Archive for September, 2013

Sep 30 2013

Bacteriophage Therapy

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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/

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Sep 30 2013

And the process continues..

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Sep 29 2013

Results of first round of purification

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Great results! On friday, after class, a few of us went into Dr. Gibbon’s lab to go check on our phage plates and the first round of purification went great! Some students had very invasive phages, but the ones that I have are much less aggressive and much more difficult to see. Despite these differences, I am still very excited to have truly begun the process of isolating a phage.

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Sep 28 2013

PUPPY!!!!

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Sep 27 2013

The Case of the Missing Agar Plates

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Sep 27 2013

False Alarm?

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On Monday I was really excited because I had a possible phage! The thought of never collecting soil again was exciting! However, when I entered lab on Wednesday, and grabbed my plate, my hope was disappointed. I definitely had something lysogenic on my plate. Something ate away some of the bacteria. However, it was most likely not a phage. A phage would eat the bacteria completely, leaving clear spots on the plate. However, my plate had rings eaten away. In other words, it appears that there is a bacteria in my soil sample that is eating away – not a phage. However, I am not giving up hope yet. I refiltered all my possible plaques from Monday. I also picked the plaques again from this plate. I just want to make sure that it is definitely not a phage! So as of now, I have a 5% hope that it is maybe a phage…but I sense that next lab I will be back digging up more soil.

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Sep 27 2013

Interesting….

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I was on the New York Times Webpage trying to catch up on the real world when I came across this… Pretty interesting, especially considering what we’ve been talking about with the extracellular matrix
ScienceTake: Bacteria's Private Line

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Sep 27 2013

A Not So Enriching Experience….

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Sep 26 2013

Results?

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Some of you were testing the hypothesis that your filtered samples were contaminated with bacteria so you refiltered the samples and respotted on Arthrobacter.
What were your results? Did you have phage? contamination? both? neither?

Please post a reply here and we will be able to see the sum of the experiment.

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Sep 26 2013

Cloudy with a Chance of Lysis

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Sep 25 2013

A brief History of My Studies in Science/Bio 1405. (And kinda what’s going on in my head)

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Sep 25 2013

Hello world!

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Sep 25 2013

Glimmer of Hope

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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!

No responses yet

Sep 25 2013

Awaiting Positive Results

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Sep 25 2013

Comment on Learning How to Fold.it by bryan_gibbon

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Sep 24 2013

Finally!

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Hello fellow Sea Phage Researchers,

So for my first blog, I decided to share a link I thought was pretty fascinating. It’s about a girl who makes an algae biofuel lab in her room- pretty inspiring stuff! Hope you guys enjoy it :)

http://www.huffingtonpost.com/2013/03/29/sara-volz-17-year-old-mak_n_2979408.html

Also, I’m so happy for the people who were able to find phage colonies yesterday! I unfortunately had contamination, so I refiltered my samples again. Crossing my fingers!

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Sep 24 2013

Learning How to Fold.it

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Sep 24 2013

Monday’s Results

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Sea Phage Researchers,

My sample yesterday still yielded no phage. I had some contamination on a plaque, but not where I put my soil samples. Therefore, I put my entire sample as negative for the Arthrobacter plaque. I filtered my third sample again and spotted a plaque to try this sample again. If this sample yields no phage, I will try an entirely new sample from around campus. Maybe this will yield better results.

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Sep 24 2013

Hope (Finally!)

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We finally got some good news this time!

Even though I did not get any plaques or lysing on my plate, there were about ten people from our class who did. I have to admit, it was disappointing seeing next to nothing on my Arthrobacter plate and rampant contamination on my smeg plate, but I am glad to know that there is some hope out there. We finally have results that suggest that finding phage that infect Arthrobacter is achievable, and that makes me even more determined to find putative phage in my own samples.

Today I did a little troubleshooting myself today and I think I have a hypothesis as to what happened with my Arthrobacter plate. I will post the picture of my plate, but it basically was a lawn except for the 10^0 section of my plate. That section had  a little bit of bacteria growing on top of the top agar, in a splattered pattern. I realized, after looking at my lab notebook from the previous lab, that while spotting my 10^0 serial dilution, I splattered the dilution, possibly from pushing down on the pipettor too quickly or releasing the liquid too far from the plate, onto the plate. The latter makes more sense, because no other section of my plate had contamination. I think that the 10^0 filtrate was exposed to bacteria in the air as I was transferring it to the plate, and subsequently caused bacteria to grow on top of the top agar. If this did happen, it makes sense that there was no other contamination on the plate, as the contamination occurred after I performed the serial dilutions.

Today I re-filtered my soil samples, and put them on a new plate. I tried really hard to minimize contamination by working quickly and keeping things covered when not in use. Hopefully, there will be no contamination and the re-filtering of the samples will result in some phage in my plate! Let’s keep our fingers crossed for Attempt #4!

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Sep 24 2013

Success at last!

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Today in lab, we looked at our samples and although there was a widespread problem of contamination, about 9 or 10 of us were able to form/find phage and plaque colonies! The old host was unsuccessful (Mycobacterium Smegmatus) this time, but for some reason (likely a better round of bacteria) a few of us (myself included) were able to cultivate some phage! This is really exciting because I was starting to question what we were going to do, since we had already attempted twice to no concrete avail. However, now, we are able to begin the isolation and purification process of the phages.

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Sep 23 2013

Contamination

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http://www.the-scientist.com/?articles.view/articleNo/37562/title/Lab-Tubes-Contaminated-with-Virus/

The article associated with the link above was interesting as we have some contamination on our plates in the lab. While in our case we have bacterial contamination, it can still serve as a reminder to handle everything carefully.

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Sep 20 2013

New Procedure

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Yesterday (18 September) all of us phage-ers used a slightly different procedure. We prepared the agar plate as usual to go along with our final samples, but we also prepared another plate with 7H9+1mM CaCl_2 agar and the host bacterium that has been used in years past: Mycobacterium Smegmatus (Smeg). We spotted that new type of plate with 0, -1, -2, -3, and -4 concentrations of each of our three phage solution samples. Today (off-day for lab) I went in to go check and see if one day was possible a better time than the five day growth time that we usually allow. With the Arthrobacter host, the results are unclear. Most of the class’s plates seemed very clean; however, my plate and Walker’s plate both showed some possible phage action: his much more so than mine, mine is likely just contamination. But when I looked in the incubator at the plates for the Smeg host, many plates showed very positive signs of phage presence: a welcome sign! I am hopeful for Arthrobacter Phage activity in at least Walker’s plate and if that fails, for some progression of research with the Smeg host.

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Sep 19 2013

New Strategy Today

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Hi Sea Phage Researchers,

Since I finally learned how to use this blog today, I can actually post something about phages. :) Today Jeremy and I did not mix up our Arthrobacter bacteria samples. So that is positive. Because our recent trials have ended in either contamination or no activity at all, we used a different agar and a different host, and we also used the same agar and bacteria we used before to test our last sample of dirt that we acquired before lab started. I used a soil from my hometown in North Dallas and I also used a sample that I acquired just 30 minutes north from Waco. Hopefully these will capture some phage in the soil. I put all 3 samples in both of my agar plates just to grab some more info and retest one of my samples. I am excited to see what will happen on Monday!

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Sep 18 2013

CDC Report- Antibiotic Resistant Bacteria

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Sep 18 2013

The Missing Phage Song

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