Friday, August 22, 2008

The DNA Network

The DNA Network

It's elemental: Chemistry movies on YouTube [Discovering Biology in a Digital World]

Posted: 22 Aug 2008 06:00 PM CDT

The Periodic Table of Videos from the University of Nottingham has 118 short YouTube clips about the elements. Wired Campus recommended the Sodium clip (below). I liked it, too. It's not quite as funny as Mentos in Diet Coke, and but it's still cute and the narrator has a haircut like Gene Wilder in Young Frankenstein.

H/T: Wired Campus.

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High school students use DNA testing to spot fishy seafood [Discovering Biology in a Digital World]

Posted: 22 Aug 2008 04:02 PM CDT

Two teenagers, Kate Stoeckle and Louisa Strauss, carried out their own science project over the past year. They visited 4 restaurants and 10 grocery stores and gathered 60 samples of fish and sent them off to the University of Guelph to get sequenced.

I like this story. One of my former students did a project like this for the FDA years ago, sampling fish from the Pike Place Market and identifying them with PCR. He was an intern, though. Here we have students identifying sushi on their own!

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A quick tour of 5 mind-blowing scientific theories [adaptivecomplexity's column]

Posted: 22 Aug 2008 03:57 PM CDT

Don't think you have time for science? ("America's Only Humor & Video Site, since 1958" - we've got humor and video here at Scientific Blogging, but we haven't been around since 1958), has a quick summary of 5 scientific theories that will make your head explode.

One of those theories is evolution:

We're all familiar with the basics of evolution: that a munificent monkey-goddess birthed us all from Her banana-scented womb. But there are some lesser-discussed implications of natural selection that are just plain weird...


Science Olympics [Bayblab]

Posted: 22 Aug 2008 03:57 PM CDT

Are you an expert at the 10m Namedrop? The Data Stretch? The Long Jump-ing to conclusions?

Whether you're doing the summer student sprint or running a marathon on the tenure track, check out these events for the Science Olympics, or come up with some of your own.

[via A Blog Around the Clock]

Lab Artifact [The Daily Transcript]

Posted: 22 Aug 2008 03:15 PM CDT

Maybe this will become the new Friday feature at The Daily Transcript ...


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Navigenics and 23andMe Given California Go-Ahead [DNA Direct Talk]

Posted: 22 Aug 2008 02:16 PM CDT

We are very pleased to see that Navigenics and 23andMe have reached a resolution with the State of California that allows their businesses to move forward with clarity offering their personal genome services to California residents. It’s great news for all– for consumers, the industry, and best of all– for innovation.

Review of Tomorrow's Table: A soothing draught and an easy glide [Tomorrow's Table]

Posted: 22 Aug 2008 11:33 AM CDT

This review just in from Edible East Bay, a quarterly newsletter that celebrates the abundance of local foods, season by season:

"Our world is facing several converging crises—environmental, social, and political—that are affecting, or will affect, the availability of food to all people. This convergence on the issue of food is making our food policies and production practices more visible than ever. Genetic engineering has become a topic of hot debate in this climate, and it is long overdue for citizens to educate themselves on the matter...

In Tomorrow's Table: Organic Farming, Genetics, and the Future of Food, we hear from practitioners in the field of genetic engineering: Pamela Ronald, professor of plant pathology and chair of the Plant Genomics Program at UC Davis, and her husband, Raoul Adamchak, a veteran organic farmer who assists in his wife's research. The two believe that the technology can be (and is being) put to work to the benefit of humanity and global environmental stewardship. In these confusing times, I for one find such creative solutions to the world's problems to be a soothing draught, and the arguments put forth in this book are compelling enough to make one want to rethink the whole matter. Ronald and Adamchak wrote the book, tag-team. It's such an easy glide that we are happily led back through lessons we once slept through in high school, like basic biology and what constitutes the scientific method. This book also includes memorable characters, recipes, and a fabulous glossary of terms useful in the debate over genetic engineering."

Cheryl Koehler

Street Corner Science [Bayblab]

Posted: 22 Aug 2008 09:50 AM CDT

I love this idea, We've been talking about doing something similar at the student pub for some time now for the bayblab podcast... But obviously this guy is in another league...

b-lactamase reporter for selecting yeast clones [Reportergene]

Posted: 22 Aug 2008 09:24 AM CDT

Large scale therapeutic protein production is not so cheap, and it is well known that pharmaceutical industry is under constant pressure to reduce the overall costs. When post-translational modification requirements allow to adopt in production yeast systems instead of mammalian cells, the cost is significantly lowered. In this latter case, the selection of high-producing clones is very important and the possibility to visually discriminate just in 3-4 classes the productivity of thousands of clones in a few days by a single operator is noteworthy, especially if the method is cheaper than classic ELISA or fluorescence/bioluminescence test.

So Hribar and colleagues from the National Institute of Chemistry of Ljubljana, started to deal with alternative "low cost" reporter genes like the beta-lactamase, to find out a rough measure of the protein of interest. The autors worked on Pichia pastoris, a yeast strain just licensed to more than 100 companies also for recombinant heterologous protein production. The short technical report published on the april number of Biotechniques, will not warm up any reporter geek - like me - that loves stupid performances (who really need 9 orders of magnitude linearity???), but the colorimetric method of such 39 kD b-lactamase enzyme would be an asset for smart bio-companies which prefer pragmaticity to geekiness.

  • Hribar, G., Smilović, V., Lenassi Zupan, A., Gaberc-Porekar, V. (2008). β-lactamase reporter system for selecting high-producing yeast clones. Biotechniques, 44(4), 477-484. DOI: 10.2144/000112730

Primary rodent neural stem cell lines [Reportergene]

Posted: 22 Aug 2008 07:25 AM CDT

Millipore Corporation's MilliTrace primary rodent neural stem cell (NSC) lines express green fluorescent protein (GFP) constitutively. GFP expression in these stem cells allows researchers to monitor the behavior of specific populations of cells as they proliferate, migrate, and differentiate into various cell lineages, depending on developmental context. The MilliTrace cell lines are the first commercially available, GFP-expressing, karyotypically normal stem cell lines, and are supplied with optimized expansion medium. Millipore Corporation

red fluorescence spectrum from soviet countries? [Reportergene]

Posted: 22 Aug 2008 07:22 AM CDT

Despite years of effort since its cloning in 1992, the GFP of the jellyfish Aequorea victoria (the most known and used green fluorescent reporter) has not been turned red... until now.

A team of Russian researchers started from a blueshifted GFP variant and performed a molecular mutagenesis evolution approach to get, not only shift toward red, but also some clues to the chromophore formation theory. Basically they made libraries of millions of mutants and sent them through a Dako cell sorter to select the best red performances that were mutated once again and analyzed iteratively until they achieved the desired shift to the red fluorescence. The results was a protein, R10-3, that has both red and green fluorescence, so a pure red protein has not derived yet (but the evolutive job is still in progress).
It is not the first time that a Russian team turns to red fluorescent reporters: some months ago we were reading the Nature Methods paper about Katushka and mKate. Is a matter of fact that red color is an innate hue in some countries: are there the basis to make a social association study about scientists, countries and reporter colors?

  • Mishin, A.S., Subach, F.V., Yampolsky, I.V., King, W., Lukyanov, K.A., Verkhusha, V.V. (2008). The First Mutant of the Aequorea victoria Green Fluorescent Protein That Forms a Red Chromophore. Biochemistry, 47(16), 4666-4673. DOI: 10.1021/bi702130s

Developing World Nuclear Revolution [Sciencebase Science Blog]

Posted: 22 Aug 2008 07:00 AM CDT

nuclear-powerNot being one to shy away from controversy (viz. my MMR and vaccination item, the intelligent Dawkins debate post and the recent flurry of global warming items, including one entitled Climate change debunked), I thought I’d dive headlong into the muddy ethical, economic, and engineering puddle that is nuclear power.

However, I am wearing a buoyancy aid, a nose-clip, ear-plugs, and protective goggles in the form of a peer-reviewed review from the International Journal of Global Energy Issues (2008, 30, 393-412), rather than skinny dipping.

In that paper, John Cleveland of the International Atomic Energy Agency, in Vienna, points out that currently nuclear power produces around 15 percent of the electricity we use worldwide. This time last year, there were 438 nuclear power plants providing more than 370 Gigawatts with 31 new units under construction looking to add 24 GW to that total, although with a few being decommissioned in the meantime.

Cleveland explains that several countries are planning to either introduce nuclear energy or expand their nuclear generation capacity, and that most of the new plants will be of evolutionary, rather than innovative design. They will incorporate improvements over existing electricity generating nuclear plant designs achieved through small to moderate modifications, with a strong emphasis on maintaining proven design features to minimize technological risks. Cleveland suggests that in the longer term, innovative new designs will help to promote a new era of nuclear power.

He argues that the increasing demand for power both in the industrialized and developing world, together with nuclear power's positive attributes, provide a solid rationale for expanding nuclear power sources:

  • Nuclear power’s lengthening experience and good performance. The industry now has more than 12,000 reactor years of experience, and the global average nuclear plant availability during 2006 reached 83%
  • Growing energy needs. All forecasts project increases. The strategies are country dependent, but usually involve a mix of energy sources
  • Interest in advanced applications of nuclear energy, such as seawater desalination, steam for heavy oil recovery and heat and electricity for hydrogen production
  • Environmental concerns and constraints. The Kyoto Protocol has been in force since February 2006, and for many countries (most OECD countries, Russia, the Baltic nations and some countries of the Former Soviet Union and Eastern Europe) emissions limits are imposed
  • Security of energy supply is a national priority in essentially every country
  • Nuclear power is economically competitive and provides stability of electricity price.

He adds that nuclear power faces significant challenges, nevertheless, including the continuing need to sustain a high level of safety assurance, implementing high-level waste disposal, and strengthening the nuclear non-proliferation regime.

Success in these areas will provide a sound basis for establishing nuclear power as a sustainable energy source.

Evolutionary nuclear plants that utilise the best of current systems are already being built in several countries, and, adds Cleveland, are likely to be the primary choice for the next decade or two. Innovative, nuclear plants, are a different matter. In general they will require a new design paradigm, construction and testing of a prototype, and then a pilot plant before commercialisation, and so may not be implemented until about the second quarter of this century.

Several innovative designs are being developed for the Small- to Medium-Size Reactor (SMR) range and could find their introduction into the increasingly power hungry developing nations, as well as in some cases into industrialized countries. In developing countries, boosting self-reliance, keeping costs down, and enhancing local work force participation and participation of the domestic industry could be important factors for the governments of those nations to pursue.


Developing World Nuclear Revolution

Around the Blogs [Bitesize Bio]

Posted: 22 Aug 2008 05:40 AM CDT

Bayblab podcast: Episode18 [Bayblab]

Posted: 21 Aug 2008 10:42 PM CDT

After a summer off the bayblab podcast is back. In this delayed episode we drunkenly ramble about non-coding RNA's, phages, science in the news and the optimal amount of beer for various activities... Don't miss out on episode 19 (and episode 7 part 4) which will be out any day now :). We'll be back with a bigger better podcast in September so refresh the bayblab podcast on your itunes or other rss clients in anticipation...

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