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single cell analysis

Creative Minds: Can Salamanders Show Us How to Regrow Limbs?

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Jessica Whited

Jessica Whited /Credit: LightChaser Photography

Jessica Whited enjoys spending time with her 6-year-old twin boys, reading them stories, and letting their imaginations roam. One thing Whited doesn’t need to feed their curiosity about, however, is salamanders—they hear about those from Mom almost every day. Whited already has about 1,000 rare axolotl salamanders in her lab at Harvard University and Brigham and Women’s Hospital, Cambridge, MA. But caring for the 9-inch amphibians, which originate from the lakes and canals underlying Mexico City, certainly isn’t child’s play. Axolotls are entirely aquatic–their name translates to “water monster”; they like to bite each other; and they take 9 months to reach adulthood.

Like many other species of salamander, the axolotl (Ambystoma mexicanum) possesses a remarkable, almost magical, ability to grow back lost or damaged limbs. Whited’s interest in this power of limb regeneration earned her a 2015 NIH Director’s New Innovator Award. Her goal is to discover how the limbs of these salamanders know exactly where they’ve been injured and start regrowing from precisely that point, while at the same time forging vital new nerve connections to the brain. Ultimately, she hopes her work will help develop strategies to explore the possibility of “awakening” this regenerative ability in humans with injured or severed limbs.


DNA Barcodes Could Streamline Search for New Drugs to Combat Cancer

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Cells labeled with barcodesA little more than a decade ago, researchers began adapting a familiar commercial concept to genomics: the barcode. Instead of the black, printed stripes of the Universal Product Codes (UPCs) that we see on everything from package deliveries to clothing tags, they used short, unique snippets of DNA to label cells. These biological “barcodes” enable scientists to distinguish one cell type from another, in much the same way that a supermarket scanner recognizes different brands of cereal.

DNA barcoding has already empowered single-cell analysis, including for nerve cells in the brain. Now, in a new NIH-supported study, DNA barcoding helps in the development of a new method that could greatly streamline an increasingly complex and labor-intensive process: screening for drugs to combat cancer.


Single-Cell Analysis: Powerful Drops in the Bucket

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If you’re curious what innovations are coming out of the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative, take a look at this video shot via a microscope. What at first glance looks like water dripping through pipes is actually a cool new technology for swiftly and efficiently analyzing the gene activity of thousands of individual cells. You might have to watch this video several times and use the pause button to catch all of the steps, but it provides a quick overview of how the Drop-seq microfluidic device works.

First, a nanoliter-sized droplet of lysis buffer containing a bead with a barcoded sequencing primer on its surface slides downward through the straight channel at the top of the screen. At the same time, fluid containing individual cells flows through the curved channels on either side of the bead-bearing channel—you can catch a fleeting glimpse of a tiny cell in the left-hand channel about 5 seconds into the video. The two streams (barcoded-bead primers and cells) feed into a single channel where they mix, pass through an oil flow, and get pinched off into oily drops. Most are empty, but some contain a bead or a cell—and a few contain both. At the point where the channel takes a hard left, these drops travel over a series of bumps that cause the cell to rupture and release its messenger RNA—an indicator of what genes are active in the cell. The mRNAs are captured by the primer on the bead from which, after the drops are broken, they can be transcribed, amplified, and sequenced to produce STAMPS (single-cell transcriptomes attached to microparticles). Because each bead contains its own unique barcode that enables swift identification of the transcriptomes of individual cells, this process can be done simultaneously on thousands of cells in a single reaction.


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