Sunday, February 2, 2014

welcome to the jungle

Hey Guys,

So we got the CRISPR system to talk about and I have a recipe at the very bottom that is my absolute favorite go-to meal to make. Before we get into science though, I figured I'd embrace my crazy cat lady for a few minutes and discuss my neurotic roommate, Bagheera. Yes, he's an all black cat. So you are probably assuming I am being very uncreative with such a name… I beg to differ my dear readers. This is no sane feline. He (and it's a boy) is probably the most strange pet I've had and I've had a siamese cat before (need I say more if you are a cat person and know what this means- cue in Chucky music). So this is a comparison of what we (or at least me) thought of when we were kids versus my reality:

(This is where you should be going "awwww! Kittteeeeeyyy!!") 

He is the sweetest thing, I will say that in the very beginning. He is also a massive pain in the ass. I have gotten a tiny glimpse of motherhood, and holy cow, I may or may not have slapped my biological time-clock to its senses. Bags is 1year and 5 months, meaning he's a baby and wants attention nonstop. At first, this was awesome. I am living on my own in western MA and knowing no one. Coming home from lab and having a living thing love you was (and is) the greatest thing a person can ask for; however, I now have established a life here (Ahem, correction: grad student life. I plan on explaining this in the next post) and Baggy does not like sharing me. 

As seen above he has this lovely habit of jumping on my shoulders and wanting to sit like a scarf around my neck. This is all fine and dandy except he is like ~15 pounds and his back claws have made quite lovely tattoos on my back side. What is cute is once the pain is gone and he is at his perch, he will head butt you on the cheek and lick your face. He doesn't just do it to me either...
(Poor Ethan)

So here is a typical morning I deal with everyday:

Alarm goes off and I hit snooze, Bagheera decides this means I should be up feeding him. He jumps off the bed and meows. I ignore him.

My 2nd alarm goes off and I hit snooze (don't judge). Bags is pissed I'm not up so he jumps on the bed, meows, and licks my chin. I push him off of me and roll over. He goes to the sliding door to the deck and moves the shades back and forth so sunlight hits my eyes.

I swear profusely at him.

He meows back.

My 3rd alarm goes off (seriously, no judging) and I turn it off and try to wake up. Since I am not immediately off the bed at this point, Bags now head butts me while purring and kneads my face/chest. I reluctantly pet him because I feel bad about how many times I pushed him off the bed.

I get up and make coffee, nearly tripping 4x as Baggy runs between my legs meowing frantically as if I never feed him (his bowl is full of dry food mind you 24/7, I only give him wet food in the morning).

I go into the bathroom and run the hot water for the shower, Baggy is now on the rim of the tub looking in and looks back at me grabbing a towel/organizing the bathroom, meowing out of concern.

While showering the cat meows frantically while sitting on the toilet lid trying to comprehend why any animal would purposely get wet. He repeatedly pokes his head through the curtain to check to see if I'm alive and if I don't respond he then begins to paw through the curtain at different spots (scaring the shit out of me since I am still half asleep and this dark figure is jabbing at me in different locations every time).

I get out of the shower and he instantly rubs against my legs happy I'm alive. I now have black fur all over my legs.

I go to dry my hair/get dressed and Bagheera follows me into the bedroom to watch the birds. While he is on his pillow he begins making the weirdest barking/purring/meowing combo noises once he spots a bird. If I don't look out the door too he then goes to the mirror and pushes it out of angle, meowing at me.

I pack up and put on my shoes. This is the signal. Bags races to the kitchen once my shoes are on.

I take out the wet food while being bitched out by this feline. I place the food down with a final "muuurrr" like I am so awful to him to make him wait.

I pour my coffee and about to head out the door. Say goodbye to Baggy and shut the door. As I lock the place up I see paws come from under the door with some muffled meowing. I poke his paws and tell him to go back to the window. One final meow and the paws disappear. I go off to work.

You may think this is cute... but it's not. It was the first month. Maybe even the second month. We are now almost 6 months in with this routine and I sometimes want to kill him as cute as he is and as much as I love him. It's like a toddler, and I was told cats are low maintenance... HA. Yeah screw that theory.

Meanwhile in the science world…

I learned about the CRISPR system in my Advanced Molecular Biology course last semester. I was completely fascinated because it sort of relates to my favorite topic, The Red Queen Hypothesis. Basically the RQH is a race between two species to keep existence. Most commonly it refers to a host and virus, where they constantly adapt to become immune and to infect, respectively. We see this in the CRISPR system used by bacteria to outwit its nemesis, the bacteriophage (virus that infects a bacteria). How does this system work and why is this such a big deal?

Well kids, let's hop on the Magic School Bus and go microscopic! Let's get Frizzled! 


… Anyway

If you haven't read my last post from ages ago, it gave a paper with supplemental data as well as an article posted about the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system; however, I was pretending to be one of you and realized you can't open the paper unless you have Science access and/or on a campus that has it. Therefore, I am going to try to quickly summarize this paper the best I can and then we will talk about the article I've pulled up and then I hope to inspire you to go off the deep end with all the fabulous applications we can think of for this system (pretend to care please).

So as I learned in class, the CRISPR system is a surveillance mechanism in bacteria that prevents bacteriophage infection (as well as plasmid infection but I won't get into that, leave a comment at the bottom if you want me to). It's sorta similar (I say this cautiously) to RNA silencing we see in eukaryotes, but the mechanisms are completely different. If you need a reference though, that's the best comparison I have for you.

So the article I linked last post, which you can look at again here, gives a really good history and summary. This kinda kills the point of me writing about it but the difference is they have to be professional in their writing… I do not. Though if anyone from a reputable job opportunity looks at this blog (I posted it on my Linkedin account and surprisingly sell this site to professors) I would love to see their faces of either, "Hey, she's funny and excited about science. Let's hire her!" or "Nope. Not in a million years." *click on delete application*. Either way this blog will either go unnoticed, be seen and approved, or completely backfire on me and I'll die with a Ph.D. but no job. The point was of this entire paragraph that I will also give a brief history and background as the article does but mine is more entertaining (if you haven't noticed yet) and you should read mine.

This system has been in the science world for a while, 27 years actually. It's not until now that we appreciate it and are trying to understand it. Basically in Escherichia coli there was a section in the genome that had random repeats (DNA gibberish is the best way I can describe it) with "spacers" that had DNA that was homologous to pieces of pathogen DNA. Picture it kind of like a fossil record of the infections this particular line of generations came into contact with. It's been found that these DNA fragments in-between the random repeats are transcribed (DNA ---> RNA) and used to guide a direct subsequent cleavage of complement viral DNA that is trying to infect the cell. So these small RNA pieces are used to destroy DNA of a virus that has just been injected into the cell that has once before tried to infect the cell. Make sense?

Now the paper I had read for class describes in detail one of three types of systems used within the CRISPR system umbrella. It's type II if anyone wants to look into it more and tell me I am explaining this horribly or (preferably) perfectly. We also focus on the genes that are always in genomic proximity of this array known as the cas genes. Cas proteins work with CRISPR and carry out the following 3 steps basically:

Phase 1) Adaptive phase:
This is basically when the cell reacts to the first viral infection and beats it. It takes a short fragment of the foreign DNA (a piece of the viral genome) and puts it in its CRISPR array. So to picture it as you've rented a movie and now you keep the movie preview in a media library so you remember what it's about.
Phases 2 and 3) Expression and Interference phases
So with this, the transcription (DNA-->RNA) of the spacer (your movie preview being played) occurs and is cleaved at a specific point that then allows it to form a functional complex with Cas proteins (Oh hey, I've seen this movie!).

Now the cool thing is that actually two different RNA fragments are part of this process. One is the pre-crRNA which is the preview of your movie which is first transcribed and not yet cleaved. The other is tra-crRNA (transactivating crRNA), which is what is complimentary to the pre-crRNA and actually is the one to trigger the processing of the pre-crRNA and activates the cr-RNA guided DNA cleavage of the infecting viral genome. Once the complex is formed, then the complex can cleave the target DNA. The important part of this system is that it can cleave one DNA strand or both of the double helix at very precise locations, depending on which protein domain of the complex you are looking at.

Why is this important? Well when it comes to genetic engineering, having precision is key. And this is where the article gets involved into our discussion. What the article is getting at is the applications involved with this CRISPR system. To someone who isn't in microbiology, picture it being the wheel already invented by nature and you no longer have to design it on your own.

So what applications do you see with this system? I'd love to have a discussion so I'm hoping some of my science (or non!) friends will pitch in ideas, critiques, post articles they've seen etc. I look forward to reading what you got!

If you made it through this post so far, I am impressed you got through my novel. This is also why it takes forever for me to write these, something I really want to get better at. So far New Year successful resolutions have been to eat more healthy, exercise, and time management. Surprisingly after 22 years I am making way on these things. Next post will be about grad school life after 6 months in and as for the science I would love to know what you think I should write about. I have some ideas but I want this as an interactive blog so keep up the comments! I get a lot of them in person or on facebook, which I appreciate, but let's give each other something to talk about on the site :).

Okay so recipes:

I have Trinidad Chicken Curry… it's a slow cooker recipe but I promise it's worth it.

13oz can of light coconut milk
3 cloves of garlic (I always add just a bit more)
1 Tbsp. fresh grated ginger
1 Tbsp. tomato paste
1 Tbsp. curry powder
1 Tbsp. turmeric
1 tsp. ground coriander
1 tsp. ground cumin
1/2 tsp. black pepper as well as salt (or to taste)
2-2 1/2 lbs od boneless chicken thighs cut into strips OR I use chicken tenders and cut them into cubes
2 sweet potatoes cut into bite size chunks
1 medium onion (I've done purple and yellow, both taste good)
1 jalapeño pepper, halved, seeded, and thinly sliced (or chopped I've done both)
1 can of pigeon peas (15 oz) rinsed and drained
3 Tbsp. finely chopped cilantro (I don't normally do this… cilantro is expensive for a student)

Add coconut, milk, garlic, ginger, tomato paste, curry poser, turmeric, coriander, cumin, black pepper, and salt to either:

A) slow cooker if you have one
B) tall pot like I have on the stove

Stir to mix well and then add the chicken, sweet potatoes, onion, and jalapeño. Stir well again. Sprinkle the peas over mixture and don't stir.

Cover and cook on high for 4 hours (or low for 8) if you have a slow cooker.

If you don't have one like me, I bring it to a boil and then simmer on low for 3-4 hrs. It's important to keep watch. There won't be much liquid at first and then there's a ton. After that you need to be careful because if you cook too long, it becomes a paste rather than a stew. I've accidentally over cooked it once and it was a weird paste, still tasted good but I wanted stew. So my warning to you is watch it and get it to a texture you like (and make sure your chicken has cooked through).