Posts Tagged ‘tools’

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.

Designing the Perfect Quantitative Western Blot

 :: Posted by American Biotechnologist on 04-02-2014

A methods article published yesterday provides a rigorous and concise workflow with specific instructions on how to produce and analyze quantitative data using western blot experiments. The paper, coauthored by Bio-Rad scientists and published in BioMed Research International, also highlights recently introduced technologies that improve reproducibility. The result is a powerful, step-by-step guide to obtaining quantitative and reproducible densitometric data from western blots regardless of the specific experiment.

Although western blotting is a well-established laboratory technique, it has recently come under fire as a quantitative method because extreme care must be taken when generating and interpreting the resulting data.

The technique is challenging and requires following a rigorous methodology to achieve reproducible and quantitative data. According to a recent survey of more than 750 labs, 41% of researchers say their western blots fail a quarter of the time.

Dr. Aldrin Gomes, an assistant professor at University of California, Davis, agrees that flawed western blots are not unusual. To compare expression of a protein of interest from sample to sample, protein abundance is commonly normalized to a housekeeping gene. “When I see a large, dense band for the protein of interest or the housekeeping protein, I cringe,” says Gomes. That dense band usually means the protein of interest or housekeeping protein was no longer within the assay’s linear dynamic range. No accurate quantitative data can be extracted from such blots.

Sean Taylor discusses the BioMed Research International paper he coauthored.

Another common reason for failure of quantitative western blots is flawed or incomplete protocols, according to Sean Taylor, the paper’s lead author and a Bio-Rad field application scientist (watch a video of him discussing the paper on the left). To address this, Taylor’s review pays special attention to experimental design and sample preparation and discusses proper definition of the linear dynamic range of protein loading, all key factors for generating meaningful quantitative western blot data.

Taylor also introduces more advanced concepts to improve reproducibility, simplify workflow, and reduce the time and cost of western blotting. One such technique is stain-free total protein normalization, which over the past year has proven superior to using housekeeping proteins or total protein staining to correct for loading errors.

With this article, Taylor hopes researchers now have a simple guide to ensure quantitative and reproducible western blot data for all research fields that rely on this technique.

To read the open access research article, visit http://bit.ly/1kCAOcr.

For additional resources please consult Bio-Rad’s guide to Troubleshooting Western Blots.

Video: How to Perform Perfect Quantitative Western Blotting

 :: Posted by American Biotechnologist on 04-01-2014

Lab on a chip….on a cell phone!

 :: Posted by American Biotechnologist on 11-18-2013

In developing nations, rural areas, and even one’s own home, limited access to expensive equipment and trained medical professionals can impede the diagnosis and treatment of disease. Many qualitative tests that provide a simple “yes” or “no” answer (like an at-home pregnancy test) have been optimized for use in these resource-limited settings. But few quantitative tests—those able to measure the precise concentration of biomolecules, not just their presence or absence—can be done outside of a laboratory or clinical setting. By leveraging their discovery of the robustness of “digital,” or single-molecule quantitative assays, researchers at the California Institute of Technology (Caltech) have demonstrated a method for using a lab-on-a-chip device and a cell phone to determine a concentration of molecules, such as HIV RNA molecules, in a sample. This digital approach can consistently provide accurate quantitative information despite changes in timing, temperature, and lighting conditions, a capability not previously possible using traditional measurements.

Read more…

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.