Showing posts with label Weird contamination "patterns" confuses microbiologist. Show all posts
Showing posts with label Weird contamination "patterns" confuses microbiologist. Show all posts

Sunday, October 5, 2008

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!

Wednesday, August 20, 2008

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.