H2SO4Hurts - Brian Krueger, PhD

Featured - A coming of age for PacBio and long read sequencing? #AGBT13

Sat, 23 Feb 2013 13:10:01 -0600

Aside from the dubstep pumping out of the Roche and Agilent booths, the volume of AGBT has been somewhat muted.  There was no grand offering of new hardware or over the top promises of sequencing genomes on what now appear to be vaporware USB thumb drives.  This is my first in person experience of AGBT, so as a virgin it seems for the most part to be rooted in the science despite; (read more)

Source: Brian Krueger, PhD - Discipline: Genetics

Featured - Next Generation Sequencing rapidly moves from the bench to the bedside #AGBT13

Fri, 22 Feb 2013 15:02:07 -0600

As the second day of AGBT kicked off, it became quite clear that this meeting would be dominated by medical genomics.  There were a few talks sprinkled in about gut or sewer microbiomes but the vast majority of the talks the last two days have been on clinical genomic sequencing.  This is fine by me since it’s exactly what we do in the Genomic Analysis Facility in Duke’s Cent; (read more)

Source: Brian Krueger, PhD - Discipline: Genetics

Featured - #AGBT day one talks and observations: WES/WGS, kissing snails, Poo bacteria sequencing

Wed, 20 Feb 2013 23:57:41 -0600

Today I dusted off my luggage and headed down to the annual Advances in Genome Biology and Technology meeting in Marco Island, FL. Historically, this meeting has been the Detroit Auto Show of Genomics where companies and labs release their beautiful shiny new products and methodologies. In past years, attendees were showered with fireworks displays and epic swag bags. The tone this year is p; (read more)

Source: Brian Krueger, PhD - Discipline: Genetics

Featured - Got fetal DNA on the brain?

Fri, 28 Sep 2012 11:33:14 -0500

Human fetus in amniotic sac One of the big stories that blew up on the internet the other day was the publication of some results that reportedly show that females who have birthed males have male DNA in their brain.  That’s pretty cool stuff!  This isn’t uncommon, it’s called microchimerism, or the deposition of cells or DNA from the fetus to the mother or vice versa.& (read more)

Source: Brian Krueger, PhD - Discipline: Genetics

Featured - Memes about 'junk DNA' miss the mark on paradigm shifting science

Fri, 07 Sep 2012 12:36:31 -0500

Credit: Shutterstock In 1990, the scientific community embarked on a landmark experiment to completely sequence the human genome.  At the time, it was assumed that knowing the exact sequence of the human genome would provide scientists all of the information they ever wanted to know about genomics and how DNA contributes to human disease.  At least this is how the project was pr; (read more)

Source: Brian Krueger, PhD - Discipline: Genetics

Featured - So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what?

Thu, 16 Aug 2012 17:32:00 -0500

Is it a hoe? Is it a shovel? It's bound to happen in every lab.  Someone is going to get distracted and for whatever reason a box full of tubes or tubes themselves are going to accidentally get dropped in the lab's liquid nitrogen container.  A lot of people might say, "Screw it," and leave those samples on the bottom of the tank.  This might be a good solutio; (read more)

Source: Brian Krueger, PhD - Discipline: Technology

Featured - Did the Internet Save Science from Arsenic Poisoning?

Wed, 11 Jul 2012 12:31:23 -0500

GFAJ-1 Credit: Wolfe-Simon et al Almost a year and a half ago, NASA ignited a media firestorm after it announced the discovery of a new organism with alien implications.  The whole fiasco began when a scientist found a new bacteria in Mono Lake that could grow in the presence of high concentrations of toxic compounds.  These types of bacteria are not uncommon on earth. ; (read more)

Source: Brian Krueger, PhD - Discipline: Science Politics

Featured - Some math...Or why posting the median salary of genders in the White House doesn't help Republicans

Mon, 16 Apr 2012 11:25:15 -0500

I recently posted a picture of the congressional vote count for the Lilly Ledbetter Fair Pay Act showing the absolutely disgusting bi-partisan divide over this vote in 2009.  Republicans should be ashamed. Credit: Rachel Maddow/MSNBC However, someone added a link to an Examiner article posted a few days ago that said the Obama White House paid women 15% less in 2011.  The artic; (read more)

Source: Brian Krueger, PhD - Discipline: Mathematics

Featured - A peril of "Open" science: Premature reporting on the death of #ArsenicLife

Thu, 02 Feb 2012 09:42:54 -0600

GFAJ-1 Bacteria Open science is a wonderful concept, but what happens when reporters start writing stories on data that has not been properly reviewed and vetted by the scientific establishment?  Before this week, I had never really considered this question.  Open science at its core is a wonderful utopian idea where scientists do their work in the open and publish their noteboo; (read more)

Source: Brian Krueger, PhD - Discipline: Science Politics

H2SO4Hurts - YouTube: Just a (PhD) Dream

Thu, 27 Oct 2011 13:06:11 -0500

Source: Brian Krueger, PhD - Discipline: Agriculture

H2SO4Hurts - Slides - From the Bench to the Blogosphere: Why every lab should be writing a science blog

Wed, 19 Oct 2011 10:03:32 -0500

Here are the slides from the presentation I gave on Monday.  We recorded a video, but I'm not sure how it turned out.  I have a feeling the audio is going to be bad so I might just sit down and do it over again this weekend on my laptop. Two of the slides are movies.  The first is a clip from "Flock of DoDos" where some lady says scientists are horrible communica; (read more)

Source: Brian Krueger, PhD - Discipline: Agriculture

Featured - Fact Checking AARP: Why soundbytes about shrimp on treadmills and pickle technology are misleading

Mon, 17 Oct 2011 09:00:00 -0500

AARP put out a commercial a few months ago deriding wasteful spending in Washington.  Unfortunately, the soundbytes don't accurately represent the full story behind the spending.  Have a watch before continuing. The main points of this mis-infomercial are: We're wasting money on a Brazillian corn institute, Poetry in Zoos, Shrimp on treadmills, and pickle technolog; (read more)

Source: Brian Krueger, PhD - Discipline: Science Politics

Featured - MHV68: Mouse herpes, not mouth herpes, but just as important

Mon, 17 Oct 2011 08:33:38 -0500

In the current political climate it has become clear that science is a major target of Republican directed budget cuts. However, the soundbytes of politics do not represent the importance of science in our lives.  Because of this, I think it's extremely important that we explain why some of our model systems are so important for understanding how viruses and ultimately human diseas; (read more)

Source: Brian Krueger, PhD - Discipline: Microbiology

Featured - @DonorsChoose update: Pictures of the materials we bought being used!!

Fri, 14 Oct 2011 09:37:13 -0500

Wow!  Mrs. Irish has posted pictures of her students using the microscope, slides and workbooks that we helped purchase for her classroom.  This is exactly why we work so hard to try to bring in donations through the DonorsChoose program. There are still 60 or so unfunded projects on our giving page, sp please stop by and help in any way you can. ; (read more)

Source: Brian Krueger, PhD - Discipline: Science Politics

H2SO4Hurts - @DonorsChoose project: Launch a Rocket of Success

Wed, 05 Oct 2011 09:15:40 -0500

Mr. Bradham in class Today's featured DonorsChoose project is: Launch a Rocket of Success.  Mr. Bradham is looking to buy rocket kits for his science class to teach his students about physics and space exploration.  He says that his students are, "eager for knowledge. Unfortunately, they lack the adequate financial means to provide for supplies that could further their unde; (read more)

Source: Brian Krueger, PhD - Discipline: Space

H2SO4Hurts - Is this supposed to be a feature, @NPGnews ?

Tue, 04 Oct 2011 14:26:39 -0500

I know, know, paper is so 1990 but I just wanted to pull a paper over at Nature to read during seminar later.  Unfortunately I used the big fat "Print" button on the manuscript page.  This is what I got: Notice anything funny about the figures? I guess next time I'll just download the PDF and print it that way.  However, even I know that if you stick blocks of tex; (read more)

Source: Brian Krueger, PhD - Discipline: Internet

H2SO4Hurts - A dose of batshit crazy: Bachmann would drill in the everglades if elected president

Mon, 29 Aug 2011 15:15:58 -0500

Source: Brian Krueger, PhD - Discipline: Environment

H2SO4Hurts - A true day in lab

Wed, 10 Aug 2011 07:57:17 -0500

Here's a true timelapse video of a day in lab.  Pictures were taken every minute for 24 hrs.  The video goes from about 4am to 4am the next day. And because someone asked...The images were taken with a GoProHD Hero camera and then compiled in Windows Live MovieMaker.  Images are displayed for 0.1 seconds.; (read more)

Source: Brian Krueger, PhD - Discipline: Research

H2SO4Hurts - A day in the lab...

Mon, 08 Aug 2011 15:00:12 -0500

Source: Brian Krueger, PhD - Discipline: Agriculture

H2SO4Hurts - More Troubleshooting

Wed, 13 Jul 2011 09:52:58 -0500

A week or so ago someone forgot to close the door on our enzyme freezer tightly.  I had just ordered $1,000 worth of NEB enzymes to make high throughput sequencing libraries too...  Before the meltdown, I made a couple of test libraries to be sure that the protocol was worked out. One of my test libraries with a perfect library smear.  We extract the DNA in between the ; (read more)

Source: Brian Krueger, PhD - Discipline: Molecular Biology

H2SO4Hurts - End to the sonication saga

Tue, 07 Jun 2011 14:56:12 -0500

A quick update on the side project since I'm procrastinating writing a short fellowship grant...  About a month ago I realized why my sonications were not working.  It turns out that when I moved to Florida from my Graduate work at Iowa, I didn't update my ChIP protocol to reflect a reagent change.  At Iowa, we had been using 16% paraformaldehyde as our crossli; (read more)

Source: Brian Krueger, PhD - Discipline: Research

H2SO4Hurts - Reflecting on a childhood whack-a-loon

Fri, 20 May 2011 12:27:42 -0500

In a recent episode of the new TV show, Happy Endings (Episode on HuLu), one of the characters, Dave, gets super excited when he runs into and reconnects with his favorite high school teacher.  The only problem is that the teacher turns out to be an alcoholic douche, but Dave spends the entire episode fawning over the guy until he realizes that the teacher is just an underachieving l; (read more)

Source: Brian Krueger, PhD - Discipline: Careers

H2SO4Hurts - University of Iowa holds Science Writing Symposium

Tue, 26 Apr 2011 09:10:34 -0500

  The University of Iowa will be holding s science writing symposium tomorrow (April 27th).  The symposium will be webcast LIVE at this address from 1PM to 5PM CST: https://webapps1.healthcare.uiowa.edu/webcast/Default.aspx There's a login screen now, but that will disappear once the talks start.; (read more)

Source: Brian Krueger, PhD - Discipline: Internet

H2SO4Hurts - Sonication success??

Mon, 18 Apr 2011 14:35:26 -0500

I've been working on this project on and off for a few months now.  You may remember my previous post about attempting sonication trials.  Unfortunately, things in lab have been busy trying to get a new graduate student started and troubleshooting problems with other experiments so I haven't had as much time to devote to this project as I would like.  I've; (read more)

Source: Brian Krueger, PhD - Discipline: Research

H2SO4Hurts - Thwart the NYtimes paywall

Thu, 17 Mar 2011 15:16:26 -0500

The NYTimes has recently implemented a paywall system where users will be charged for access after a certain number of page views.  Whatever your opinions of this system are, there is an easy way around it.  I heard rumors on twitter that following a link from twitter or facebook to an article would not count against your "free" pageview limit.  Someone has started a twi; (read more)

Source: Brian Krueger, PhD - Discipline: Internet

H2SO4Hurts - Circle of life

Thu, 17 Mar 2011 09:55:27 -0500

Today I noticed my Tomato Clownfish acting a little friskier than usual.  A few days ago I saw a white bump under the female's anal fin and thought it might be a fungal infection because it had a goofy gray tinge to it.  I figured I'd just wait and see what developed.  Well today I noticed that it was much bigger and longer...It was her ovipositor (egg laying t; (read more)

Source: Brian Krueger, PhD - Discipline: Marine Biology

H2SO4Hurts - Curing a plague: Cryptocaryon irritans

Wed, 09 Mar 2011 11:13:02 -0600

Every once in a while I find myself having a "grass is greener" moment in science.  I sit at the computer thinking about all of the annoying things in lab that aren't working and wonder, "If I could answer any question, given unlimited resources, what would I choose to study?"  This, my friends, is where I prove my unhealthy obsession with fish.Credit: Colorni and Burgess, 1; (read more)

Source: Brian Krueger, PhD - Discipline: Marine Biology

H2SO4Hurts - Video: First new fish in 6 months!!

Wed, 02 Mar 2011 09:37:41 -0600

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 an; (read more)

Source: Brian Krueger, PhD - Discipline: Marine Biology

Featured - Don't ever get a sun tan...on your eye balls

Tue, 01 Feb 2011 10:14:54 -0600

"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.------My scientific career has been filled with plenty of misadventures and scr; (read more)

Source: Brian Krueger, PhD - Discipline: Research

H2SO4Hurts - #Scio11: Collaborative tools in industry and academia

Wed, 19 Jan 2011 11:22:56 -0600

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 ne; (read more)

Source: Brian Krueger, PhD - Discipline: Technology

H2SO4Hurts - The first step is the most important

Thu, 30 Dec 2010 14:37:53 -0600

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 ; (read more)

Source: Brian Krueger, PhD - Discipline: Molecular Biology

Featured - Have we really found a stem cell cure for HIV?

Wed, 15 Dec 2010 11:40:24 -0600

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… HIV Virion Credit: NIH Human immunodeficiency virus (HIV) wa; (read more)

Source: Brian Krueger, PhD - Discipline: Molecular Biology

Featured - This paper saved my graduate career

Tue, 14 Dec 2010 09:43:41 -0600

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 v; (read more)

Source: Brian Krueger, PhD - Discipline: Molecular Biology

Featured - Valium or Sex: How do you like your science promotion

Tue, 23 Nov 2010 10:19:30 -0600

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 pict; (read more)

Source: Brian Krueger, PhD - Discipline: Science Politics

H2SO4Hurts - A wedding pic.

Tue, 16 Nov 2010 12:00:00 -0600

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

Source: Brian Krueger, PhD - Discipline: Misc

H2SO4Hurts - To rule by terror

Tue, 09 Nov 2010 14:32:05 -0600

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. N; (read more)

Source: Brian Krueger, PhD - Discipline: Careers

Featured - Summary Feed: What I would be doing if I wasn't doing science

Wed, 06 Oct 2010 09:00:00 -0500

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.   Credit: Gaeten Lee/CC3.0 1. DamnGoodTechnician says that she'd probably have majored in sociology and become an administrative assistant if it wasn't for her high ; (read more)

Source: Brian Krueger, PhD - Discipline: Careers

H2SO4Hurts - "You have more Hobbies than anyone I know"

Tue, 05 Oct 2010 14:46:56 -0500

I thought about this question probably everyday of my graduate school career.  My days usually went like this: 1. Get to lab at 7am2. Start 12hr experiment3. 7pm, experiment failed4. 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&#; (read more)

Source: Brian Krueger, PhD - Discipline: Careers

H2SO4Hurts - Hiccupping Hubris

Wed, 22 Sep 2010 00:00:00 -0500

Credit: Jens Lagner 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 Iow; (read more)

Source: Brian Krueger, PhD - Discipline: Health

H2SO4Hurts - A death in the family :(

Mon, 20 Sep 2010 12:00:00 -0500

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 fis; (read more)

Source: Brian Krueger, PhD - Discipline: Marine Biology

H2SO4Hurts - The new lab fish!

Fri, 10 Sep 2010 14:25:56 -0500

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. 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 hav; (read more)

Source: Brian Krueger, PhD - Discipline: YouTube

H2SO4Hurts - What I wish I knew...Before applying to graduate school

Tue, 07 Sep 2010 14:32:53 -0500

Credit: Rohan BaumannI’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 whe; (read more)

Source: Brian Krueger, PhD - Discipline: Careers

H2SO4Hurts - Stopping viruses by targeting human proteins

Tue, 29 Jun 2010 00:00:00 -0500

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 w; (read more)

Source: Brian Krueger, PhD - Discipline: Molecular Biology