Wednesday, October 29, 2008

A Five Year Old's Perspective on Virology

When Niecey came to visit me back in August she of course spent time in every room in my apartment, this of course included the home office/plant room (and thankfully the bathroom, she was a late potty user and almost didn't get to come because I said she had to be potty using in accordance to the state law to be allowed to visit). In said home office/plant room there is a wall that has dark wood paneling. This nasty paneling is actually featured through much of the apartment. I have seen worse but either way I am not a fan of it. To make it more livable for me I decided to cover/decorate it with my GIANTmicrobes collection and some family pictures. Now I actually like the wall, and so did Niecey. There was one microbe in particular that caught her eye, it is the plush for E. coli.

Every year there is this huge student-run/organized (somewhat mostly, the university seems to have a huge hand in it) campus-wide celebration that lasts a week but the main bash is on the weekend. This occurs in April, usually the weather is starting to get better and the frozen tundra begins to thaw so the fact that the buses are totally rerouted that weekend isn't quite as upsetting to me (I am usually stupid enough to try to work that weekend). Every year I try and make a point to visit the undergrad micro club's display and will often buy a shirt from them (they also sell giantmicrobes and sometimes other stuff). Last year they had made little replicas of bacteriophage (aka phage) out of a styrofoam ball, a wood peg and pipe cleaner and were giving them to whomever bought something from them. I was going to buy something anyway but really really wanted the phage. Phage are viruses that infect bacteria. Well I decided to put this little phage on the E. coli plush and thus my tangent now connects with the original logic train.Niecey can be a very curious child, as are most children her age, and so she wanted to know what that thing was doing on that microbe. I gave her a watered down version of phage:bacteria interactions and how viruses work. I am not 100% how well she understands virology at this point, but she does have some conception of it and this is her rather good interpretation of how it works:

This picture is one of my absolute favorites and I will keep it forever! I plan to eventually frame it, she was so happy that I put it on my fridge that I have left it there for now. I love how easy it is to make a child's face light up and their little chest swell up with pride! That is why I always try to pay attention when there are little kids around instead of ignoring them. A kind word from an adult can totally make their day and not much else makes my day better than making someone else's, adult or child but children are usually easier, lol.

Picture 1: Picture Niecey took when she found my camera, this features some of the microbes wall and some of the plants.
Picture 2: Another Niecey pic, this one features the E. coli plush (football shaped with string coming down) and the phage (round thing on top of plush).
Picture 3: Niecey's depiction of a bent rod shaped bacterium being attacked by two phage, the one on the left appears to be injecting its genetic material into the cell while the one on the right appears to be in the attachment phase.

Tuesday, October 21, 2008

"Tastey" Tuesday

Yesterday I went to the clinic and my amazing nurse sprayed the live attenuated flu vaccine up my nose (get vaccinated!). On the way back to my building across campus I decided I was hungry and since the library is between the clinic and my building and has a cafe this seemed like a good choice. The problem with this location is that the sidewalk leading into the library is a "free speech zone", and is often populated by clubs/people pushing an agenda. It is potentially irritating enough under normal circumstances but as we are quickly approaching the season finally of the "reality" show that is this year's presidential election (November 4, 2008: Find out who the American people will give the rose to and who will get voted off the island. Obama wins the swim suit competition but there is something about a man in uniform...), this area is often infested with annoying politically minded individuals. What's a poor microbiologist to do you ask? Why what she does every night, try to take over the world... oh wait wrong show. The trick to making it through this area unbothered is to not make eye-contact, walk quickly, and look occupied. Luckily for me my wonderful nurse gave me the vaccine info sheet, so I suddenly became engrossed in "reading" it and made it past all of them unscathed. I almost lost it at the register to vote table, they had a hilarious poster thing with people shaped cardboard cut outs with black and white pictures of the candidates' faces stuck on the heads. I wanted to get a picture but there were people manning the table that smell attention just as sharks sense blood.

So I made it past the insanity sidewalk and went to the cafe. All the sandwiches looked gross* and so I decided to not bother with solid foods (I could totally have gotten a cookie, you should all be totally impressed with my healthy choice!) and went to look at the drinks. I found this "health" drink stuff and looked at all the weird juices and concoctions they had to offer while longingly thinking about the AE milk in the next cooler over (I am a milkoholic but need more than just dairy in my diet). I decided the "Chocolate Protein" drink looked the most useful and had the highest probability of being drinkable, plus I decided that it was probably something my dietitian would approve of since she was talking about me drinking ensure and stuff like it to replace meals I don't eat. I think Doc and I need to have a chit chat about the dietitian thing, not sure she is "what the doctor ordered". Perhaps if I go through with the follow up with her it will be more useful if I have more of an idea of what we are aiming at with my seeing her. I have very mixed and confused feelings/thoughts after my first visit with her. Some of it reminded me of the last time I "allowed" Doc to refer me, which was a disaster**.

I actually had warmed up to the idea of seeing her (shh don't tell Doc, it would ruin my reputation) and was hoping she might have had some suggestions of foods I could eat and not get as sick on but she didn't really. Most of the time was spent with my defending myself because she could only see parts of my chart and on paper without context I come off as the worst patient ever to plague a doctor and that I was a waste of his time and hers and she was a waste of mine. But then she switched a bit and wants me to follow up next month, my sucking up to try and get her to not hate me and not think I am a total waste of everyone's time worked I guess. Not sure if she is going to earn a place on Team Karen or not, I think giving her one more try is in order but if the second visit is like the first then I won't go back again. I have enough trouble with feeling like I am a hypochondriac whining to Doc as much as I do and often allow my condition to get really bad before I cave and call him, and like many people I have insecurity issues that cause me to feel that I am a waste of his time (he does NOT make me feel this way). It has taken me quite awhile to realize this and I have been trying to overcome it since it is not healthy to let things go as much as I do, but having a professional practically tell me I am a waste of time does not help.

Anyway, back on topic, I bought the chocolate soymilk drink and left the library. This time I messed up, I glanced back at the poster that amused me earlier and one of the voter registration kids caught me. I quickly told her I already registered and intend to vote but thanks and she threw back a request that I volunteer to help them out, even if for only an hour. I told her sorry but I can't, need to be back in the lab and then I walked away as quick as possible. I am so not standing outside in the freezing cold to try and con idiot children to vote, I figure that if someone is not registered at this point that they have no intention of doing so and that is their choice, besides they are either informed and hate all the candidates or not informed and I don't like the idea of them voting anyway if that is the case. After making it out of that area I took my drink back to my office and made a video for your enjoyment, I think this is the first time I have ever drank soymilk, I've tried a few soy products but not that. Note I did not go to the campus book store, I have no idea why I said that since I am boycotting them and have been boycotting them for a year (they screwed me over). I was too lazy to redo it and besides my camera was running low on battery so it may not have been able to take another video. So here you go, my first soymilk experience and a product review on it.

~~~~~Copy LiteralDan Section~~~~~
*I am a picky eater in general but with my stomach issues I have become extremely picky since I have trouble digesting and can have a food "haunt" me for many hours. The food looked fresh and perfectly edible if it didn't contain nasty (by my definition) ingredients.
**What Doc says goes in the end, he lets me have input (awesome!) and he will let me get away with stuff as long as it won't hurt me so it is kinda like getting my own way and makes me feel more in control of my issues (which some days I totally need). If Doc says I am going to the GI then I am going to the GI, I try and convince him not to send me because I don't like the idea of it and I hated the last doc he sent me to (wrist doc). It is all his fault, if he wasn't so perfectly suited to my personality and the best doctor ever then I would not be quite as reluctant to see someone else. Another factor is the thought of cameras being shoved everywhere and it costing me who knows how much to run worthless tests (I have insurance but it is best for clinic visits). I find the whole thing kinda scary, especially if Doc "gives up" on me, psychologically I kind of see it as if he lets me get away with my crap that means I am not as sick.

Save Edna Jester

So I was checking my AOL mail and I often get distracted by the headlines and click them, especially funny sounding ones. Well I came across this gem and decided to share it with those of you paying attention to the less important news, such as the train wreck upcoming election (that is as political as I plan to get on this blog). Basically it is about an 89 year old woman who was arrested and is being charged with petty theft because some kid(s) threw a football in her yard and she was holding onto it to teach them a lesson.

The neighborhood is divided on this issue, according to the video this has been an ongoing issue with her and the neighborhood kids/families (or at least the one). To me I think the fact that she has made it clear she is annoyed with the kids having their balls go into her yard and got to the point of keeping them for however long to reinforce this that the parents' of these children should use it as an opportunity to teach their children about respecting their elders/neighbors, hell they should have already taught them. Is she being harsh, perhaps, but at the same time I would be very frustrated myself if someone was being disrespectful of me and my property (something I had to deal with in the lab yesterday) and if it was a kid that their parents did not teach them manners. According to the youtube video I found the "kid" is a teenager who got a job and bought it with his own money. I'm sorry but if a kid is old enough to have a job they should be old enough to know better than to mess with their elderly neighbor and perhaps old enough to go to the nearest park to play if their yard is too small.

Perhaps it is the way I was raised, I was expected to be polite and respectful of my elders. When we went somewhere I was expected to follow the rules of that place, even if it was something that was otherwise considered fine behavior for home. I plan to raise my potential offspring in the same way. If I knew my neighbor was bothered by something I or my kids did then I would try to talk it out with them to come up with a solution/compromise. Is it Edna's place to try and teach a little respect to the urchins next door, not really, but at the same time what are her other options if the parents don't do their job? Perhaps it is a silly issue to make such a big fuss over but at the same time it does bring up valid points, and really what means something to one person may mean something else to another.

Perhaps I am relating to Edna and reading too much into the issue given my issues with one of my coworkers (Prof Wannabe for those keeping track). But that is for another post.

FYI: I am working a lot right now and it is significantly limiting my blog writing and reading. I have set myself on a schedule that does not involve days off, it is not as bad as it sounds, some days I have very little to do so it is practically a day off, but there is always something that needs doing that totally gets in the way of blogging. Plus I didn't want to post and have my contest get burried (check it out, post below this, contest deadline has been extended to the 31st). Hopefully I can catch up at some point, miss you guys!

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 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!

Saturday, October 4, 2008

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