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Archive for the ‘cool tools’ Category

Stunning images of the human brain

 :: Posted by American Biotechnologist on 03-27-2012

Are you a stumbler? While I don’t spend oodles of time bouncing through StumbleUpon, every once in a while I come across a gem that I just need to share. The Human Brain, is a collection of the most amazing images of, wait…you guessed it…the brain, that you have ever seen. It includes detailed views of every angle, with the ability to zoom in and out and add clear labels if desired. It also included histological sections which can be zoomed in right down to the cellular level.

I urge you, if you want to experience jaw-dropping images, to visit the human brain website.

Researchers Print Live Cells with a Standard Inkjet Printer

 :: Posted by American Biotechnologist on 03-19-2012

Researchers from Clemson University have found a way to create temporary holes in the membranes of live cells using a standard inkjet printer. The method will be published in JoVE, the Journal of Visualized Experiments, on March 16.

“We first had the idea for this method when we wanted to be able to visualize changes in the cytoskeleton arrangement due to applied forces on cells,” said paper-author Dr. Delphine Dean.

She said other researchers have been using this method to print cells onto slides, but that they have only recently discovered that printing the cells causes the disruption in their membranes for a few hours. Creating temporary pores allow researchers to put molecules inside of cells that wouldn’t otherwise fit, and study how the cells react.

“The authors have used an extremely innovative approach for bioprinting cells. Moreover, this approach can be used for applications other than cell printing,” said JoVE Science Editor, Dr. Nandita Singh. “Matrix proteins can be printed onto substrates with this technique for cell patterning. This JoVE publication will make this approach simple and approachable and enable other labs to replicate the procedure.”

The printer is modified by removing the paperfeed mechanism and adding a “stage” from which to feed the slides. The ink is replaced with a cell solution, and the cells are printed directly on to the slides.

Using this method, the researchers are able to process thousands of cells in a matter of minutes. Dr. Dean’s team used the holes to introduce fluorescent molecules that illuminate the skeleton of the cell.

“We are actually interested in the cell mechanics of compressed cells. This method allows us to push on the cells and watch the response easily,” said Dr. Dean. “We are interested in cardiovascular cells, and how they respond to mechanical force.”

Dr. Dean chose to submit her method to JoVE, the only peer reviewed, PubMed-indexed science journal to publish all of its content in both text and video format, because, according to her, “until you’ve seen it done, it’s hard to understand the process.”

To watch the full video article, please click here: http://www.jove.com/video/3681/creating-transient-cell-membrane-pores-using-a-standard-inkjet-printer#

Spliceman to the rescue

 :: Posted by American Biotechnologist on 03-12-2012

In a brief paper in the journal Bioinformatics, Brown University researchers describe a new, freely available Web-based program called Spliceman for predicting whether genetic mutations are likely to disrupt the splicing of messenger RNA, potentially leading to disease.

“Spliceman takes a set of DNA sequences with point mutations and computes how likely these single nucleotide variants alter splicing phenotypes,” write co-authors Kian Huat Lim, a graduate student, and William Fairbrother, assistant professor of biology, in an “application note” published in advance online Feb. 10. It will appear in print in April.

Spliceman can be found at fairbrother.biomed.brown.edu/spliceman.

Read more…

Analyzing complex plant genomes with the newest next-generation DNA sequencing techniques

 :: Posted by American Biotechnologist on 02-27-2012

Richard Cronn and colleagues (from the USDA Forest Service, Oregon State University, Brigham Young University, and Linfield College) have published an overview of newly developed, up-and-coming DNA sequencing techniques as one of a series of articles in a Special Issue on Methods and Applications of Next-Generation Sequencing in Botany in the American Journal of Botany. In their article, Cronn and co-authors summarize “targeted enrichment” strategies that can be used to obtain specific DNA sequences from complex plant genomes. Articles in the Special Issue provide a detailed snapshot of how “next-generation” sequencing is transforming plant biology.

“Plant genomes range from simple to exceptionally complex,” noted Cronn. “Combining next-generation sequencing with targeted enrichment allows plant scientists to reduce the complexity of plant genomes and focus on specific genes or unique regions that are easy to analyze.”

Read more…

The special issue also includes a comprehensive review article on NGS technologies. Click here to read the review.

Turning a Star Trek Vision Into Reality

 :: Posted by American Biotechnologist on 01-16-2012

Those of us in the medical research community think of ourselves as contributors to patient heathcare both in the areas of disease diagnosis and treatment. However, our contributions are not always recognized and it can be challenging to directly correlate the results of our experiments with a practical medical application. However, I believe that a new research challenge issued by the X PRIZE Foundation and Qualcomm Foundation may change all that and give medical researchers the recognition they deserve.

According to the announcement, the goal of the challenge will be for teams to leverage technology innovation in areas such as artificial intelligence and wireless sensing – much like the medical Tricorder of Star Trek® fame – to make medical diagnoses independent of a physician or healthcare provider.
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