Wednesday, August 13, 2014

you're as cold as ice

Hey guys,

Just wanted to show the video of my ice bucket challenge (thank you Julie!) and help spread ALS awareness through as many portals of social media as possible. Please donate and help a very good cause (I donated $15 and I'm a poor grad student…no excuses)! Any amount is a great amount and will impact many lives :)

A post will be coming soon I've been dying to update life stories and put up my Darwin vs Dating post but this summer has been crazy awesome busy. Thank you for your patience and enjoy!

PS: And yes... we used an autoclave bucket…

Thursday, April 10, 2014

it's the final countdown

Hey Guys,

So the title of this post literally is the theme for April for myself and most graduate and undergraduate students. I have a really fun post I'm working on about "Darwin, Dating, and Cooties" that will be up hopefully by the end of the weekend. I hope it makes you laugh, get offended, and make you ask questions about our society and microbes (because everyone does that right?). In the mean time, I am writing a proposal for class and wanted to send my idea out to you, my science and non science readers, to get a feel for what you think. Years ago in my microbiology population genetics class we did this exercise of sharing our ideas via blogs so that before we wrote the darn thing, we already had critiques on our ideas.

So, I am writing about nitrogen loading effects on microbial communities in streams. Nitrogen loading is a huge issue across the US, a silent "contaminant" that stimulates eutrophication in watersheds. This basically means that is destroys aquatic life and in result, ecosystem services. The New England area in particular has a serious issue with nitrogen (as well as other nutrients) loading in our watersheds (Casco Bay, ME is one example). The reason why I know all this is because a couple years ago I was an intern for the EPA Region 1 Headquarters in Boston looking at how to approach this nitrogen/nutrient loading problem we're having. There are certain sources of nitrogen: Point Sources, which are waste water treatment centers, and Non-Point sources, which include land run-off from agricultural/developed land as well as atmospheric nitrogen. These sources all go into watersheds (rivers, streams, lakes, and estuaries interconnected in a certain land area) and cycle through. Now under normal circumstances this is fine; however, with the increase of nitrogen from these sources, there is too much nitrogen/nutrients in the water and can no longer be retained in marsh lands and used up by the microbes/plant life. This rising nutrient level then causes algae/phytoplankton blooms and in turn, eutrophication. It is of great importance that we find a way to approach this issue.

You can see my old TEDxYouth Talk here about this issue too (was also on an old blogpost).

Anyway, because my next rotation involves soil biota and carbon cycling, I decided to combine the papers I'm reading to prep for the rotation and twist it so I am also reading them for this proposal (yay efficiency)…plus it's all pretty fricking cool.

So my thought was that you could look at the microbial communities in stream bed sediments and see how they are reacting to these point and non-point sources. By understanding the community shifts (bacteria populations shifting in ratios), the functions that are present in the community (looking at extracellular enzymes), as well as how the nitrogen is affecting the carbon/nitrogen cycling of the community (rate of cycle, labile vs recalcitrant carbon, etc)… We may be able to utilize what we learn to coming up with new forms of bioremediation. Not to mention this research, since it's considered "field work", could be applied to nitrogen loading models (such as SPARROW) that I believe look at microbes as a "black box" in their equations, rather than individual communities responding to each type of source. That part I still need to check, but I do know that when it comes to global climate change models and looking as microbial communities as a variable, it would be helpful to have this data.

….
*This is an updated note after I received some feedback:

When looking at the effects and relating it to the course (Cell Physiology), we had learned how cells make energy, how cells compete/interact using that energy, etc. This study would focus on determining the dominant method of energy production, how nitrogen is utilized/the rate of which it is utilized, as well as how the community, in it's competition to survive in a dynamic environment, alters with pathways/products in response to each other.

Good questions brought up as well such as what are the seasonal effect (I do have papers on that!) and what other factors could be affecting the shift (iron, phosphate, etc).

Final point that I forgot to mention was I am trying to think of ways to test these communities in the lab to see if nitrogen is truly having an effect. Once again, reading a ton of papers as I type.
….

I literally came up with this yesterday evening, so I would love feedback. I am aware that different literature have approached this in different ways (such as using a model, looking at C:N in the soil and other biochemistry approaches, using sequencing to determine the microbial communities and any changes, etc) but from what I can tell, it hasn't been approached in this particular manner and looking at these many variables (though there may be a reason for that too I haven't stumbled upon). Please tell me if I'm wrong though!

If you understood all that, what I'd like to know is:

1) Does this make sense?
2) Did someone already do this?
3) Do you see flaws in the idea already?
4) Are there other questions maybe I should be asking? Or maybe not asking?
5) Do you need more info than what I gave thus far in order 1-4? (you can comment and just write "#5")

Hope you enjoyed my mini spiel and look on the blog soon about Darwin, dating, and cooties! (Oh and a first date story that's priceless).

Please make comments (or vote on the blog poll)! And you can be mean, it's okay, I'm used to grant reviewers… Have skin of steel now.

Monday, March 10, 2014

lady on the water

Hey Guys,

If you haven't guess yet, I figured I'd give a quick post about my ice fishing adventures. As most of you know, I am dating Ethan, aka "mountain man" as Janhavee (college friend and fellow Hugh Jackman fanatic) put it. Therefore, I am now hiking, fishing, camping, canoeing, and other various things that I never felt the need nor desire to do (aren't relationships great!?).

The sad(?) thing is I like this outdoors crap... who knew.

Just so you understand the stark contrast of the past 4 years, my ex of two 2 years just prior to Ethan was allergic to grass and trees. We went camping once in Bar Harbor and it was a complete disaster (oh there's another hilarious story, maybe another time). So then later I began dating Ethan and it has been one fear factor after the next with him just grinning ear to ear at me like, "Isn't this great?!" while I'm thinking, "You crazy bastard. Why am I here?".

Ah love.




My first trip was just Ethan and I trying to catch some dinner (because god forbid we just go to the store). The problem was it had been a long 48 hrs for me with school and then driving up north. Though it was my own fault, I did not want to be awake never mind drilling holes into the ice by hand that afternoon. Nevertheless, we set up the holes, the shanty, the tip ups, and sat down to begin the hunt. To make things interesting, we made a bet that whoever caught the most fish got a massage from the loser (my idea, cardio kickboxing class killed me that week). Ethan then taught me how to jig the line and what to do if I felt a tug (pull very quickly up and then reel in). Then we started to talk about… something... See, I might have fallen asleep at one point while he was talking to me…. great girlfriend right? In my defense, when he was my TA (prior to dating or even thinking I'd see him again) I used to sleep in the front of the class when he gave his lecture for lab. (Probably not helping my case huh?)

Fine, maybe this will be a better defense: I had borrowed the heated seat I got him for Christmas and had a blanket… I was toasty and his voice is very soothing.

I can relate to this so much you have no idea:



Even with my snoozing, I totally kicked his ass and caught 4 fish while he caught 1.  Nothing was big enough for dinner, but it was fun seeing how he fishes and once I woke up, to spend quality time talking (that and getting a massage!).




My second trip was with Ethan and Marcus, participating in an ice fishing tournament at Club Pond in New Durham, NH.

Once again I had very little sleep the two days prior (Notice a trend? My subconscious is always in denial). I had stayed up late Thursday night closing out a bar with some friends in NoHo (Northampton) and then Friday night I went to the microbio departmental TGIF and then drove two hours to Dover that night. I didn't get there until 12:30 AM and this time we had to leave by 7AM to make the tournament starting at 8AM. It was a long morning and I was getting nothing despite moving around the lake and making the place into swiss cheese.

After about 3 hours of staring into a pit of watery darkness and swigging back a nip of tequila… I felt a tug.

A tug! Finallythank God. I yelped out of excitement and started reeling it in, hoping maybe I could contribute to the men's pile and prove that I could be a fisherman too.
How I felt at that moment.
I pulled it up waiting to see a huge Perch, or maybe a bass, or maybe something that I don't know the name of! … Well I got the third one right at least. I caught a baby Pickerel… or as Ethan said (trying not to laugh) a "slime dart" when I frowned and held it up.
And cue *frown*
Meanwhile, literally not even 20ft away, Marcus all of a sudden is making a lot of noises (mainly "I think it's a big one!") and then all of a sudden dives his hand into the water. He triumphantly whips the fish into the air: a 3lb and 2oz large mouth bass.

…Really?!…. <20ft away?!?

I was happy for him (and bummed by tournament rules we couldn't keep it for dinner) but now I was glaring at my hole with disdain. Traitor. The last 3 hours I drank a PBR and dozed in and out at my hole (too tired to make another after 4 that day). Not a single bite. 6 hours on the ice and one slime dart. Yeah, screw you too mother nature.

Despite the fish doing this behind my back:

                                

We had fish tacos that night :) … and a sunburn on my face. It's what I get for falling asleep with my face pointing at the water…sigh...

Side note, I thought this article sent to me by my friend Jen was entertaining about luxury shanties.

I showed Ethan the article and his first response?

"…I think it's funny people are willing to pay that much for them…I can tell you they aren't true sportsmen haha… They build their own!"

Oh and in case you were wondering? He has built his own shanty back in Michigan.

Sometimes I wonder….
Okay, before I end this post I am trying something new. There are a couple polls on the left side of this blog (below my picture). I would love if you at least participate in the polls if you don't want to comment.

For those that have fishing experience in the NE area and want to comment below, all I ask is maybe just say the pond/lake/river where you've had the best luck? Looking for places to try out this summer/next winter and could use your help. If you want to brag on your catch too, by all means! (photos are welcomed!!)

Enjoy!

Monday, March 3, 2014

life in eden had changed

*Attention: If you are looking for science related posts, this is not one of them. I accidentally wrote a novel on my personal life and I decided I should probably do another post soon just on science. Sorry, just wait a bit.*

Hey Guys,

The title of this blogpost is from "Eden" by Sara Bareilles. This particular song I love because it has a lot of meaning for me once I settled into western Mass. It's a little on the morbid side for her, the lyrics describe her dislike of her old home and why she left. For me, I loved "home" (UNH). What I can relate to is the idea of growing out of a place over time and that "life in eden had changed." I visit Durham and Dover still on a regular basis but it isn't like visiting "home" anymore. A place I enjoy? Most definitely. It’s how I enjoy it that’s different. It was funny because I didn't realize it until I went up in the beginning of the school year. I was waiting downtown for Ethan to finish up his lab work so we could go to Portsmouth. I went to Breaking New Grounds to get a coffee and I made note that all the people that worked there had filtered out. I ordered the special as usual and went outside to sit and people watch by the stone benches that people typically never see (there's a lot of trees and its sorta hidden between the bagelry and hair shop). I saw freshmen walking around with their parents and getting textbooks. The "bleed blue" t-shirts everywhere and of course, the tremendous about of spandex and flip flops from the new comers and the younger undergraduates. I felt like I was in a glass box just watching it. Weirdest moment of, well, one, I miss when my ass was that small and I actually could have worn spandex like that, and two, I wasn't coming back that fall to start class. I then drove "home" (Granby, MA) that Monday morning and slowly over the past 7 months have morphed into my new "Eden".

In one of the posts I had written about all the new stuff I found and the great people here (also there is a secret post in another blog site that I put a link to for those that want to try to find it). It was more of list really and just me still getting excited and trying new things. Now? I actually have a routine.

To clarify, I have a grad student routine. I figured I would share this life with you since when people ask me what grad school is like all I can think of is well, a lot like undergrad, but I have to act like an adult and now I get paid to stress out, pull long nights studying, and take exams… not to mention complete lab work and come off across some what intelligent in between dancing in lab with huge skull candy headphones when no one is around.

Now I haven't had to do this as much as others because I'm new (though I see it on the horizon starting as the weeks continue… 8 westerns in 1 day? Challenge accepted.) but with grad school, you don't have a "weekend" or a "9-5". You come in when your experiments need you on the weekend and when you are home you are studying for your exams or prepping review sessions for your undergrads. Actually for most of us, you are constantly reading science literature to stay up to date on your project. With undergrads, "C's get degrees". For graduate students? You need a B minimum for some courses, or like right now, an A- is the lowest I'm allowed to get in my Cellular Physiology course this semester to qualify for candidacy. You actually have to earn your degree beyond the classroom… so it's nothing like undergrad life. Not to say we don't have fun though. I was told by a history professor once that graduate school would be the best years of my life and put my undergrad memories to shame. I am gladly willing to take that bet, after all, life in Eden had changed.

For one, it's amazing how once you actually see the receipt of a gym membership how much you then want to use your pass. It's unreal. As an undergrad, everyone who knew me would have known that I was super athletic in high school but in college? Ha. Maybe went to the gym a handful of times a year, if that. Now? I get my calves, hamstrings, glutes, biceps, abs, etc handed to me in a pile of mush Monday-Wednesday (Thursday/Saturday is yoga, not as extreme). Cardio Kickboxing? Oh yeah, I'm becoming a regular. I used to make fun of the girls that went when I was at UNH, calling it a "biddy fest". Now I am one of the oldest there and sweating like a pig in heat in a baggy t-shirt and soccer shorts amongst spandex and tiny little waists that I could break with one finger. Spinning Class? Nothing says "I hate myself" like cycling for an hour and not gaining any distance other than away from sanity. And finally on Thursdays it's sample day for me. Pick a class and see how it goes. Piloxing was my favorite so far of "Oh dear god, never again". I mean, my arms were on fire and I'm pretty sure I could hold up for like 5 seconds now if I did an arm wrestle with Ethan (hockey player… goalie actually… so big arms); however in this class she made us shimmy. Yeah, shimmy. Grown 22+ yr old grad students shimmy with students that we probably are TAs for at some point in the following years. If that is not a humbling experience, I don't know what is.

Actually I lie, I do.

She then at the end had us do this three step move and yell "sexy, strength, and power!"… my lips were shut tight. If you haven't picked up on it already, I don't go to these things alone. There's about 5 of us that try to go to these classes together. If I didn't have them (and the receipt hanging in my kitchen) I probably wouldn't be as dedicated. What's nice is the evening classes, though insanely crowded, are after most of us have finished lab work and have hit the point of "If I don't get out of lab soon I will start making evil fingers with the P1000 tips" (don't worry if you don't get that, that's a good thing). Especially us first through third years still dealing with classes, the preliminary exam to be considered for candidacy, TAing, and then our actual lab work. The gym is a release at this point, but I say that with also a big hint of endearment. I really do enjoy the comradery I have with these 4 people. Not to mention The Pub (cue heavenly angels singing). Nothing says a Thursday then having an embarrassing/tiring/funny/etc workout followed by a $5 special (burgers, tacos, etc) at The Pub with a beer. May or may not be a huge highlight of my week.

Secondly, as a first year we do rotations to get a feel of not only the department, but what would we like to do for the next 5 years. Meaning I join different labs for a semester each and then at the end of spring/summer I figure out which lab I would like to work in. In a sense, it's speed dating. Think about it. A semester is 4ish months. How many of us say that when dating the 3 month point is the "hump" month. Either you stay to invest in a long term relationship because you've seen what this person is like for the most part and the honeymoon stage is fizzling down or you run out of the room screaming never to return. Aka: rotations. Well, okay not really. But not only do you get a feel for what the lab is like, they also are getting a feel for you. It's a good set up and there are no surprises in what you are getting into. At first, to be honest, I thought it was a little silly. Just get your degree, who cares as long as it gets you to where you need to be in the end. Now, I see its importance. I've enjoyed the two labs I have been in. As mentioned prior in a post I was working with anaerobic bacteria dealing with environmental biotechnology, something I have never done before. The work reminded me of my undergrad (bio-energy aspect) so that was slightly familiar but still, completely new. My current rotation I am working with aerobic bacteria focusing on cell cycle and protein degradation. No environmental at all, but gaining techniques I only read about as an undergraduate or saw the TA do an example of. Two completely different labs (and two different buildings even). I'm getting a sense of what I want to get out of my degree as well as who I see myself as research scientist.

Finally, in case some of the prospective students creeped on facebook and found me (I noticed a spike in views for the blog since the Microbiology Retreat) here’s just a quick glimpse into the random crap you will get yourself into that makes it clear life in Eden has changed when you enter into this realm of academia.

You will do things you said you’d never do. For instance, I have now gone ice fishing... twice. If you plan correctly and save up, you can still take trips. I just took a four day trip in January to Florida to see Machayla and Colin (thank you Ethan for the wonderful Christmas present again). You will also find entertainment everywhere. I am going to Michael Jackson The Immortal World Tour by Cirque du Soleil this week on campus and a Boy and Bear concert late this March in Cambridge. You will become athletic to keep your sanity… there’s now like 5 or 6 of us running a Cosmic Run in Hartford in April. 

Yet when all is said and done… You are still in your twenties. You will still have those nights where next thing you know you and your friends are drinking, eating fruit dipped in chocolate, and desperately trying to follow the “Just Dance” video game icon and the others secretly video taping you slamming your knee into the coffee table...

There’s so many more stories I want to type out but this is literally 3 pages long (I wrote it in Word first)… so I should stop; however, next post I have some cool stuff I’d like to talk about I learned in class as well as maybe going into more detail with certain events that occur (ahem, ice fishing… twice.) For now I am going to advertise some music but this time I am plugging for a local band… which happens to have my mother in it. Yes folks, Valerie (or as my friends know her, "Val") is a paid singer (yay mom!). The band is called Wooden Soul, which specializes in acoustic rock (though they also do way more than that. Check out their playlist) and is a duo of my mom and Rudi Glenn Ridosh. Restaurants, weddings, private occasions, you name -they do it. I may be biased but they are pretty damn good so if you are in the southern NH area you should go to the local places they sing at… just saying.

Please follow them on Facebook here

Check out their YouTube videos here

Enjoy!

PS: Anyone got some good stories from first year out of college please share!

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:

6:30AM
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.

7:00AM
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.

7:15AM
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.

7:20AM
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).

7:25AM
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.

7:27AM
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).

7:45AM
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.

7:50AM
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.

8:10AM
I pack up and put on my shoes. This is the signal. Bags races to the kitchen once my shoes are on.

8:15AM
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.

8:20AM
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).

Enjoy!