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Archive for the ‘cool tools’ Category

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.

A Revolution in Scientific Publication

 :: Posted by American Biotechnologist on 07-30-2014

Since we are talking about impact factors and Journal related stuff, (see When JIF Becomes a Dirty Word), I wanted to share with you a very cool concept that I saw recently in F1000 Research.

Aside from it’s move to the digital world, scientific publication, as we know it, has remained relatively constant for over four hundred years. Papers are written in a scientific method-based theme and broken down into bite size sections. Papers are very much there for scientists to communicate their findings with us and for the investigators to provide us with their personal interpretation of the data. While a sort of 2-way communication often happens via editorials and personal communication, the presentation of the data remains static and one dimensional. Results, which represent the heart of the researchar, often presented in tabular or pictorial format. Much of the effort and funding allocated to a research project can be distilled down to several figures and maximizing the communicative ability of these results is essential to successful publication. That is why the methodology used to publish a recent paper in the journal F1000 Research may, in fact, revolutionize the world of scientific publishing.

In the newly released article, German professor of neurogenetics, Bjorn Brembs, published a proof-of-concept figure allowing readers and reviewers to run the underlying code within the online article. Instead of presenting readers with a static figure that can only be interpreted by the author, Dr. Brembs submitted the figure’s underlying code to the journal, allowing readers and reviewers to render the figure in various formats giving them more control over interpretation of the original data.

According to Brembs, the ultimate goal is to set up all journal submissions in such a way that authors will no longer have to deal with figures. They will simply need to submit text with links to data and code, and the rest will be up to the reader.

The recent rise in retraction rates of scientific articles proves that attempts at reproducibility by other labs are crucial to cross-checking our understanding of science. With only one or two figures to choose from in the past, authors were incentivized to pick the view of the data that best demonstrated their conclusions. “The traditional method of publishing still used by most journals today means that as a referee or reader, the data cannot be reused nor can the analysis be checked to see if all agree with the reported conclusions”, said Brembs. “This slows down scientific discovery. We are pleased to be able to pioneer these two interactive figures with F1000Research, which will hopefully be the start of a big shift in the way journals treat their figures.”

Cell Isolation – The Two Worlds of Cell Separation

 :: Posted by American Biotechnologist on 06-30-2014

A Simple Way to Label Your Own Antibodies

 :: Posted by American Biotechnologist on 03-13-2014

Bio-Rad Laboratories announced the launch of its ReadiLink antibody labeling kits, one of the market’s simplest antibody conjugation solution for labeling microscale amounts (50–100 µg) of antibody. These kits are ideal for researchers interested in labeling their own antibodies for flow cytometry and cell sorting applications.

Using the ReadiLink antibody labeling kits, researchers can label their antibodies in two easy steps. The protocol takes only 70 minutes, and the labels are as bright and photostable as traditional dyes. Bio-Rad offers 10 different fluorophores whose excitation/emission wavelengths range from UV to infrared.

ReadiLink antibody labeling kits permit fluorophore conjugation of antibodies in two simple steps.

“The labeling kits will benefit a wide range of researchers,” said Mary Ferrero, Bio-Rad Product Manager in the Gene Expression Division, Life Sciences Group. “ReadiLink antibody labeling kits are ideal for researchers who are using a rare antibody, are interested in an antibody that is not commercially available with the appropriate fluorophore, or who want to label an antibody with a fluorophore that will fit into their multicolor flow cytometric experiment.”

Bio-Rad also offers additional reagents and consumables for each step of flow cytometry experiments, such as the ReadiDrop™ cell viability assays and primary antibodies.

For more information about Bio-Rad’s antibody labeling kits, please visit www.bio-rad.com/antibodylabeling.

How Google Glass Will Change Science

 :: Posted by American Biotechnologist on 01-23-2014

Google Glass is still in its infancy, however, the potential breakthroughs that it can offer in the fields of medicine and science are astounding.

Surgeons at the Ohio State University Medical Center are already using the device as a training and consulting tool while in the midst of surgery. Physician wearing Google Glass are able to transmit a live video feed to colleagues and medical students anywhere in the world. This is a true game changer in education as it gives students valuable exposure to live surgery in real-time from a surgeon’s point of view.

Aside from it’s communicational value, Google Glass has the potential to actually be used as an integral part of surgical practice. Physicians hope to be able to call up medical images or other important patient data during the course of surgery.

Now imagine combining Google Glass with procedures that incorporated fluorescently labeled dyes capable of differentiating cancerous tumors from benign growths or nerve from muscle. Surgeons such as Quyen Nguyen are already currently shining light onto labeled tumors and nerves to accomplish this goal (see Lighting up the operating room). With Google Glass, this procedure would become so much easier.

While medical applications sound very cool, what will be of most interest to our readers are the potential laboratory bench applications. How about using Google Glass for fluorescent imaging at the bench? Or calling up protocols while setting up an experiment? The possibilities are endless.

What applications can you imagine for Google Glass in your daily research?