Archive for December, 2013

Dec 06 2013

Almost there!

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I’m finally about to catch up with most of you guys in lab! Yesterday, I went into lab and prepped/purified my DNA pellet for DNA digestion. Thankfully, I had help from Dr. Adair and was able to conduct the procedures without much trouble.  Otherwise, I probably would have been stressing out.

Something funny that did happen though–when we placed the microcentrituge tubes into the mini-centrifuge to spin/dry the filter for the final time, we heard a loud click as it began spinning.  We didn’t think much of it, and assumed that it must’ve been something snapping into place as the tubes were spun.  We were wrong.  When we looked inside the machine after the two minutes was up, we found that the plastic microcentrifuge tubes had cracked and shattered.  It’s never happened before, but luckily, my columns with the were undamaged, meaning my phage DNA is still safe! Yay!

I’m not even sure what I would’ve done if my phage DNA just splattered everywhere in the centrifuge.. I probably would’ve had a mini melt down. No joke.

I’m really excited to start the digestion today! I can’t wait to finally see the infamous DNA that we’ve been studying for so long.

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Dec 06 2013

Finally Moving

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Dec 05 2013

Roar

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Dec 05 2013

Electrophoresing Amigo

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Dec 05 2013

Comment on Waiting for Supername by yasmenewarrad

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You could name your phage amiga and our phages can be best friends… or Aragog. Thats good too!

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Dec 05 2013

Already the end?

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Where has the time gone? It feels like yesterday that I was awkwardly digging through the soil, trying to find a phage. But literally just yesterday I basically completed the lab – I finally got my picture of the gel! (I essentially know what the DNA of my phage looks like!) I had the opportunity to tell a few of my friends what I have been doing in this lab, and they were amazed. They thought it was incredible that I had the opportunity to do all of these advanced laboratory procedures. And looking back, it has been crazy! In the beginning I did not even know what a microcentrifuge tube was. And I cannot wait for next semester when we spend time in the library researching and further understanding everything we learned in the lab.

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Dec 05 2013

Comment on It’s Coming to an End… by Saiaparna_Konde

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Dec 05 2013

Pizooky!

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So today, I was able to name/archive my phage. Because discovering that I had a phage made me as happy as eating a pizookie, I named it after the best dessert in the world. 

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Dec 05 2013

Comment on Sad Day by allenkarstens

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Yeah! Mine broke too! I feel like they are super easy to accidentally tear! What was crazy was when she was looking at mine you could still see the tear moving! haha crazy.

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Dec 05 2013

Bittersweet

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Today I finished my restriction digest. It was kind of stressful in the since that sometimes when pipetting .69 micro litters, its hard to tell if anything is actually being pipetted! (And not to mention the entertaining frenzy of everyone on that same step fighting for each of the enzymes and their perspective buffers!) But now that thats all done, i’m moving onto the final steps including the electrophoresis. This part of the lab has been so cool because i’ve gotten to work first hand with some unbelievable equipment for any undergraduate, especially for a freshman! (Heck, I even got to troubleshoot the photo spectrometer!) So I really am sad to see this experience go, but next semester is where we get to actually dive into our results and that too is exciting.

I remember when I first applied to this program. I was expecting to see some pretty cool stuff under a microscope and actually get some biology lab experience. But it really has turned out to be so much more. It still blows my mind with all the stuff that we’ve been able to do this semester! I want to believe Dr. Gibbon when he says that next semester is super cool, but I feel like comparing it to this semester is going to be pretty tough!

 

Oh, and I found a really really interesting study for my last blog post! So be on the lookout.

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Dec 05 2013

It’s Coming to an End…

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Dec 04 2013

Waiting for Supername

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Dec 04 2013

Just a lonely cell living in a 3D world

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Dec 04 2013

Comment on Robots=Humans? by Kirby

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I agree, there is a very fine line between allowing the ease of technology to provide a relief from tedious work and using said technology as a crutch for incompetent individuals. I believe this branch of science still recquires a lot of research and work but I look forward to seeing more of this robotic technology in the future

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Dec 04 2013

So we meet again….

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Dec 04 2013

Sad Day

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So on Monday I was able to check the concentration of my DNA using the spectrophotometer. The concentration of my DNA was surprisingly low. I don’t know what the next step will be, I think I’ll be making a gel, but today I will be making a grid because I was not able to make a grid last time as it was breaking apart. Let’s hope I can find a phage today.

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Dec 04 2013

Oxytocin can Help Autistic Children

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I read the article at http://www.sciencedaily.com/releases/2013/12/131202162115.htm and found it very interesting. It is about how a nasal spray of oxytocin can help autistic children. I really liked this article because my best friend’s little brother is autistic, so I am always interested in new treatments for these sweet kids.

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Dec 04 2013

Long time no post

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Hey everyone!

Our first semester is coming to an end and unfortunately, I won’t be with you guys next semester! I switched my major to biomedical engineering a couple weeks ago and turns out that biology isn’t a part of the degree plan for BIOmedical engineering. Hmm…Weird. But, it is what it is!

But on a more exciting note–I am SO pumped about our EM phage photos! I literally squealed when I saw mine.  I was just a litttttle too excited. All the more reason I switched into biomedical engineering! The technology is just so fascinating.

On Monday, I plated a spot test for my ten 10-fold dilutions of my newly purified lysate. When I was spotting the 10 microliter drops of lysate dilutions, the drops didn’t form a circle/drop. The top agar seemed to be solidified (I waited about 7 minutes and doubled checked to make sure it wasn’t runny or moving). Either way, the drops spread out and made odd shapes, only to be absorbed by the TA within seconds.

My concern is that the drops ran together and will affect the titer calculation.. Hopefully this won’t be a huge problem since we only really look at the lower concentrations for calculations. Fingers crossed!

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Dec 03 2013

Everybody, meet mis Amigos…

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This past week I have been able to finally get a close up look at just what it is that we have been working towards this entire semester. As strange as it sounds, I feel so incredibly proud of those tiny little black spots with tails because they are representative of every hour we have spent working and researching in the lab. It is such a great feeling to be able to look at the finished product of your work and be able to say “all of that time and effort has paid off”. Those itty-bitty little clear spots we were working with at the beginning of the semester have matured  (not really, but it feels like it) into a fully grown phage with DNA we can look at and analyze. I’m looking forward to completing the next steps in the process, whatever they may be.

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Dec 03 2013

Comment on Close Encounters of the Phage Kind by allenkarstens

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Hahahaha! I love the name of the post (and the phage too) puns are hilarious! (When in good taste) But your phages seem a lot clearer and more defined than mine looked, but that might be because my grid ripped and she was somehow able to still find a picture!

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Dec 03 2013

A day in the life…

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Well not every day in research is worth bragging about.. yesterday was one of those days where not much got done and there wasn’t too much anyone could do about it. Yesterday I learned how to operate the spectrophotometer. While this is an amazing piece of equipment that at the end of the day did its job, it goes to show that sometimes things just don’t go as you planned. But! I did get my concentration for the DNA sample. I’m not sure if mine was really that concentrated, or if there is some contaminant DNA hiding somewhere in there.. but! I’ll be ready to calculate and perform my restriction digest on Wednesday!

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Dec 03 2013

Yours, mine, or ours?

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Firstly, my apologies for having not blogged in a very, very long time, but life got hectic and I tend to get forgetful when that happens. So here begins the first post of a sequence of several to follow within the following week and half.

Since my last blogging adventure, a lot has happened. After selecting a plaque from a serial dilution of my ninth sample, I proceeded to run my three rounds of purification, which included unfathomable numbers of arthrobacter plates and serial dilutions. These steps ran very smoothly, so smoothly in fact that I had a nagging feeling that something must have gone wrong (let’s be honest here, when has anything in this research project run smoothly without one single kink?). I guess you could say I was right. Somehow, between rounds 2 and 3 of my purifications, the phage I had been purifying became contaminated by Yazmine’s hulk-strong phage; and thus, the phage I had been purifying was no more :(.
Unfortunately, I did not realize this at the time and continued to perform the next few steps as if everything was normal. There were a few passing suspicions that we were both working with the same phage based on plaque size and the distinctive halo which formed around each lysogenic spot; however our titers were so drastically different that those suspicions were, for the most part, ignored. Even if we had caught the mistake at this point in the process, there wasn’t much that could have been done about it since all of the old plates containing my phage had been disposed of and it was already too far into the semester to begin again from the soil sample.
Needless to say this has been an interesting experience, but informative nevertheless as I am now aware of just how little it takes for contamination to occur and have become much more aware of my aseptic technique. This has also allowed me to see the variation that can exist between experiments even when they are done using the same methodology. While this may not have turned out like it was intended to, if everything always went as it was supposed to in a scientific experiment, the scientific community would miss out on the numerous numbers of innovations that have stemmed from mishaps. While it is still disappointing that I wasn’t able to analyze my own unique phage, I am still glad that I was able to contribute some assistance to the isolation and purification of Yazmine’s ultra-phage, Amigo, who now going to be sent off for sequencing. Adios Amigo! See you next semester.

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Dec 03 2013

Comment on Isolating and Purifying DNA by katelynpruett

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Thanks for forging the way for Group 5!

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Dec 03 2013

Comment on Tie between ALS and Genetic Mutations by katelynpruett

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That’s a really cool story Abby! I agree that a personal motivation like yours can be very inspiring.

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Dec 03 2013

Comment on contaminated lysate by katelynpruett

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I have now added #phageworldproblems to my daily vocabulary. Thanks for coming up with that!

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