Things have started to calm down a bit on my weekends so I've had more time to attend to fish. One of the crappiest things about owning a saltwater fish tank is that you can't just add fish to your system immediately. The fish come from the ocean covered in parasites, so you have to take extra special care of new additions to be sure they're clear of parasites and infections before you add them to your main "display" tank. Quarantining fish is absolutely a necessary evil. A lot of people neglect to do this, but it saves a ton of headaches. Trust me on this, you would much rather lose an $80 fish than get your $3000 display tank infested with a parasite!

Anyway, the fall got clogged with trips and holidays. Some of you may remember that back in October I tried to quarantine a yellow longnose butterfly fish and a powder blue tang that both died from a nasty bacterial infection. Given that quarantining fish takes at most 2 months if they get sick, I didn't have enough time to cycle in more fish before Turkey Day! Once Christmas passed, I was working on setting up an office tank for Whitney, so my quarantine system has been occupied with her inhabitants for the past two months... Finally I was able to pick up a new butterfly fish a few weeks ago. . . . More

"This is the one thing you never want to mess around with. You'll wake up in the middle of the night crying like a baby and you'll have no idea why." These were the sage words of my undergraduate advisor, it's too bad they got discarded with everything else that I learned in undergrad.

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My scientific career has been filled with plenty of misadventures and screw ups. Most of them are really boring mistakes that didn't involve bodily harm, and only resulted in weeks of repeated work or extended nights in the lab re-preparing samples. Though, every good scientist has an epic fail story locked away in their skeleton closet. I think many of us go into science in the beginning thinking that we're unstoppable know it alls. That is until some event punches us in the gut to tell us, "Open your eyes and pay attention or else next time I'm going to aim a little lower and negatively affect your chances of reproduction."

When I was in undergrad, I worked on a bunch of projects ranging from ecology field studies to molecular biology projects in plants and fish. One of the last projects I worked on was one where we were trying to determine if fish bacterial infections could be transferred from mother to egg. This project involved c . . . More

I'm finally coming out of my Scio11 coma. It was a super exciting weekend filled with talks about technology, blogging, and new media. On Saturday, Kristy Meyer, Dr. Isis and I led a panel discussion on the use of new communication tools in academic and industry science.

The discussion covered a wide range of topics. One of the first that was brought up was how new media tools might be used to increase collaboration between science and industry. One participant stated that she was surprised by the lack of collaboration between academic and industry scientists in the Research Triangle Park area. She said there really was no resource for expert discovery and thought that the creation of a local database would be helpful in finding connections.

Expanding on this researcher database idea, I asked the audience to talk about their use of currently available social networking tools like LabMeeting, MyNetResearch, BioKM, Mendeley, ResearchGate, etc. One biotech researcher said that his company was open to using these tools privately, and that's really what I have seen and heard of over the years. Companies and institutions want to find bette . . . More

I'm beginning a new project in lab. It's a series of ChIP-seq experiments and the first step to doing ChIP-seq properly is optimizing sonication conditions. Here's a trial run with the sonicator I plan on using. The DNA shown in the gel is from cells containing latent herpes virus. We're looking to shear the DNA so that the bulk of it is between 100 and 600bp. For ChIP-seq we extract and purify the DNA in the 100-300 range in the gel. Looks like about 13 cycles of sonication should do (sonication past this point doesn't result in smaller fragments, don't want to risk over sonicating)! Actually, I think I'm going to do this again on Monday. I looked back at some old data and I should be able to get the fragment sizes a bit smaller by increasing the pulse time. I'll post an update soon!



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Yesterday there was some buzz over at Huffington Post about a stem cell cure for HIV. I first ran across the article via a link a friend of mine had posted on Facebook. The HuffPo piece is scant on details, so I’ll provide a quick run down on what’s going on here. But first, a lesson in HIV virology…

Human immunodeficiency virus (HIV) was first discovered in the 1980’s when gay men and IV drug users started turning up in hospitals with very odd opportunistic infections like Kaposi’s Sarcoma Herpes virus. These individuals had severely compromised immune systems and the original name given to the condition was gay related immunodeficiency disorder (GRID). The discovery of a viral cause of the disease came in 1983 from the labs of Luc Montagnier (recently won the Nobel Prize for this work) and Robert Gallo (recently didn’t win the Nobel Prize and is kind of pissed about it).

Genetic tests have shown that HIV originated in African monkeys and is related to a similar condition in monkeys called Simian Immunodeficiency Virus (SIV). It is thought that the virus was passed on to humans through the consumption of “bush meat” in sub-saharan . . . More

In a previous post I mentioned that I spent the first year of graduate school working on a dead end project that was going nowhere. I’m going to present and discuss the findings of the paper that changed the direction of my thesis project and ultimately lead to the completion of my PhD.

In the fall of 2006, I was finishing up the last few experiments on a project trying to link P53 (a very important protein in cells that helps to prevent cancer) to one of the most important transcriptional activators, P-TEFb. I should probably pause for a second here to give a little bit of background on P-TEFb so that what follows is somewhat understandable. Positive transcription elongation factor b (P-TEFb: Pee Tef bee) is a protein kinase (read as on/off switch) that regulates RNA polymerase II transcription of most genes. RNA polymerase II is the protein responsible for messenger RNA (mRNA) transcription or the process of turning DNA into mRNA. Without mRNA, the transfer form of DNA, proteins cannot be made by the cell, and life does not exist. Essentially, P-TEFb tells RNA polymerase when it’s ok to start making RNA. You can think of P-TEFb as the starter at a track meet, you know, the guy th . . . More

With the launch of this year’s “Rock Stars of Science” campaign, there’s been a lot of talk about how to best promote science. I’m no marketing guru, but I am a scientist. This latest campaign is better than last years', only because it’s more diverse, but I think it really misses the boat. Is the public really going to be inspired by a couple of pictures in GQ of scientists looking uncomfortable and over dressed in the presence of Rock Stars? The most appalling aspect of this campaign is that there is no highlight of the researchers or their science. There truly are some science all stars in this group, many of which are well spoken.

However, the Rock Stars of science pages in GQ only list the scientist’s name and title, while the “Rock stars” get a one or two sentence summary of how awesome they are for standing in on these pictures. What’s the real focus of this campaign? To promote Bret Michaels’ latest reality TV dreck? If a reader wants to actually understand why these scientists were chosen and what they’re doing to cure disease, they have to visit the website. I find it hard to believ . . . More

I'm back! And here's an early treat from my photographer and good friend, Todd Adamson

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When I started graduate school at Iowa, I went in there with a chip on my shoulder.  They didn’t choose me, I chose them.  They weren’t a highly ranked “elite” institution, so to make my mark I had to work for the biggest and the best that Iowa had to offer, or so I thought.  I sought out the highest profile researchers at Iowa and picked the one that best aligned with my interests.  No matter what school you look at, there’s always, “That Professor.”  You know who I’m talking about.  The professor who publishes the most papers, who has the most respect.

I did my homework on my mentor.  I read a bunch of old papers, I understood the direction and the goals of the lab.  I remember our first lab meeting vividly, well, I remember how I felt after the lab meeting.  I was exhausted.  My brain physically hurt.  I thought I knew it all going into that meeting and I realized I didn’t know anything.  It was a wake up call, but I think I liked that feeling.  It was fresh and challenging.

During my rotation, I put in ungodly long hours, not because I thought it was expected of me, but because I wanted to.  At this point in time I was enamored with the science.  It’s funny how this changed for me as I look back on my four and a half years in t . . . More

Today is: "What I'd be doing if I wasn't doing science" blog post theme day. The goal of this post theme is to let our readers get to know who we are and what our non-scientific interests are.



1. DamnGoodTechnician says that she'd probably have majored in sociology and become an administrative assistant if it wasn't for her high school sweetheart and his penchant for genetics.

2. Dr. O was involved with every group and club under the sun in high school and really wanted to become a broadway performer and until recently she had her heart set on teaching high school science but research sucked her in.

3. Evie would be everything. First she'd be a ninja kung fu master, then she'd learn how to talk to dolphins, create world peace and turn earth into an atheist utopia. Evie needs to lay off the caffeine pills

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I thought about this question probably everyday of my graduate school career. My days usually went like this:

1. Get to lab at 7am
2. Start 12hr experiment
3. 7pm, experiment failed
4. 7:15pm set it all up again for tomorrow

Eventually I got everything to work but that 12hr period in the middle was filled with:

"I bet me engineer friends don't have to deal with this shit, and they're getting paid 6 times as much as me."
"I should have just become a web designer. I have fun doing that AND things usually work the first time."
"I want to run away to the cirus and become a Barker."

My PhD mentor once told me that I was the weirdest person he'd ever met because I have too many hobbies. He didn't think I could be successful in lab if I ran a website, went to the gym for two hours in the middle of the day, maintained my saltwater fish tank etc. I think he saw all of these things as distractions, or more like, "If he spent that energy in lab, he'd have a billion papers by now." Well, Honestly I can only take so much science and I need all of these hobbies to keep me sane. Further, I think I could turn any of my hobbies into careers.

In middle school, my mom worked for a computer training c . . . More

I'm going to preface this by saying that I am not a medical expert. I don't even begin to pretend I know anything about medicine or how to cure diseases. I do watch those cheesy "Untold stories of the ER" shows on Discovery and TLC though, and sometimes I partially remember things they say about diagnoses.

This story begins back when I was finishing up my PhD at Iowa. I had successfully defended my thesis (thank god) and was out on a drinking excursion with "the boys" the weekend before I was moving down to Florida to start my new job. The evening started out just like any other, we pregamed at my buddy's apartment drinking cheap beer, cooking up some quick dinner and bullshitting about how much being a graduate student sucks. You know, the typical poor graduate student routine.

We finally got a cab and made it down to "downtown" which in Iowa City consists of 3 businesses and 75 bars filled with helplessly drunken co-eds. I swear it wasn't more than 15 minutes into the night when my buddy, who shall be referred to as "Dr. Millner" from here on out, started hiccuping. These weren't your normal "Hiccup for 10 minutes and be done with it" type of hiccups, these things were going to last for hours. Of course, being a medical student an . . . More

I came into lab yesterday to a disaster. I took a look at my quarantine tank and it was filled with a white bacterial bloom, the bottom of the tank was covered in what looked like leftover food and fish poop, and the water smelled like rotting fish. To top it off, the Powder Blue Tang could not right itself, and was swimming upside down and in circles. For those of you that have never owned fish, upside down and in circles is usually referred to as the "death roll." The yellow longnose butterfly fish seemed just fine though. I have absolutely no clue why there were feces and food all over the tank. I'm the only person in lab that messes with the fish and everyone knows that if they touch anything to do with the tanks without asking me, they're liable to get their hands whacked off with the guillotine paper cutter. Both fish were doing just fine when I left them on Saturday and did their daily feeding and tank cleaning. The presence of the amount of food and feces in the tank was very surprising. I do a 25% water change EVERYDAY on this tank AFTER feeding to clean up any uneaten food and feces from the night before. I'm convinced someone messed with it, because there's no other explanation. I rushed to do a massive water change. This involved making . . . More

This is kind of stupid, but I thought I'd share a video of my new lab fish. Who knows if they'll survive quarantine, but we can bask in their beauty for a while.

*This entry contains a YouTube video*

The blue-ish one is a powder blue tang approximately 3" long and the yellow one is one of my favorite fish of all time! It's a yellow long nose butterfly fish. The tang is covered in a pretty common parasite so they have to stay in quarantine for a few weeks. The treatment regimen is to lower the salinity by 70% and then let the fish hang out in that for 4 weeks. Amazingly, saltwater fish can survive in very low salinity water, the parasite can't and eventually dies out as all of the eggs hatch. Although, the unfortunate thing is that salinity can be reduce drastically over a one hour period, but the salinity must be raised back up to normal much much more slowly. It usually takes a week and a half to bring the quarantine tank's salinity back up without killing the fish. I'm sure there's some interesting physiology involved there ;) So maybe in 6 weeks I'll post another video of these guys swimming in the main tank!

*This entry contains a YouTube video* . . . More

I’m totally late to this party. I spent the morning writing my rebuttal to DrugMonkey and Co, doing the news, and cranking out a few pesky experiments. Ah, to live the life, right? Anyway, I’ve noticed that all of the good topics are now taken so I have to scrub the bottom of the bucket. I think one of the most important decisions I made in my scientific career was when I decided where I wanted to go to graduate school. The factors that play ball in this game are numerous and obviously not the same for everyone, but here’s my rundown of all of the things I wish I knew before heading off to graduate school.

Not to be too bitter about my undergraduate experience or anything, but the graduate school preparation was horrendous. No one told me from the beginning, “If you want to go to graduate school, here’s the X, the Y and the Z.” This may all sound like common sense, but some of it is not and having someone tell me all about X, Y, and Z my freshman year would have been helpful.

Do grades matter?

YES. They matter as much as they do for your annoying pre-med classmates, especially if you want to go to a . . . More

One of the biggest problems facing the eradication of hard to kill viruses such as HIV is that viruses mutate readily. A standard technique for creating lasting immunity against viruses is the creation of vaccines. These have been used for years to eradicate a multitude of viruses. There are three standard types of vaccines that have been used in the past. There are attenuated viral vaccines which use a weakened form of the virus to challenge the immune system, killed virus vaccines which use dead viral particles to trigger the immune system, and finally there are peptide vaccines which use the expression of a specific viral protein to trigger the immune system. Although these approaches work readily for many viruses, in the case of a small subset of human pathogens, such as for HIV, these techniques cannot be used to create lasting immunity. In these cases, the virus mutates so readily that any immunity gained is quickly lost because the immune system can no longer recognize the virus.

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