The Rogue Gene

Illumina Sequencing MRSA

2010-01-25T12:30:00.000-06:00

Illumina, one of the 3 major next-gen sequencing platforms on the market is back in the news with this article by MIT's Technology Review. The article explains the efforts made by the Sanger Institute to track and understand the evolution and spread of MRSA, the antibiotic-resistant form of Staphylococcus aureus by sequencing its genome using Illumina sequencers. Unfortunately, there was no link to any actually published work, nor did they mention what sequencer they were using (probably a 'Genome Analyzer II'), but I will poke around the web and try to dig up some more info. The article is very interesting, regardless.

A New Hope...

2010-01-11T12:15:00.000-06:00

Readers,

Well, it was quite the drought, and even though the idea was to have a "rebuilding break", not much was accomplished. The blog does have a new catchy name and I'll be adding some subject avatars shortly, but other than that, not much has changed.

Due a recent lack of home internet service, I will once again be posting mostly from my phone and work which will delay (even further) the aquisition of an actual domain name, as well.

So enjoy....

Attention

2010-01-08T15:58:00.000-06:00

Ok. It's coming. A new blog soon! Stay tuned!

Note to readers:

2009-10-08T11:22:00.003-05:00

Readers,

I am very sorry for the recent lack of posts on this blog. I have been working really hard on a couple of articles that I would like to post soon and I am trying to move the blog over to its own domain. I assure you that I will mitigate this drought of content, and try to expidite the publishing of those new articles ASAP.

Also, in an effort to maintain the usefulness and depth of the site, I will be adding some new writers soon to help post content. These new writers will be very specialized in other fields and their science and technology credentials are consistent with the integrity you have come to expect from Science.Blog.Science.

I will admit, also that I have been distracted recently, mostly because of the purchase of my new iPhone (which is consuming a lot of my time now but should help create more content in the future).

Please continue to e-mail me any relevant news stories, topics, and feedback. They are all very essential to the preservation and continuation of this blog.

Thank You,

Nick

So why aren't we doing this???

2009-09-28T12:58:00.008-05:00

Normally the bumps on Adult Swim are mildly funny and somewhat informative, but this weekend they had one that really grabbed my attention. They showed this image of how much area it would take to power the globe on solar panels. Keep in mind most of these areas are deserts.

click on image below to enlarge

To quote Adult Swim, "So why aren't we doing this...".

Of course they go on to explain why with another image of Uncle Sam, well, lets just say befriending an oil derrick.

Lack of Sleep, Alzheimers linked

2009-09-28T09:47:00.002-05:00

In a new study published this week in "Science", researchers at Washington University witnessed a significant increase in accumulation of the protein Amyloid beta in mice when they were deprived of sleep. High levels of Amyloid Beta that populate the extracellular space are a hallmark for Alzheimer's Disease and this link to sleep levels will raise concern for those who suffer from insomnia and other sleep related issues. The study also links orexin, a protein associated with the regulation of sleep cycles, with the increased levels of AB. When the mice were injected with orexin they stayed awake longer and the amount of AB increased dramatically, but when orexin was inhibited in the mice, AB decreased over time. This shows hope as a possible treatment for Alzheimer's disease in the future.

Face Full of Pathogens: Shower Heads and Your Health

2009-09-24T16:25:00.000-05:00

This morning I woke up, desperately flailed my arm against my alarm clock, streched, brushed my teeth, and then jumped in my shower to remove all the diverse microbial communities that had built up on me since my last shower. As soon as the water is hot I stick my face under it and let it massage my face for a few seconds before I begin my cleaning routine. What I did not realize was that I was getting a face full of morning pathogens, many of which I inhale along with the steam clouding the inside of the shower.

In a recent publication from the University of Colorado, and as reported by futurity.org, your shower head could contain massive amounts of Mycobacterium avium in biofilms inside of it. M. avium, a pathogen linked to pulmonary disease, can exist in aggregates up to 100X the normal "background" levels of your municipal water supply.

I highly recomend the article on futurity and also the video posted below. The article is a cliff-hanger, though, since it doesn't give you any good method of cleaning your shower head and eradicating the pathogenic colonies that reside in it. The bacteria seems to have a resistance to bleach and chlorine (and since it is in our water supply I would assume flourine as well), and when they did clean the shower in a different study with bleach, a similar pathogen Mycobacterium gordonae actually increased 3 fold! I would guess due to the elimination of competing microbes.

SciFest in St. Louis

2009-09-23T11:46:00.002-05:00

Yes, it's that time of year again. SciFest is back at the St. Louis Science Center this October 7-11. For those of you that have never been to or heard of the annual event (since they don't publicize it very well,), Scifest is a five-day celebration of science with over 60 different sessions and lectures. Most of what is available for view is pretty watered down for the general public, but some of the lectures are quite informative. I really recomend a lot of the events on Saturday and Sunday (since the weekday sessions are for school children on field trips).

Some of the more interesting events (at least to me) include:

Rock Guitar in 11 Dimensions
Bionic You
Honeybees in Crisis
What is Reality?
Can The Moon Save the Earth?
Feeding The World
The Science of Ted Drewes

Unfortuanately, the Schlafly science of brewing will not be there this year. I don't know why, it just isn't.
Ticket prices are as followed:

Single ticket for day session - $6
Single Ticket for Evening Session - $10
All Day Pass - $10 for Science Center Members. $20 for non-Members.
Extravaganza Ticket - $100

UPDATE: I will probably be getting a whole bunch of free session tickets since I am volunteering on Sunday and my employer is sponsering the event. If you want some contact me or comment below.

Science Spotlight: Alan Turing pt.2

2009-09-16T08:59:00.000-05:00

In 1936, Alan Turing theorized a simple computer that consisted of a reader and an endless reel of symbols (numbers, letters, etc). Even though he wrote about this machine almost a decade before the first electronic computer was developed, this basic theory has become the backbone of modern algorithmic computation. Check out this link for a workable Java "Turing Machine". The machine threorized by a young Alan Turing had the possiblility of bridging the gap between human cognition and mechanical artificial intelligence, since it mimics basic cellular processes and computation.

Turing's AI work didn't stop with his machine however; he later developed the Turing Test, a test where a blinded interrogator must ask questions to a human and a machine that are both trying to prove themselves human. If a machine is able to "trick" the questioner, then it is said to have passed the test. Here is the original paper writen about the Turing Test, I really recommend reading it if you like mind puzzles. Also here are some relational maps describing the debate on whether computers can actually 'think' and if the Turing Test actually works.

Science Spotlight: Alan Turing

2009-09-14T08:45:00.006-05:00

Last week Prime Minister Gordon Brown apologized to Alan Turing on behalf of all of England, calling Mr. Turing "a real war hero". Over half a century has passed since Alan Turing committed suicide instead of facing a prison sentence or continued estrogen injections; the two options for being gay in England at that time, but his revolutionary endeavors are still changing academic thought in computer science, chemistry, mathmatics, biology, and cryptoanalyics.

This week Science.Blog.Science will be dedicating a series of posts to the work of Alan Turing and the effect he has had on all science and humanity. As always, I really appreciate any relevant posted material or links to the subject.

Free Online Journals!

2009-09-09T13:13:00.000-05:00

Unfortuanately, not everyone is currently enrolled at a university nor do their employers pay for acess to a robust set of scientific journals, but there is a large group of interested individuals who would like to stay on top of developing research without it being filtered through some news site or blogger (ugh...wait a sec?). I encourage everyone to check out this website which provides a large conglomeration of free online journals. Now it won't contain your Nature's and your Science's, your screwed there. It does contain a large repository of open-access journals, some of which are great if you are a novice or an expert in that field. Check it out, the Directory of Open Access Journals (DOAJ), is a really easy to navigate website and who knows you might learn something.

Liquid Gold: Liposuction and Stem Cells

2009-09-08T11:05:00.002-05:00

As reported by The Stanford School of Medicine, researchers have found that adult fat tissue can be coaxed into becoming pluripotent stem cells (iPS cells). Not only is this new resource readily available, research shows that converting fat cells to iPS cells is 20 times more effiecient than the traditional conversion from skin cells. Not only are they getting a greater amount of cells to change, but they are also getting them to change quicker!

This is a great advance into developing patient-specific iPS lines in the future. I'm going to try to renew my JSTOR account today, so hopefully I can add a little more to this article once I read the published paper.

Nintendo Power!

2009-09-02T08:38:00.000-05:00

Can Tetris improve brain function? According to a recently published study in BMC Research Notes, playing Tetris for 30 minutes a day can increase brain efficency and cortex size in the BA regions that control critical thinking, reasoning, language. and processing. The image below of both hemispheres of the brain show the areas of increased cortical thickness (Red) and the increased brain function (Blue).

I'm sure further studies will follow, but I am suprised that there was no comments made about increased brain function regarding spatial relationships (an area I would assume would improve, if any).

And if this wasn't awesome enough, According to Science Daily, an initial Oxford study shows that playing Tetris may help reduce PTSD flashbacks, also!

Lets get Sequenced!

2009-08-31T13:16:00.003-05:00

After browsing the the websites of http://www.23andme.com/ and http://www.navigenics.com/, I am really amazed that there is a competitive, viable market for personal genotyping. These services (just two of a whole emerging online market) both offer what seems at first glance to be quality genotyping services, but I'll concentrate just on 23andme's product since it is much more affordable (ranging from $99 to $399) compared to navigenics ($999, expensive but seems more robust).

So what is personal genotyping? Why get it done? Well, first of all let me explain the difference between genotyping and sequencing. Genotyping is the process of identifing genetic variants within a genome, in this case using SNPs. This process is just finding a small fraction of regions in your DNA and comparing them to historical medical data. Now sequencing on the other hand is laying out all the A, T, G, C's for a large region or whole genome. For a more in depth but easy to follow tutorial on this I really recommend PBS Nova's flash shows (a little outdated though, but informative none the less). Sequencing is a lot more robust, expensive, and time consuming, but apparently, according to Ivan from scientificsolutions there is a new company out there that will sequence your whole genome for $5000.

The benefits of genotyping your own DNA is arguable. In fact, everything I have read seems pretty inconclusive one way or the other. Regardless, the ablitly to analyze your own DNA against ever-growing medical data of known mutations of certain genes would mean you can see, within reason, if you have a high probability of a developing a specific genetic condition. Of course, this is not a diagnosis, but may help you predict such diseases as Crohns Disease, Type II Diabetes, and BRCA Cancer Mutations (and over a hundred more, but some are pretty obvious without the testing).

The sites also offer you the ability to compare you data to other people, whether that be family data (but they warn you that you may find out your adopted, lol) or you can just compare against friends to see who is the most genetically superior!

UPDATE: here is a related article regarding why you may not ever want to get this done. Insurance companies could deny you based on a genetic predisposition to a certain disease!

Firefox upgrade scaring porn collectors

2009-08-27T08:53:00.003-05:00

LOL! I don't know what to say about this article, it speaks for itself.

http://www.pcpro.co.uk/blogs/2009/08/26/porn-collection-put-people-off-upgrading-to-firefox-3/

Check the comments to prevent your porn bookmarks from being discoverred!

Computer Programmers Needed!

2009-08-26T13:17:00.004-05:00

Now that biology, specifically genetics, is becoming more automated for the purpose of high-throughput, I have seen more and more job opportunities arise to fill the rift between scientists, engineers/computer programmers. These liason positions trouble me greatly. They highlight a major inneficiency within organizations. You have to hire an excessive amount people to compensate just the terminology gaps that two cross-trained individuals could easily tackle, not to mention that your end products are always full of problems and bugs mainly because programmers do not fully understand what the needs of the biologist are, and biologists rarely understand the limits of the programming languages.

If you're a biology major: TAKE AS MANY PROGRAMMING CLASSES AS POSSIBLE!!!! In fact, double major, if you can (or at least minor). I cannot believe there is not more stress put on this, especially in grad school programs. If you have both degrees, then your marketablility is limitless.

If you're a CS major and are intersted in working in science: Take an advanced biology course (and all the prerquisites, of course). If your programming for a genetics lab, then take a genetics class. Understand the terminology, and the basic priciples that dictate the science.

UPDATE: Not an hour after posting this, my boss just asked during a meeting if anyone could write PERL scripts, because our normal PERL programmer just got fired, lol!

Trial for Global Warming???

2009-08-26T10:24:00.002-05:00

The LA Times reported yesterday that the largest business lobby, the US Chamber of Commerce, is trying to mimic the Scopes-monkey trial by calling for a hearing regarding the legitamacy of human caused global warming and it's harmful effects on the human population.

Despite an overwhelming concensus among published papers and scientists, the US CoC wants to bring this issue up in court in hopes to create the illusion of "discord" among the scientific community, and ultimately allow their members to avoid paying higher taxes/fines regarding emmision and pollution standards.

The EPA, who is primed to initiate legislation that would make greenhouse gases regulatable under the Clean Air Act, has already called such a hearing a "waste of time", but the CoC may pursue this in a higher, federal court.

CCD marker found for bees

2009-08-25T10:53:00.002-05:00

A new marker for Colony Colapse Disorder was found in a study featured in the Proceedings of the National Acadamy of Sciences this week. According to genomeweb; the University of Illinois researchers were using microarrays to analyze gene expression patterns, and found a significant difference in fragmented ribosomal RNA (rRNA) in their guts.

The CCD-affected bees had higher amounts of fragmented rRNA, which could, if infected with a virus, harm ribosome performance; thus hinderring protien manufacturing in the cells.

"If your ribosome is compromised, then you can't respond to pesticides, you can't respond to fungal infections or bacteria or inadequate nutrition because the ribosome is central to the survival of any organism," Berenbaum said in a statement. "You need proteins to survive."

This discovery should be able to lead to earlier diagnosis of CCD infected colonies and brings the whole research-effort one step closer to understanding the underlying factors that cause CCD, a disease that has wiped out massive amounts of bee colonies all over the world.

Synthetic Life

2009-08-25T08:53:00.004-05:00

As the UK Times reports, the private scientist Dr. Craig Venter is getting close to creating the first synthetic life. Though the possible applications in the eventual refining of this technique are limitless, are there ethical questions that should be addressed?

I assume that the culmination of his efforts will be misperceived by many people, and that the unknown will once again be feared, ostracized. But there should be a very serious discussion of what is happening.

I really recommend reading the entire article posted by the UK Times.