Posts Tagged ‘Protocols’

A Revolution in Pipetting

 :: Posted by American Biotechnologist on 08-05-2014

A team of Whitehead Institute researchers is bringing new levels of efficiency and accuracy to one of the most essential albeit tedious tasks of bench science: pipetting. And, in an effort to aid the scientific community at large, the group has established an open source system that enables anyone to benefit from this development free of charge.

Dubbed “iPipet,” the system converts an iPad or any tablet computer into a “smart bench” that guides the execution of complex pipetting protocols. iPipet users can also share their pipetting designs with each other, distributing expertise across the research community. The system, created by researchers in the lab of Whitehead Fellow Yaniv Erlich, is described in detail in a letter appearing this week in the journal Nature Methods.

Erlich says that today’s experiments frequently rely on high-throughput methods that combine large numbers of samples with large scale, complex pipetting designs. Pipetting errors can lead to experimental failure. Although liquid-handling robots would seem to be a logical choice for such work, they are also extremely expensive, difficult to program, and require trained personnel. Moreover, they can be plagued by technical snafus, ranging from bent or clogged tips to an inability to capture liquids lying close to the bottoms of individual wells.

“We needed an alternative to costly robots that would allow us to execute complex pipetting protocols,” says Erlich. “This is especially important when working with human samples that are often in limited supply.”

iPipet illuminates individual wells of standard 96- or 384-well plates placed on top of a tablet screen, guiding users through the transfer of samples or reagents from source to destination plates according to specific designs. Users create their own protocols in Microsoft Excel files in comma-separated format and upload them to the iPipet website, which generates a downloadable link for execution on a tablet computer. Included on the iPipet site are a variety demos and an instructional video.

So, how well does iPipet work? Beautifully, according to members of the Erlich lab. In a test of the tool against a liquid-handling robot, iPipet enabled nearly 3,000 fixed-volume pipetting steps in approximately seven hours. After significant time spent on calibration, the robot accomplished only half that number of steps in the same allotted time. To date, one of the only challenges lab users have encountered is keeping well plates in a fixed position on the tablet screen. For that, Erlich’s team provides a solution: a 3D printed plastic adaptor that users can create with a file accessible via the iPipet website.

“The entire iPipet system is open source,” says Erlich. “We want to maximize the benefit for the community and allow them to further develop this new man-machine interface for biological experiments”

Thanks to Whitehead Institute for Biomedical Research for contributing this story.

How to avoid leaky SDS-PAGE gels

 :: Posted by American Biotechnologist on 06-03-2013

Here’s a great video tip from LabTricks.

Please note that this video is unaffilated with Bio-Rad Laboratories.

A SMART(er) way to track influenza

 :: Posted by American Biotechnologist on 07-11-2012

Brown University researchers have created a reliable and fast flu-detection test that can be carried in a first-aid kit. The novel prototype device isolates influenza RNA using a combination of magnetics and microfluidics, then amplifies and detects probes bound to the RNA. The technology could lead to real-time tracking of influenza. Results are published in the Journal of Molecular Diagnostics.

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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.

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Introduction to High Resolution Melt Analysis

 :: Posted by American Biotechnologist on 03-05-2012

In our last post we told you about how Bio-Rad Laboratories very own Sean Taylor and Francisco Bizouarn were crowned the kings of MIQE. Today we’d like to bring you another classic from his majesty Frank. In the slideshow below, you will learn the basics of High Resolution Melt Analysis (HRM), applications, important considerations, assay design and optimization and analysis software. Enjoy. And all hail the king!