Contamination Fairy Drawing Contest [Updated]

Once upon a time, a long time ago, in a lab far far away there worked a microbiologist. For several years this microbiologist did her job, learned how to work with her cultures and developed methods that would allow her to test the objectives of her projects. She had her share of problems along the way, perhaps more than her share some might argue, but that was in the past and she was ready to put it all behind her as much as possible and move forward. About this time she was asked to help get another grad student trained in the art of working with her cultures. This concept made the microbiologist a bit nervous, the last time she had been in charge of training someone had been in her days of being a deli slave and it had not always gone well. As a deli slave whenever they hired someone it tended to be someone older that her and they did not always take kindly to a "stupid kid" trying to teach them how to do something. She quickly found out that V was not like that, working with V was great!

For awhile everything was happy and productive in the lab far far away, the only problems the microbiologist and V had were minor and they got through each of them without any trouble. They worked so well together, the microbiologist did not feel as isolated being the only one not working with pathogens and under a different professor in the lab anymore. And then one day the microbiologist looked at her plates and noticed that there were different looking colonies on her plates and when she looked at them under the microscope they were not the same, she had contamination! She decided that perhaps she had been using the same stock tube to get her cultures from too long and switched. That seemed to fix the problem at first until V showed the microbiologist her new plates, they were beyond contaminated, the Bifidobacteria had been totally overrun and there was nothing but contamination visible. They went back and forth a few times, sometimes V's plates were contaminated and the microbiologist's were fine, sometimes the reverse has been true, sometimes they have both had contamination...

About a month of testing and the source did not reveal itself and the microbiologist and her boss decided they should try moving forward again. And so they did, V made a new batch of yogurt and the microbiologist did her final preliminary run before getting going on her project at long last. The microbiologist waited anxiously for V's plates to come out of the incubator so she could look at them to see if she spotted any problems, and they looked fine. Then she took her own out, and they were quite obviously contaminated, she was crushed! The joy of getting back on track was derailed much like a toy train in the presence of a toddler. Being one that does not like to show such emotions in front of others the microbiologist took a few deep breaths and did what she does in such situations, she tried to make it funny, laughing is way better than crying! And thus the Contamination Fairy was conceived.

The Contamination Fairy is an evil fairy that likes to mess with the poor microbiologist's head. It randomly attacks the microbiologist and V's cultures leaving no trace of how it came in so the microbiologist is helpless to stop it from getting in that way again. It has been said that in order to beat your enemy you have to know your enemy, and this is where you come in dear readers. I am asking you and or your kid(s) to draw me pictures of what you/your kid(s) think the contamination fairy looks like. To give some incentive I am offering the winner their pick of one of the GIANTmicrobes. Here are the rules:

1. Each person can submit one picture, it can be anything from being drawn on paper using crayons/pencils/marker, it can be drawn with a computer program like adobe or pc paint, it can be a picture of a play doh/clay sculpture, as long as it is in good taste it can be entered. If you have several kids who can be conned into playing then each can make their own and be entered. To make it easier please make one comment per individual on this post, I will publish your comment after I receive the picture so you will know that I got it.
2. Electronic submissions are best, you can upload them on a hosting site and drop me a link in the comments, use this contest as blog fodder and link me to your post about it, or e-mail them to microblogologist@yahoo.com. I will allow certain people to mail me entries (no anonymous requests, I have to have some sort of proof that you are not a serial killer ;)), e-mail me and we'll discuss it.
   
3. Since I am allowing the idea of snail mail I will arbitrarily have the contest end on October 31, 2008 to give time for it to get here, I must receive all entries before 5pm central (3pm west coast, 6pm east) on the 31st. Winner will likely be announced that evening or on the 1st of November depending on how busy I am.
   
4. I have an international reader or two I think, not sure of the logistics of sending you the prize but I am more than willing to try to figure it out if you want to participate and have your art chosen.
5. This is just a silly contest and the prize is a silly stuffed toy that costs about $8. Don't take it too seriously and get mad if you don't win or something. Trying to sue me would be pointless, I owe the bank more than I am worth. (This should be unnecessary but you never know...)
   
6. Keep it clean, I will disqualify any entry I wouldn't be willing to show my niece (who is 5) and like the idea of decorating my lab bench with them.
   
7. Since I am only going to allow for one winner and have this open to everyone I plan to use a random number generator or something like that to pick the winner. I HATE picking favorites of pretty much anything and one cannot really compare a drawing done by an adult or older child with a younger one. This is why I ask for one comment per entry.
   
8. GIANTmicrobes inc is not aware of this contest, they are not liable for anything having to do with it (please don't sue me GIANTmicrobes, I love you guys!)
9. A few lines explaining why you/the kid made it the way they did would likely amuse me greatly (and would be a hilarious blog post that would totally write itself) but you don't need to, I would like to know the age of the kiddies so I can do the "That is sooooo cute!" thing.
10. Most importantly be creative and have fun!

**Edited to extend the contest deadline since I have not gotten a single entry =(. Niecey and Cheryl both made me pictures (I am not counting them in the "contest"), they are awesome and are currently hung with pride on my lab bench. Perhaps they will help spark someone's imagination:
Oh and special thanks to Deb, she wrote a totally sweet post about me and pimped this contest, it made my day! She is one of my favorite bloggers, which makes her the equivalent of a celebrity in my world, not only does she write hilarious posts but you get a bonus mini-post if you read the labels she puts on her posts. I totally try to copy her with mine but definitely do not have her talent for it! Oh and her linky love caused a huge jump in my google analytics stats, I have named the spike in the graph Deb's Peak. Thank you so much Deb!

Spread Plating and Guess That Gizmo

Before I showed you streak plating, that is a method that is often used when checking for contamination and is supposed to result in isolated colonies that originate from a single organism that lands on a spot and grows there until it forms a visible area of growth in the form of a dot. Spread plating is a very common method that is used to enumerate the bacteria in a sample. Most of my studies have to do with how well my bacteria survive in different environments and so I do dilutions to get a smaller number of bacteria per mililiter and spread plate the dilutions and see how many colonies I get, the concept behind said colonies is the same as for streak plating.

The two dilutions I commonly make are 1 in 100 (1 part of sample into 99 parts diluent) and 1 in 10. When I plate the sample I plate 0.1 ml so that adds another 1 in 10 dilution in the end. I multiply the number of colonies on the resultant plates by the number of times I diluted and it gives me the number of cells per ml in the original sample. Not diluted enough the bacteria form a smear across the plate, if too diluted then only a few colonies if any are present, I want approximately 20-250 colonies to have what is considered statistically significant results. And at risk of losing all of my beloved readers and having Baby Sibling make fun of how incredibly dorky I am I have made a video of me doing a dilution set and spread plating it:

Here are two plates, the one on the left I used the spread plating technique and the one on the right I streak plated:

You are still here??? Great! Now that you have gotten to laugh at me how about giving me a laugh or two (with you not at you), it is time for the next Guess That Gizmo!
Sorry about the not so sticky biohazard sticker, they just don't make 'em like they used to I guess:
And remember, this is a semester long contest so new readers can participate too, here are the rest of the Fall 2008 Semester GTGs:
Gizmo 1
Gizmo 2
Gizmo 3

Contamination

The contamination I spoke of earlier appears to be more widespread than we originally thought, as in I now have two out of four of my cultures showing signs of it. The "patterns" are still rather random and I am having trouble figuring out what caused it, I can't fix it unless I find the source (I suspect it is either the stocks or myself at this point). Once a pattern seems to emerge a result comes along that throws it out. V asked what we are going to do, I suggested hitting our heads on the lab bench until we don't notice/care anymore. My boss graced the path lab with her awesomeness, it was amusing that she has the same approach to looking at slides under the scope that I do, stare at one, switch to the second, go back to the first, second, first... Then go cross-eyed and look at the plates awhile before going back to the microscope. She got tired of it and said "This is why I'm a chemist." So much for my trying to convert her! The bugs look similar under the scope, hence the switching, and also we really really want them to be the same and the right bug, but alas when Dr. M looked at them he confirmed my (and likely her) sneaking suspicion, they are most likely not. Good thing I don't have stomach acid or I'd have an ulcer by now!

I have options, we will get through this, it is just very frustrating that I am once again stalled and poor V is as well. I feel extra bad for V since she has been going insane with this too and it originally looked like it could be "her fault" now it looks like it is not (it could be mine). Hopefully I will get to the point of posting more regularly, I have posts swimming around in my head but it takes time to get them written, and some require photoshop and possibly Baby Sibling. Plus I really need to get my progress reports done, they are a pain and two are late (the two I don't care about as much and protest having to do).

In the mean time here is a video I made of what I am recently doing a lot of. I actually made three, at risk of scaring you all away and having Baby Sibling laugh hysterically at me I am posting the one that I narrated. What I am doing is called "streaking" it is often used to test the purity of a culture, in my case I am actually spreading what are pretty much pure cultures onto plates that I added a chemical to that makes my research organism (Bifidobacteria) turn blue and the others stay white. This will likely confirm that I have contamination in at least two of my cultures. Oh and I wore the lab coat just for you so feel special, I rarely wear one, that's how much I love you guys.

Bon Voyage

Today I met V in the lab, haven't seen her in awhile since she is a morning person and I am a vampire. We went over our game plan for trying to figure out what is going on with the culture that keeps getting contaminated for her but not me. Her technique from what I've seen is solid, hell if we were unknowingly being judged she would kick my butt since I have developed short cuts that are not in the official rule book. We suspect there is a chance her pipette is contaminated, but that would make more sense if all the cultures were contaminated and not just the one... Oops, sorry, went into analyzing mode, I'm back. If you cannot tell this issue is somewhat of a big deal.

Microbiologists are obsessed with purity, contamination is generally one of our greatest enemies. We fight it with fire, chemicals, and good technique. Of course contamination led to one of the greatest discoveries in medicine. Dr. Alexander Fleming was actually looking for antimicrobials, he often worked with Staphylococcus aureus (the bacterium that causes food poisoning and is a common hospital acquired infection, it puts the SA in MRSA). Well he had some plates of S. aureus lying around (perhaps he had plate hoarding OCD like I do!) and one of them was contaminated with mold and he noticed that there was no bacteria growing by the mold. Turns out this mold was Penicillium notatum, which produces penicillin. I've had quite a few plates contaminated with mold but none have been quite that spectacular, though some are really cool looking! My coworkers likely question my sanity more than usual when I find a plate contaminated with a cool looking mold and dub it my "pet mold" and watch it growing until the plate dries out or it just stops. That picture is of one of my pet molds, this one formed a rather intricate pattern and has been fun to watch.

Well I finished with all that and was tinkering/loitering in the lab for a bit and got roped into helping order lab supplies for a bit. Then I noticed the time, it was 3:40, the next bus was at 3:50 and I wasn't sure if the post office closes at 4:00 or 4:30 (yes the post office here closes insanely early!). I almost rudely take my leave, one of those the person keeps asking you stuff after you tell them you have to go several times. I detour on the way out and google the local post office, it closes at 4:30, I had a shot at making it. The 3:50 bus gets me home at 4:00, then I had to throw crap into the box I found, tape it up, and address it before jumping in the trusty oldsmobile and hightailing it to downtown. I made it with 10 minutes to spare and the line was miraculously short given that the invasion of undergrads has doubled the population of this town in the past week.

I hand the nice lady the box and tell her it is the most important box she will have for the day. She looked at me as if I were totally mental and likely was considering pushing the emergency "crazy person is here, send backup!" button that I so know they have, telling her that it contained a priceless treasure didn't help my case either, until I mentioned that it was a ratty satin bow that a certain 5 year old loves to death. Then she got the "awwwww" look and was super sweet and told me I was such a wonderful auntie as she was getting the quote for overnight. When I heard that it would be over $20 I informed her that I am not THAT wonderful of an auntie! Besides, every time I have talked to Niecey one of the first things she has said was "Why haven't you mailed me Big Bear's old bow yet?", because she totally thinks that the USPS has same day delivery or something, she's gotta learn sometime... Ok fine, I'm cheap! But I did upgrade from the $4.70 or so "It may or may not get there in the next 6 months" option to the 2-3 day priority mail at a whopping $4.95, that makes me at least a sorta wonderful auntie right? The nice postal lady said she will likely get it Saturday since it is only going a state over.

I didn't attempt to insure it, though I have been contemplating the philosophicalness (oh hell yeah I can invent words) of it. To Niecey this is a priceless treasure she would trade just about any of her other possessions for I suspect. To pretty much anyone else it is a ratty piece of crap that they would carelessly toss in the trash. Thankfully my ingenious idea to have Big Bear "guard the car" when we go out somewhere that I came up with awhile ago automatically transfered to whatever lovie she brings on a trip and so there was less worry about losing the bow in public. Oh and FYI the car almost got stolen by TWO car thieves while we were in the lab, but thank goodness Big Bear was there guarding it and bit their butts and they ran away! Big Bear is so my hero!

And so dear readers who have followed the saga of Big Bear's old bow it is time to officially say goodbye, at least for now. Bon voyage Big Bear's old bow, have a safe journey back to Niecey Poo!

Oh and don't tell but under the fake grass skirt (another thing Niecey forgot here) there is candy, lots of candy. If Daddy or Baby Sibling read my blog they will have a heads up and likely intercept it, if they don't and Niecey opens the box unsupervised they may wonder why she is crawling on the ceiling >=) hahahaha!

Letters to bacteria

Dear Bifidobacterium breve,

You know I have a special place in my heart for you. You have always been my star bug surviving in whatever situation I put you in like a champ, I wish your siblings would behave as well as you do! That being said I have to bring up your recent bad behavior. It seems that lately you have been falling in with the wrong crowd. While I appreciate your domain's* diversity and recognize that it makes a total mockery of what human beings consider diverse I ask that you remain in pure culture and only hang out with the yogurt cultures that are intentionally put in with you. I know this seems harsh but how can you shine if you are overgrown by some bully organism? And poor V, she has worked so hard to learn how to treat you just how you like it and just when she is getting all independent and confident in her abilities you throw her this curve.

And don't you try and pretend you aren't contaminated, even my lab assistant was able to tell the difference between you and the impostor organism. Is this a ploy to drive us insane, because it is working!? I am glad that V decided to test you out before moving ahead with her project, she was on to you and your sneaky tricks. And that was very sneaky, behaving for me and not her making me think it was all a fluke. You will be in so much trouble if your stock** is contaminated! There had best be no other organisms growing on your plates currently in the incubator, and don't you think I won't check, you have definitely earned yourself some time under the microscope.

V and I would really like to get past this rebellious phase of yours and be able to get some real research done. Don't you want your name in the journals with us writing about how wonderful you are? Well that is never going to happen if you keep stalling us like this! So please, just go back to behaving like the wonderful organism I know you are.

Love,
Karen

First picture: Image of B. breve taken through a light microscope, 1000X magnification. Notice the irregular shapes and sizes of the cells (the little dots and lines), Bifidobacteria tend to be irregularly shaped rods.

Second picture: Image of unknown contaminant, same details. Notice the uniform perfectly formed rods, this is a pretty good indicator that this is not a Bifidobacteria sample.

*Based on genetics all lifeforms currently fall into one of three groups called domains, bacteria, archaea and eukaryota. Bacteria are the most diverse group, in comparison human beings are all the same, to me it shows how ridiculous prejudices based on genetic traits (like skin pigmentation and the like) are given how infinitesimal the differences really are.

**A stock refers to a stored sample of an organism, there are several different methods of storing them including freeze drying (like the yeast in the Super Yeast post), and frozen stocks (aka glycerol stocks). I prefer working with frozen stocks, which are prepared by mixing glycerol into a pure sample of an organism in broth and keeping it in a -75 C freezer. The glycerol makes it so when the sample freezes it has less ice crystals, ice crystals are sharp and can shred the cells you are trying to save.