Monday, August 4, 2008

The DNA Network

The DNA Network

DNA sequencing and bioinformatics, part I: a case study from the classroom [Discovering Biology in a Digital World]

Posted: 04 Aug 2008 07:42 PM CDT

What happens when high school students clone and sequence genomic DNA?

DNA sequencing is a wonderful tool for discovery and a great technique for getting students involved in molecular science. This fall, Bio-Rad will officially begin selling their DNA cloning and sequencing kit. Now, students across the country will have the tools in hand to begin their own projects cloning and sequencing plant genes.

Of course, without bioinformatics there's no way to know what's been cloned or sequenced.

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Pfizer will donate dollars to science education- but only if you vote [Discovering Biology in a Digital World]

Posted: 04 Aug 2008 06:29 PM CDT

Pfizer has pledged to donate up to $10,000 to the cause of science education, through, but only if enough of you, dear readers go to Big Think: Think Science Now and vote for your favorite video.

If you're not familiar with Pfizer, they're a pretty well-known drug company. You probably read about one of their products every time you delete messages from your e-mail in-box.

You don't even have to watch the videos, just vote.

I strongly recommend watching the videos, though. They are all profiles of scientists who work at Pfizer or other research organizations. It's pretty interesting to hear their stories and learn about their careers.

The fund raiser will have a limited shelf-life, but hopefully BigThink will keep the profiles up for a while. This is a great resource for providing students a snapshot of scientists and their careers. I'm also impressed with Pfizer for profiling the most diverse group of scientists that I've ever seen outside of a real lab.

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Link For Consideration? => Submit to! [Think Gene]

Posted: 04 Aug 2008 03:52 PM CDT

We at Think Gene, like all websites, occasionally receive emails from other websites asking for reviews, promotion, and link exchanges.

We are happy to promote relevant, quality genomics-related content. However, we have a web application specifically for link promotion: Please submit your web content to news.thinkgene if you’d like to be considered for promotion. Why?

  • You earn relevant promotion from our users by submitting to the news.thinkgene list even if we do not mention you on the Think Gene blog
  • It helps us organize and review new content
  • It’s an easy filter to weed out mass-mailers and low-quality content

You are welcome to make as many submissions as you like to news.thinkgene as long as they are relevant and interesting. Typically, essays, videos, and archives of factual content do better than home pages, factual articles, and press releases without a personalized response.


-Andrew Yates
Senior Editor, Think Gene

Medical Education Evolution: A Growing Community [ScienceRoll]

Posted: 04 Aug 2008 10:34 AM CDT

Some weeks ago, we launched the Medical Education Evolution project which aims to connect the tools of medicine 2.0 to traditional medical education. Now we have about 40 members and there are several active discussions about different aspects of the problem.

If you think you have visions and ideas about how to change medical education, please join us and tell us your opinion.

You should also check out the wiki Deirdre Bonnycastle just created.

Anthropology of YouTube [ScienceRoll]

Posted: 04 Aug 2008 09:21 AM CDT

One of the best slideshows I have ever seen:

(Via Johnnie Moore’s Weblog)

DNA Education: Back to School Edition [The DNA Testing Blog]

Posted: 04 Aug 2008 08:56 AM CDT

As the end of the summer nears, students and teachers alike prepare for the start of another school year. This is a perfect time of year to remind educators and parents of school-aged children that DDC's DNA Education Corner contains dozens of activities meant to educate and entertain even the youngest budding scientist about DNA [...]

Nuclear Magnetic Reporters [Reportergene]

Posted: 04 Aug 2008 08:05 AM CDT

With the advantage of tomographical data set and detailed anatomical information, magnetic resonance imaging (MRI) features an unsurpassed space resolution (micrometers!) in the field of in vivo imaging. Conversely, imaging of optical reporters like luciferase and GFP, still suffers from short-sighted resolution, often requiring longer post-mortem analysis (i.e. immunoistochemistry) to identify and deconvolve photon emission sources of in vivo datasets. From this "topological" standpoint it is easy to understand the growing awareness and demand of new "superparamagnetic" reporter genes to be detected according to their "relaxivity". NMR gene expression strategies thus far introduced in recent literature include:
  • detection of beta-galactosidase activity;
  • targeting of amide protons of expressed proteins;
  • expression of natural iron homeostasis proteins such as transferrin, ferritin, MagA.
Nonetheless, those "magnetic" papers had very low followup, and a transgenic paramagnetic reporter mouse still don't exists. MRI reporters classically suffer from low sensitivity (lot of reporter need to be expressed in order to be detected) and low dynamic range (the detection don't discriminate very well different reporter concentrations). It is possible to conceive a reporter gene with high space/time resolution, high sensitivity and high linear range? With multimodality imaging a super reporter mouse can harbour a vector containing more than one reporter (for different imaging modalities). This is very fashionable in leading imaging labs, and lot of cut and paste have been made with reporter sequences. Do you know any super-mouse?

Muscle Pain from Statins? Time for a genetic evalutaion! [The Gene Sherpa: Personalized Medicine and You]

Posted: 04 Aug 2008 05:24 AM CDT

In a wonderful demonstration of how successful genetic research on pharmacogenomics needs to be done. The SEARCH Collaborative Group successfully demonstrated the power of GWAS nested in other...

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Sunbathing, Frozen Fleas, and Heavy Metal [Sciencebase Science Blog]

Posted: 04 Aug 2008 03:08 AM CDT

Spectroscopynow.comI’ve got a whole new clutch of science news in my latest column on spectroscopy NOW for you this week:

Magnetic insights - A new MRI technique has been developed to allow physicists to see deep within tiny magnets. The technique could improve our understanding of magnetism at the fundamental level and lead to better computer hard drives and perhaps even new small-scale MRI instruments.

Salty solution to desalination - NMR spectroscopy has been used to assist in the development of chlorine-resistant membranes for use in water desalination plants. The new membrane materials could avoid degradation by chlorine disinfectants and reduce operating costs and inefficiencies and so make desalination a more viable prospect on a larger scale in the developing world. I asked the team leader Benny Goodman about the prospects for this system. “We anticipate a 3-5 year timespan to commercialization,” he told me, “The remaining obstacles are to demonstrate large-scale, continuous membrane production and to further tune the chemistry of the materials to be highly rejecting for seawater purification applications.” He added that, “Our current vision is that these membranes would be made in such a way that they could be used to swap out existing membranes.”

Summer screen - Wear sunscreen! It has been the advice of the medical profession, governments, and parents everywhere for several years, and is a topic I’ve touched on in how to sunbathe safely, on Sciencebase. Now, a report published this summer by the Environmental Working Group suggests that many popular sun protection products are at best ineffective, and at worst hazardous to health.

Reflecting on frozen fleas - US scientists have synthesised an antifreeze protein from the Canadian snow flea. The X-ray structure of this, and a synthetic enantiomeric form, could lead to an improved understanding of how this protein inhibits ice crystal formation and could have implications for transplant surgery.

Ordure, ordure! - A new study of soil fertilised with bovine manure reveals that soil quality can be improved significantly compared to that possible with modern “inorganic” farming methods. The study suggests that even poor quality land can be farmed for crops such as maize using manure as a soil improver.

Absorbing work on heavy metal - Chemical analysis and a powerful microscopy technique have been used to work out how toxic heavy metals, such as hexavalent chromium of Erin Brokovitch fame, can be adsorbed on to magnetic nanoparticles. The work could help in the development of a novel remediation technique for water contaminated with the carcinogenic hexavalen chromium.


Sunbathing, Frozen Fleas, and Heavy Metal

RNase and DEPC: Dispelling the Myths [Bitesize Bio]

Posted: 04 Aug 2008 12:47 AM CDT

DEPC. IF you work with RNA, you’ll know this stuff. It’s vital for ridding solutions of RNases that would otherwise destroy your samples or probes. But just how well do you know it?

An important way of learning techniques, especially when starting out on a career in the lab, is by word of mouth from a more senior colleague. The downside of this approach is that the wisdom passed down from generation to generation is often taken as the whole truth; the original literature is not consulted and sometimes there is no literature at all, only know-how.

This lack of reference to the original concepts undoubtedly leads to the generation of myths, which grow arms and legs as the years go by. RNA techniques are particularly prone to this because, working with such delicate molecules, people tend to add a bit more paranoia-fuelled tweaks/rituals/voodoo charms to their protocols.

One of the things we love to do here on Bitesize Bio is to strip away those myths and give our readers the facts about commonly used techniques. We’ve talked about RNase work before (here and here), but the guys at Ambion also publish a good amount of documentation on facts and tips for RNA work.

One of these is a really nice article about the truths and myths behind DEPC treatment for RNase contamination. In it they test and report on 6 commonly held beliefs about DEPC treatment… here’s a summary of what they found:

FALSE: RNases re-nature after denaturation by autoclaving, so autoclaving is no good for RNase decontamination.

Tests on RNase A before and after autoclaving showed that most of it’s activity was wiped out by autoclaving, so maybe RNases aren’t so invincible after all. That said, some RNase activity remained, so while not invincible RNase are certainly hardy.

TRUE: Autoclaving inactivates DEPC

Well thank goodness - DEPC is indeed inactivated by autoclaving. The mechanism is hydrolysis of DEPC to produce ethanol and water. 0.1% DEPC/water solutions should be completely DEPC-free after autoclaving for 15 minutes/ litre.

FALSE: DEPC solutions should be odor-free after autoclaving
The solution will still smell of ethanol, but also sweet-smelling volatile esters formed by the reaction of ethanol with trace carboxylic acids.

TRUE: Tris-containing solutions cannot be treated with DEPC

The amino group on tris interacts with DEPC, making it unable to do it’s job of decontaminating the solution.

FALSE: 0.1% DEPC is sufficient to inhibit any amount of RNase in solution.
DEPC is not catalytic so the amount of DEPC required for full RNase removal increases with the concentration of RNase, as shown by a neat experiment in the report.

TRUE: 1% DEPC is better at removing RNase than 0.1%

It is certainly true but higher DEPC concentrations mean that there is likely to be more left-over DEPC/DEPC by-products after autoclaving, and these can inhibit downstream applications. The report documents that the efficiency of an in vitro transcription reaction decreases with as the DEPC concentrations used to treat the water are increased.

It’s been 2 great years… [My Biotech Life]

Posted: 03 Aug 2008 10:13 PM CDT

It just dawned on me this afternoon that MBL had recently turned 2. Yeah, two years since I started this blog. Time truly flies when you’re having fun.

I’ve made many friends and many doors have opened as a result of setting up My Biotech Life. I must thank everyone that came by and thought I had anything interesting to say.

Let’s see if I can keep this thing going strong for another 2!

It’s been 2 great years…

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