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Archive for the ‘cool tools’ Category

The Cell: An Image Library-CCDB Launches a New Tool for Cell Visualization

 :: Posted by American Biotechnologist on 06-13-2013

Guest Post by David Orloff:

The Cell: An Image Library-CCDB launches their new Pivot View tool for a new experience in exploring the images in the Library. The Pivot View, now featured on the home page http://www.cellimagelibrary.org, allows one to explore the whole library in just moments.

You can view images, by cell type, cell line, organism, image mode, attribution, and media format or any combination of these.

Want to re-use some of the images? Now you can search on the licensing requirements just as easily.

For a really interesting experience select the different criteria you are interested in and then be sure to hit the graph view button (circled in red here).

click to view image in new window

This is currently a beta release please, if you encounter any problems email Cellimagelibrary@mail.ncmir.ucsd.edu.

We welcome all feedback.

Fast new, 1-step genetic engineering technology

 :: Posted by American Biotechnologist on 05-22-2013

A new, streamlined approach to genetic engineering drastically reduces the time and effort needed to insert new genes into bacteria, the workhorses of biotechnology, scientists are reporting. Published in the journal ACS Synthetic Biology, the method paves the way for more rapid development of designer microbes for drug development, environmental cleanup and other activities.

Keith Shearwin and colleagues explain that placing, or integrating, a piece of the genetic material DNA into a bacterium’s genome is critical for making designer bacteria. That DNA can give microbes the ability to churn out ingredients for medication, for instance, or substances that break down oil after a big spill. But current genetic engineering methods are time-consuming and involve many steps. The approaches have other limitations as well. To address those drawbacks, the researchers sought to develop a new, one-step genetic engineering technology, which they named “clonetegration,” a reference to clones or copies of genes or DNA fragments.

They describe development and successful laboratory tests of clonetegration in E. coli and Salmonella typhimurium bacteria, which are used in biotechnology. The method is quick, efficient and easy to do and can integrate multiple genes at the same time. They predict that clonetegration “will become a valuable technique facilitating genetic engineering with difficult-to-clone sequences and rapid construction of synthetic biological systems.”

Thanks to the American Chemical Society for contributing this story.

Extracting and Purifying Human DNA in Under Three Minutes

 :: Posted by American Biotechnologist on 05-07-2013

University of Washington engineers and NanoFacture, a Bellevue, Wash., company, have created a device that can extract human DNA from fluid samples in a simpler, more efficient and environmentally friendly way than conventional methods.

Conventional methods use a centrifuge to spin and separate DNA molecules or strain them from a fluid sample with a micro-filter, but these processes take 20 to 30 minutes to complete and can require excessive toxic chemicals.

UW engineers designed microscopic probes that dip into a fluid sample – saliva, sputum or blood – and apply an electric field within the liquid. That draws particles to concentrate around the surface of the tiny probe. Larger particles hit the tip and swerve away, but DNA-sized molecules stick to the probe and are trapped on the surface. It takes two or three minutes to separate and purify DNA using this technology.

Read the full story on the UW website.

Accelerating the discovery of the hammers and tongs of life

 :: Posted by American Biotechnologist on 02-25-2013

Researchers at the University of Wisconsin-Madison have found a way to significanlty increase the processing speed at which mass spectrometers identify proteins. Professor Joshua Coon and colleagues from the department of chemistry and biomolecular chemistry, used isotope tags to enable the mass spec to differentiate between as many as 20 different samples at once. The new technology is expected to make mass spec cheaper, faster and more accessible to the scientific masses clamoring to be part of a technique that is on the forefront of biology.

As one astute observer put it:

Proteins are essential building blocks of biology, used in muscle, brain, blood and hormones. If the genes are the blueprints, the proteins patterned on them are the hammers and tongs of life.

With Coon’s new technology, the discovery of the hammers and tongs have life has just been kicked up a notch.

For more information, read Analytical trick may accelerate cancer diagnosis.

The Science Game Center – Video Games that Teach Science

 :: Posted by American Biotechnologist on 02-20-2013

The Science Game Center (SGC) launched on April 19, 2012 and serves as a clearing house for all types of games for science education – card games, board games, video games and more. Games that also generate science data are also featured. For example, Eyewire is a brand new game from MIT that intends to map the human brain my crowd sourcing. Eyewire is from Sebastian Seung’s lab at MIT.

Serving as a central resource for educators to find games to use to teach students and as a resource to assist game developers in reaching their audience, the SGC is a valuable resource in a growing field. Key to the value the SGC offers is the opportunity for educators, scientists, and players to post their reviews of the games. Not only will these reviews inform teachers about how the games have been used by others, reviews will provide constructive feedback to the game developers about the accuracy of the scientific representations and about how much players enjoy the games. To make the SGC as useful as possible, we need reviews of games by the scientific community. Help us out; review some games. Take a break from reviewing technical papers, give one of the games a try, then try it again with your kids and submit your thoughts. Your reactions as a scientist may help guide teachers seeking games, and your review will be tempered by the comments of 5th graders.

For additional comments or questions, please contact David Orloff, Project Director or Melanie Stegman, Ph.D., Director of Learning Technologies Program at the Federation of American Scientists (FAS). The FAS has also developed its own game Immune Attack and is currently developing the sequel, Immune Defense.This project is supported in part by a competitive grant from the Entertainment Software Association Foundation (ESAF). FAS has supported research in effective learning technologies since 2001. See www.fas.org/programs/ltp for more information about Learning Technologies at FAS.

Connect with us.
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LinkedIn: http://www.linkedin.com/groups/Science-Game-Center-4708136/about
Twitter: @scigame and @melanieanns

Thanks to David Orloff for submitting this guest post.