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Author: Brian Krueger, PhD | Views: 7892 | Comments: 2
Last by Brian Krueger, PhD on Oct 17, 2011, 11:55am
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.

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Author: Brian Krueger, PhD | Views: 7590 | Comments: 0
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 disease work.

In the lab that I run, we currently work on mutating two different herpesviruses. One of these is Kaposi's Sarcoma Herpesvirus (KSHV) and the other is Murid Herpesvirus 68 (MHV68). Both of these viruses are gammaherpesviruses. In humans, KSHV only really ever becomes a problem in individuals who have a compromised immune system such as those infected with human immunodeficiency virus (HIV). KSHV is an interesting virus because its default program is latency, meaning that once it gets into your cells, it turns itself off and waits for conditions which allow it to grow and take over. This is akin to a bear hibernating in the winter. We do not understand how or w . . . More
Author: Brian Krueger, PhD | Views: 7038 | Comments: 4
Last by Brian Krueger, PhD on Oct 24, 2011, 8:40am
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 communicators and the other is the AARP shrimp on treadmills commercial.

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Author: Brian Krueger, PhD | Views: 6912 | Comments: 0

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. Life seems to find a way to thrive at all extremes and a salty lake in California is no exception to this rule. Researchers have discovered a diversity of life in hot springs, at undersea volcanic vents, and on the cold arctic sea floor. The discovery of this new bacteria; however, was remarkable because the researchers believed that it could use arsenic in the place of phosphate. To the general public, this may sound trivial, but many of the biochemical reactions that provide life require phosphates. The reason why arsenic is so toxic to humans is that it injects itself into all of the processes that use phosphate and prevents those processes from working properly. For example, the molecular backbone that keeps our DNA together is composed of phosphate; the energetic molecules that are produced by the power factories in our cells are composed of phosphate; the specific addition of phosphate to some proteins turns them on or off. Phosphate and its derivatives are essential for life, so to find a bacteria that could function without phosphate and use arsenic in its place was an amazing discovery.

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Author: Brian Krueger, PhD | Views: 6365 | Comments: 1
Last by Evie on Dec 18, 2010, 11:17am
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
Author: Angry Scientist | Views: 6390 | Comments: 3
Last by Mike Bramnik on Mar 26, 2011, 11:09pm


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Author: LabSpaces.net | Views: 5663 | Comments: 21
Last by JanedeLartigue on Oct 15, 2010, 12:49pm
I recently got an e-mail from David Bradley asking my opinion of Web 2.0 as it relates to science, where it’s heading, and how we can get scientists more involved in web 2.0 / data sharing / and the semantic web. I thought this would be a great topic for me to write a real post on since I’ve been involved in this field and trying to promote the ideas of web 2.0 in the sciences for the last 5 years.

For starters, I really have no idea what it will take to get scientists to be fully engaged with the on-line world. It's hard enough to get them engaged in the real world (I wish that was a joke…). I think for most scientists to get involved with a network, we're going to have to develop something that significantly increases scientific productivity, and I'm not talking just a free reference management site or being able to post lab retreat pictures to a profile. The last 4-5 years have showed us that scientists really are not interested in FaceBooks for science. The marginal success of ResearchGate, NatureNetwork, and LabSpaces can't be cited as triumphs because very little of wh . . . More
Author: Brian Krueger, PhD | Views: 5661 | Comments: 0

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 understanding of science concepts." Mr. Brandham is looking for a "hook" to get students interested in and excited about science and from past experience with rocketry programs he has found that students are captivated by rocket launches and this provides a stepping stone for him to teach other science concepts in the classroom.

I can't argue with Mr. Bradham's logic. I remember when I was a kid and I got a hold of my first rocketry set. It was a basic ESTES model that I had to glue and assemble myself. I really enjoyed learning about the physics and chemistry of the launches. Launching the rockets in my local park was always a blast, but the hobby was expensive! The engines for my rockets were like $5 and for a grade schooler with a tiny allowance of a couple dollars a month it was hard to fuel my obsession. I think it's very sad that Mr. Bradham can't get the funding from his school for this project because he teaches in a high poverty district. I see enormous value in this type of activity as a teaching tool. The excitement of a rocket launch can quickly translate into student fervor in the class room to try to understand how to make the rockets fly higher and faster.

Mr. Bradham has a long way to go to fund his project though, so we need your help! Every little bit counts, so please donate whatever you can to make this happen.

You can view more projects by visiting our giving page.

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Author: LabSpaces.net | Views: 5271 | Comments: 0
I have finally added blogs to the website. Now you can write your own blogs that relate to the news stories on this site.

In the future (like later this week):

add RSS feeds for all bloggers blogs
Add blogger links to link to outside sources

When I get more time (and more server space):
Allow picture uploads and image hosting

Test out the blogs for me and let me know if you find any bugs. I'm always looking for good suggestions for improving the site!

-Brian . . . More
Author: Brian Krueger, PhD | Views: 5603 | Comments: 8
Last by americanbiotech on Mar 10, 2011, 12:22pm
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.

If money, fame, and science groupies weren't a priority, I'd spend my time and resources trying to find a cure for Cryptocaryon irritans, which is better known in the tropical fish industry as white spot disease, Ich, or Crypto. Crypto is a nasty little bug. It's a protozoan ectoparasite that lodges itself in the epidermis of fish where it grows until it drops off to mature into an Aliens inspired cyst that spits out 300 new little bastard parasites that go on to infect more host fish. In the open ocean, this guy isn't so terrible because its chances of infecting a host are minimal considering the massive amount of water a parasite has to travel through to find a new host. This is a completely different story at an aquaculture facility or in the home aquarium where fish are typically stocked to capacity in relatively small volumes of water. A single cyst can quickly turn into a fish killing epidemic. . . . More
Author: Angry Scientist | Views: 5209 | Comments: 6
Last by JanedeLartigue on Oct 15, 2010, 12:42pm
24hrs or less to live. Gotta make the most of it!

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Author: Brian Krueger, PhD | Views: 5037 | Comments: 0
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.

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Author: Angry Scientist | Views: 3845 | Comments: 4
Last by Will on Oct 28, 2010, 5:09pm
I've had this one floating around in the back of my mind for a while.

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Author: Brian Krueger, PhD | Views: 4647 | Comments: 2
Last by Brian Krueger, PhD on Jun 29, 2010, 8:48am
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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Author: Angry Scientist | Views: 2899 | Comments: 3
Last by Suzy on Jan 29, 2011, 10:52am


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Author: Brian Krueger, PhD | Views: 2771 | Comments: 3
Last by Evie on Dec 18, 2010, 10:48am
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
Author: Brian Krueger, PhD | Views: 2820 | Comments: 5
Last by microbiologist xx on Sep 26, 2010, 8:15am
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
Author: Brian Krueger, PhD | Views: 2625 | Comments: 11
Last by Thomas Joseph on Jan 04, 2011, 7:47am
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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Author: LabSpaces.net | Views: 2335 | Comments: 0
Over the last year, there has been a question on the minds of thousands of people that continues to be for the most part unanswered: Why do disinfectants and hand sanitizers kill only 99.9% of germs and not the full 100%? Or, more succinctly, why is there always 0.1% survival? Many people have surmised that the 0.1% is due to the presence of those superbugs we keep hearing about. Others have suggested that the 0.1% is just not killable. Then there’s the suggestion that the 0.1% is just a way to keep the fear of germs in the mind of the public. While these may seem like good explanations, none of them are true.

As a microbiologist who has been involved in the testing of antimicrobial products, I’ve been testing disinfectants, hand soaps and hand sanitizers for years and I can tell you that both 99.9% and the resultant 0.1% is nothing more than a statistical anomaly.

When we do testing of these products, together known as antimicrobials, the goal isn’t to determine whether 100% is killed. We want to develop a statistical analysis to show that on a regular basis, the product will kill a certain amount of microbes. We accomplish this by using a certain amount of a particular bacterium, virus or fungi (what we call a challenge) that could never be 100% kil . . . More
Author: Brian Krueger, PhD | Views: 2552 | Comments: 9
Last by Brian Krueger, PhD on Jan 20, 2011, 12:17pm
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
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