Monthly Archives: October 2013

Chutes and Ladders

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!

Disappointment, then excitement!

I felt quite stupid during Wednesday’s lab…but that is normal in a first year bio lab I am told! Well, I pulled out my 5 plates, which I had plated by possible plaque on. I knew that my -1 and -2 samples should have the highest concentration of phage on them. But when I looked at the plates, there was nothing! It was essentially just my lawn of M-Smeg. But then I pulled out my -3 and -4 plates, and noticed there were spots of clearing on them. I figured it was contamination and started preparing to get soil. However, I quickly wanted to check with Dr. Gibbon to make sure I was doing everything correctly. He quickly looked at my samples and said, “Wow, you have a lot of phage!” Thinking I knew better than him, I quickly proceeded to explain that my -1 and -2 samples should have a higher concentration, but they have nothing on them. Therefore, it didn’t work. He just laughed and quickly explained that I had so much phage on my -1 and -2 plates, that all of the clearings ran together and covered the entire plate! That is how my lab on Wednesday quickly turned from disappointment to excitement!

Some Phage Today

Hi Sea Phage Researchers,

Today after class I went and looked at my plaques, and I believe I have a phage! There was some contamination, but I think I can harvest some phage from my plaque. I obtained the phage from a flowerbed outside the BSB.  I will start my purification on Monday after I have let my phages grow some. None of my other 6 samples showed promise of a phage. I was hoping to find some more phage in my other samples, but hopefully I will be able to harvest the phage I harvested from the BSB flowerbed. Next week should be promising.

Intelligent scalpels?

I know that the majority of you are pre-med and some of you might be headed toward a career in surgery. My father was a pathologist and one of his important tasks was to perform frozen sections on surgical specimens from patients on the surgery table to determine if the surgeon had excised past the margins of the tumor. When I was a teenager I would sometimes accompany him to the lab if he had a call on a saturday. The procedure is fairly simple, the tissue is placed on a metal post, covered with a viscous gel matrix, placed in a cryostat to freeze and then sections were cut from the frozen block using a microtome in the cryostat. the sections are then fixed to a glass slide and stained before the pathologist analyzes the samples to call back to the surgical suite to tell the surgeon whether (s)he needs to excise more or not. The problem is that this takes at least 20-30 minutes for each sample, all the while the patients are sitting on the table  under anesthesia and the surgical team is just waiting.

I bring this up because earlier this week I saw a feature in Science that a company has developed a ‘smart’ scalpel, the iKnife, that can detect whether it is cutting cancerous or normal tissues. The scalpel can essentially sniff whether or not cancerous tissue is being cut. It does this by using a cauterizing (heated) blade that volatilizes compounds from the cells like phospholipids, metabolites, etc. Then a small port near the blade sucks in that smoke and volatile material and it is analyzed by a mass spectrometer. The pattern of molecules can be used as biomarkers to discriminate healthy tissue from cancer tissue. Pretty cool stuff!

http://news.sciencemag.org/2013/07/smart-knife-sniffs-out-cancer-cells

Mycobacteria in Aquariums!

As I was reading articles on the Tropical Fish Hobbyist website, I like keeping fish weird I know, I came across an interesting article. I have had many different fish over the years ranging from simple freshwater fish, to jellyfish or lion fish but I have never heard of Mycobacterium in aquariums! Mycobacteria usually are not pathogenic to humans, except for a few such as tuberculosis and leprosy, so this was an interesting find since some of us are working with mycobacteria. M. marinum can be found in any type of tank (freshwater, saltwater, and brackish) but luckily are rare infections to contract.

M. marinum infections can be pretty difficult to diagnose considering that there are few doctors that know about the various infections originating in the aquarium; also the fact that M. marinum has an incubation period of four weeks doesn’t help. The bacteria gains entry into the body by small cuts that are exposed to the infected water. Once inside the bacteria are quickly phagocytosed by macrophages, such phagocytosed material is normally degraded in lysosomes; however, mycobacteria resist lysosomal degradation and somehow manage to survive and even multiply within macrophage phagosomes!  In an effort to contain the infection these macrophages clump together to form granulomas, which are mainly found on the superficial layers of the skin in an M. marinum infection.The bacteria gains entry into the macrophages via receptor mediated phagocytosis and certain plasma membrane cholesterol recognition. Certain antibiotics deprive the macrophages of this cholesterol so that the mycobacteria have no means of entry. This inhibition of uptake is specific for mycobacteria, as other microorganisms can still enter cholesterol-depleted macrophages.

This bacterial infection isn’t as virulent as tuberculosis, but can be pretty annoying as it can persist for one hundred and sixty days on average! So next time when you’re fumbling around in you’re aquarium, hopefully I am not the only one who does, look for cuts on your hands before putting them in the tank, or else you might contract a mycobacteria infection! Just thought you’d like to know!

 

Update

So today, I observed my plates and saw that my agar had slipped. However, I did see my phage! Thankfully the agar problem didn’t affect the phage. Although my phage is pretty weak, it is very uniform throughout. Today, I repeated the the purification process once more (this is my second time). I’ll have to repeat the plaque assay procedure one more time before moving on. Hopefully my phage doesn’t die! I’ll do my 3rd purification step on Monday.

Proud New Parent (of a phage)

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!

It’s Here!!

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.)

What is Going On?!?!

I got to check out my plaque assays today and found no phage whatsoever. I can’t really tell if I made a mistake when doing the plaque assays or if I’m cursed. I’m pretty sure it’s the latter. Anyways, I think the issue might have been with the top agar as it was having some issues with solidifying again. This time I picked the plaques from the spot test that I did for these plaque assays instead of the actual “0″ samples so that could make a difference. I made sure I was extra careful while doing the plaque assays and the TA that I made seemed to be working pretty well, especially since it actually solidified. Well…here goes nothing.