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Brian Krueger, PhD
Columbia University Medical Center
New York NY USA

Brian Krueger is the owner, creator and coder of LabSpaces by night and Next Generation Sequencer by day. He is currently the Director of Genomic Analysis and Technical Operations for the Institute for Genomic Medicine at Columbia University Medical Center. In his blog you will find articles about technology, molecular biology, and editorial comments on the current state of science on the internet.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Jaeson, that's not true at most places.  Top tier, sure, but 1100+ should get you past the first filter of most PhD programs in the sciences. . . .Read More
Jun 24, 2013, 8:39am

All I can say is that GRE's really do matter at the University of California....I had amazing grades, as well as a Master's degree with stellar grades, government scholarships, publication, confere. . .Read More
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Hi Brian, I am certainly interested in both continuity and accuracy of PacBio sequencing. However, I no longer fear the 15% error rate like I first did, because we have more-or-less worked . . .Read More
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Great stuff Jeremy!  You bring up good points about gaps and bioinformatics.  Despite the advances in technology, there is a lot of extra work that goes into assembling a de novo genome on the ba. . .Read More
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Brian,I don't know why shatz doesn't appear to be concerned about the accuracy of Pacbio for plant applications. You would have to ask him. We operate in different spaces- shatz is concerned a. . .Read More
Feb 25, 2013, 8:01am
Monday, September 20, 2010

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 up 15 gallons of fresh saltwater, heating it to the right temperature for an hour and then slowly adding it to the tank to acclimate the fish to the new conditions. Neither fish was happy during this process and the Tang looked to be getting worse by the minute. After replacing 75% of the water, I waited an hour and did another 50% water change, just to be sure whatever was causing the odd behavior was completely diluted out. I assumed the Tang's behavior was due to either a swim bladder infection (nearly incurable) or ammonia toxicity. I left the lab to go home and figured I'd find the tang dead in the morning.

I came in today and the tang is doing fine, but the butterfly fish died. WTF!!! You can see a red patch on its side in the picture that could be a battle scar from a fight with the powder blue tang, but I've seen no aggression between the two fish in the week that I've had them. This death is very odd, I thought for sure that the Powder Blue Tang was the goner. I guess its possible that the yellow longnose butterfly fish had some other disease that was aggravated by the stress of a ~90% water change. This is one of the few things that sucks about owning a saltwater fish tank. I hate it when fish die and I don't know why :(

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I think you need a fish tank spy cam.

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That really sucks! Huge bummer.

Washington University School of Medicine
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Weird. You should go all CSI and dust for prints. According to my TV, you'll know who did it, what happened and what they had for breakfast in about 3.75 minutes.

Brian Krueger, PhD
Columbia University Medical Center
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@Nikkilina, Haha, or if I had a shitty security camera I could just super zoom on the water reflection to get a picture perfect image of the perp's face :P

I just hope the powder blue tang makes it. It looked ok today, but its still very stressed. It has white stress blotches all over its body :(

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So, you cleaned the tank on Saturday and it was filled with feces on Monday, and to you this means someone messed with it. I can follow that logic, but sounds to me like you are suggesting someone collected up some fish feces over time, stored them in secret, and then sneakily managed to re-add them to the tank yesterday in your absence, filling the tank with feces to sabotage your fish, which is some *serious* hatred from a lab mate....yikes

Prof-like Substance
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That sucks, I hate it when fish die. But what size is the tank? Tough to do saltwater in less than 50gal. It's not so much the water changes as the fluctuations in the chemistry variables that can fuck the fish up. You probably know this, though.

Brian Krueger, PhD
Columbia University Medical Center
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I've been doing saltwater for 5 years now. I had a 120 gallon reef tank in my basement in Iowa. When I moved to Florida, we bought a house with wood floors. My fiancee saw how much water I spilled all over the place in Iowa and said, "NO!" But my new boss here let me set up a 75 gallon reef tank in the lab :)

Definitely the bigger the tank, the more stable the chemistry, but chemistry in my experience is really only a problem for inverts and corals. The fish are pretty bullet proof as long as you have the nitrogen cycle under control. Obviously, the nitrogen cycle got hosed in my 20 gallon quarantine tank. Most fish (excluding angels, moorish idols, and Acanthurus sp tangs - like the powder blue :P) are oblivious to salinity (as long as it's above 11ppt or 1.010SG), pH between 7 and 9, and temperature between 72 and 86. I guess it could have been an issue of over stocking, but that tank should be able to support at least 10 inches of fish, and the two fish that were in there were 3 inches each. It's a mystery to me, but I'm still suspecting foul play. The other 4 fish in the 75g display all survived quarantine in it :) I'm just surprised the butterfly fish died. They're extremely hardy fish in my experience.

Brian Krueger, PhD
Columbia University Medical Center
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The powder blue tang looks normal today and the water tests show the tank is stable again. I'm pretty freaking annoyed (but it's good both fish didn't die :) ).

Washington University School of Medicine
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Glad you got it under control.
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