first figure!  Six pictures neatly arranged, with arrows.  Also, I was running a gel today that contained proteins.  Unfortunately, the gel broke where I believe my protein was expected to appear.  I guess I will find out tomorrow what happened!

"Don't walk behind me; I may not lead.  Don't walk in front of me; I may not follow.  Just walk beside me and by my friend." -- Albert Camus

Wednesday, July 2, 2014

The Best Feeling

One of the best feelings is success.  Success can be defined in many different ways, but I would like to define it as "a performance or achievement that is marked by success, as by the attainment of honors" (dictionary.com).  While my lab results have not demonstrated the outcomes wanted, like today where I expected to see bands on the Western blot, yet knew my protein was on the membrane.  This is a big relief, as my protein was properly transferred.  A western blot is a gel that contains the protein you are trying to detect, and is transferred to a membrane that can be used to detect the protein through an antibody that gives off a signal.  I have my protein, as marked by a red dye, but no signal was received from the antibody.  Going into problem solving mode, we determined that the source of the error may be the conditions of which the antibody was put on the gel. Tomorrow, I will rerun and determine if that is the issue, as my protein is there.  While I did not see the results I wanted, I was successful in getting my protein to transfer from the gel to my membrane.

The greatest feeling of success I have had comes from the application of my knowledge.  In the last few days, my lab professor has commented on the application of my knowledge, and is thoroughly impressed.  I have taken what I have learned from other classes, and applied it to lab.  This is mainly in the form of controls.  A control for each experiment is important, as it can dictate if the experiment was carried out properly ie. if the enzyme works or not.  In addition, I have used the background knowledge I have gained from writing my thesis to ask questions that impress my professor.  In my opinion, I have been successful as I have demonstrated a performance of my knowledge.

I have also sent a draft of my thesis introduction to a good friend of mine, who also studied Biology with me at Scripps.  She thought it was a great first draft, and had no major changes to make!  Step 1 of thesis: complete. (Step 1 was writing a draft of my introduction).

As many of you know, I have a very sweet tooth.  I put my sweet tooth to work over the past 26 hours and baked pancake muffins and cookies.  Not just any cookies however….cake batter oreo sprinkle cookies!

Recipes are as follows:

Pancake muffins:
Made 21 muffins.

-3 cups all-purpose flour
-1 tbsp. baking powder
-3 tbsp. sugar
-3/4 tsp. salt
-2 1/2 cups (skim) milk
-1 tbsp. white vinegar
-2 eggs
-1 tbsp. vanilla extract
-4 tbsp. butter, melted
-semi-sweet chocolate chips

Preheat the oven to 400 degrees.  Stir together the milk and vinegar, and let sit for 1 minute.  Whisk in the vanilla and eggs.  Add baking powder, sugar, salt, and flour.  Then add the melted butter and stir.  If the batter becomes too thick, add a little bit of milk.

Grease the muffin-pan, and fill each cup 2/3 of the way.  Add 4-5 chocolate chips (or more if desired) on top.  Bake for 8-9 minutes.

Eat fresh, at room temperature, or heat up in the microwave for 15 seconds!



Cookie time!

These cake batter oreo sprinkle cookies may be seen as over-kill.  I mean, they contain cake batter, oreos, sprinkles, chocolate chips, and butter-scotch chips.  However, they are so delicious!

Cake batter oreo sprinkle cookies:
Made 63 cookies (I would expect to make less)

-1 1/4 cups all-purpose flour
-1 1/4 cups funfetti cake mix (you can also use yellow or vanilla if desired)
-1/2 tsp. baking soda
-3/4 cup unsalted butter, softened
-1/2 cup granulated sugar
-1/2 cup dark brown sugar (can use light as well)
-1 egg
-1 1/2 tsp. vanilla extract
-10 oreos, crushed (I used cookie dough but any flavor works!)
-2/3 cup sprinkles
-2/3 cup semi-sweet chocolate chips
-2/3 cup butter-scotch chips

Cream the softened butter, granulated sugar, and brown sugar together on medium speed until smooth.  Add the egg, mixing on high until combined (about 1 minute).  Add in the vanilla, and continue beating until combined.  Add the baking soda, cake mix, and flour and mix on low speed until combined.  Add in the oreos, sprinkles, chocolate chips, and butter-scotch chips.  I mixed with my hands, but you can also use a spatula.

Cover the dough with plastic wrap and put in the refrigerator for a minimum of 2 hours and no more than 3 days.  I put in the fridge for about 17 hours.  Roll dough out as you are using it.  The refrigeration step is important, as the dough will spread too much when cooking if bakes from room temperature dough.

Preheat the oven to 350 degrees, and place balls of cookie dough on an ungreased baking sheet.  I made smaller cookies, using a little less than 1 tbsp of dough per cookie.  Shape the balls to be tall and thin.  I made sure that that there were either oreos, sprinkles, or chocolate chips at the top of cookie dough ball before baking.  This makes them prettier.  Bake cookies for 10-12 minutes.  The center of the cookie will appear very soft, but they will set as they cool.  Let them sit, and then enjoy!



I think that is all for today.  Life is good, I am not sore anymore and my sunburns from the hike are going away, I was able to run this morning (if only for one mile), and I am happy.