So I was expecting to just walk in and do my last plaque assay and be on my way last Wednesday.  So I walked in and found that there appeared to be more than one phage on my plates (still??) so I had to pick both the “halo’ed” and the “non-halo’ed” plaques and see if they are two different types! This meant I had to do 10 plates of plaque assays to get the question answered no big deal… yet. As I was diluting my samples and labeling my plates it seems that people were walking around and asking to borrow a bit more than normal, so came out of my world of pipetting to find that we were running out of TA, and pretty fast. So then after what feels like a longer story that it probably was, I ended up doing two streak tests and two plaque assays to account for our lack of TA. I stopped by the lab on Friday and it looks like the two plaques might be the same thing! So in the end at least I got to really learn how to do a streak test. But! i’m ready to move on and flood!

Finally! It seems that most of us in the lab are in the stages of purifying. This is so exciting.  Pretty soon we’re going to be sequencing our own, individual, cute little phages! Go us.

Since this is a late post, it’ll probably be a pretty lengthy one.. I’ll try not to be so boring.

On Monday’s lab, I found out that my group’s Phage Buffer had been contaminated. (Curse you, contamination!)  So, I’m sure you all know what that means.. EVERY plate was contaminated.

My 10^0 plate was completely contaminated, while the rest of the plates had these dots of contamination.  Literally like perfect randomized polka-dots.  Cool stuff.

However, I was able to pick an isolated phage from my 10^-3 plate, a tiny little area that was pretty far from contamination!  If you look really, reaaaally closely, you can see the lysed area between the “(6)” and the date.

Hope everyone is having no issues with contamination! It seriously is a pain in the butt.

I am very proud to announce that I have finaaaallly found a phage! Despite the dearth of 7H9 Wednesday, Sierra and I were able to do plaque assays, so hopefully we have positive results on Monday!

I have finished all three rounds of purification and yesterday I flooded my 10(-1) plate. My phages are extremely small but there are hundreds on each plate. The top agar on my 10(-3) plate slide so I had to count my 10(-2) plate instead and there were 795 phages! By the time I had finished counting I was seeing little dots everywhere! I have been trying to think of names for my phage so I would have some ideas when the time comes but it’s really hard, I think I may just pick a name from a hat at random because I can’t decide!

Hey y’all!

I know that there has been a lot of problems with calculating titer (I know that it is hard for me to grasp exactly what needs to be done), but I have found this video on YouTube that has step by step instructions on how to calculate the titer of your plate. One of the professors from Ouachita Baptist University’s SEA Phages Program made the video pretty recently, so I guess her students are on the same step that we are. I thought it was really helpful in understanding what needs to be done and why you are calculating titer. She also explains it at a slower pace, which I know was beneficial to me. I think that now, when I get to that step, I will be more prepared for and efficient at calculating my titer.

Hope it helps you guys too!

Here is the link: http://www.youtube.com/watch?v=P14-ep2kag8

I have found that these past couple months have been like a really unlucky game of chutes and ladders. Every time we roll, we make some progress, but then we somehow always end on a chute. But last Thursday we rolled again and hit a ladder! We found a phage! Now onto purifying. Hopefully from now on we will keep having good rolls and hit all the ladders along the way. May the odds be ever in your favor!

I know that failure is supposed to be part of science, but failure still is not fun. I know Dr. Gibbon and Dr. Adair would probably say that all this time spent not finding a phage is a good lesson for us, but I am just so happy it is over. Finally, the end to enrich, grid the plate, serially dilute, etc., repeat is over! Bethany was kind enough to hand over her phage to my clumsy (but loving) hands and now we get to end the monotony of the past two months and work with an actual phage! Let the purifying begin! Tomorrow we get to check our purified phages and make more progress!

Today, I adopted an M. smeg phage from Jade! (THANK YOU SO MUCH)

After trying almost ten soil samples, I just wasn’t finding either Arthro. OR M. smeg.

I just think I had bad luck when it comes to finding phages.

But anyhoo–as of right now, I’m in the process of purifying the phage I picked today and hopefully, I’ll be able to isolate a single phage with no contamination or major problems.

Thankfully, we’re all used to the lab setting now and aren’t having too much trouble finding materials or preventing contamination (yay!).

Either way, I can’t wait to see the plates I spotted next week!

Like the many others in the lab, fingers crossed!

So my phage finally decided to show itself. While there’s a small part of me that really wanted to keep trying arthrobacter… I’m very glad to be moving on with the research! Now that i’ve done my first plaque assay, it looks like there are actually multiple types of phages in my one sample! ( I feel like the m-smeg is mocking me…) But certainly no complaints there! So its time for the purification process and getting this phage by itself!

An on another semi-biological note, on my home page there are always little grab-bag news stories, and they found this fish that can grew 18 feet long! Turns out this was an oarfish. They apparently only live in water that is thousands of feet deep, and are rarely seen dead or alive. (Insert Bon Jovi pun here.) The fish was found dead in the shallow waters around Catilina Island, which is of the coast of California. Not sure if this was just to make the Time article more interesting or if this is true but the article said that this is the fish believed to be behind many sea monster stories! So the fish was buried and the marine biologists who found it are waiting for it to naturally decompose before retrieving its skeleton. (I watched the video of it and the lady who found it was wearing a Texas A&M shirt… So lets be honest, this is cool, but not that cool.)

I know some of you, like myself, are getting a little discouraged with all the lack of phage, so I thought I could comfort you with this article!
It’s called Bacteriophage Therapy and it talks about all the clinical advances made because of bacteriophage. Phage are extremely effective in killing specific host bacteria, are safe to produce commercially, and can be genetically modified to accommodate mutations in bacterial strains. These qualities make phage ideal therapies to combat bacterial infections like lyme disease, laryngitis, gingivitis, in addition to many other common illnesses.
The article also tells of the history of phage therapy and all the trials and failure many scientists had to go through in order to make it to the point where the scientific community accepts phage therapy as “potential useful.” So don’t give up! Even though are research is not as near as complex as phage therapy, if they have some success, we are bound to have success.

Read the article below:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC90351/

Still no phage you guys. Because of phage buffer contamination, I repeated my serials dilutions for samples 4,5, and 6 and plated them again using new phage buffer. And I collected and prepared new enrichment cultures for two new samples, just to be ready to try more soil in case nothing is on the plate. Hopefully plaque show up on one of these samples, and there is no contamination.

But instead of dwelling on the lack of phage, I thought I would share this video my little sister sent me of bacteriophage. She is in freshman biology in high school, and I guess they watched this in class.  It’s really coincidental since we seem to be having an epic science video war in class. She was like, “Is this really what happens?!”Either way, I thought it was hilarious but really cool at the same time, and I’d like to think that when phage eventually infect my Arthrobacter, it will go something like this:

http://www.youtube.com/watch?v=rzdwfwuVWUU

It is possible that the reason for our grainy agar (and lack of plaques) is not due to the concentration or age of our saturated culture, but instead the temperature of the incubator that the top agar plates were grown in.  Can you design an experiment to test this hypothesis?

Monday, September 23, 2013 could be my breakthrough day in the lab…or it could all be a fake. When I entered the lab I soon discovered that I had a possible plaque on my soil #3 arthrobacter sample! Though there is only a slim chance that it is actually phage, it is still exciting. One problem I am encountering though is contamination. On September 18, I prepared two plates. One used all three soil samples, with SMEG. My other plate consisted only of soil sample 3, with Arthrobacter. My SMEG plate was horribly contaminated. However, on this plate I put a control (plain phage buffer), and even that was contaminated. Therefore, that means that it was actually my phage buffer that was contaminated – which is not normal. Also, even with my Arthrobacter plate, there was contamination, but under the contamination there was possible plaque growth. I am excited to see my plates tomorrow. On Monday I picked the possible plaque – therefore, tomorrow will be the moment of truth as to whether or not it is actually a phage. On Monday I also re-spotted soil 1 and 2 with Arthrobacter. Therefore, I will see if any possible plaques arose on that!