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Archive - Aug 29, 2017


DroNc-Seq, A Technology That Merges Single-Nucleus RNA Sequencing with Microfluidics, Brings Massively Parallel Measurement to Gene Expression Studies in Complex Tissues

Last year, Broad Institute researchers described a single-nucleus RNA sequencing method called sNuc-Seq. This system enabled researchers to study the gene expression profiles of difficult-to-isolate cell types, as well as cells from archived tissues. Now, a Broad-led team has overcome a key stumbling block to sNuc-Seq's widespread use: i.e., scale. In a paper published online on August 28, 2017 in Nature Methods, postdoctoral fellows Dr. Naomi Habib, Dr. Inbal Avraham-Davidi, and Dr. Anindita Basu; core institute members Dr. Feng Zhang and Dr. Aviv Regev; and their colleagues reveal DroNc-Seq, a single-cell expression profiling technique that merges sNuc-Seq with microfluidics, allowing massively parallel measurement of gene expression in structurally-complicated tissues. The article is titled “Massively Parallel Single-Nucleus RNA-Seq with DroNc-Seq.” Researchers struggled in the past to study expression in neurons and other cells from complex tissues, like the brain, at the single-cell level. This was because the procedures for isolating the cells affected their RNA content and did not always accurately capture the true proportions of the cell types present in a sample. Moreover, the procedures did not work for frozen archived tissues. sNuc-Seq bypassed those problems by using individual nuclei extracted from cells as a starting point instead. sNuc-Seq, however, is a low-throughput technology, using 96- or 384-well plates to collect and run samples. To scale the method up to the level needed in order to efficiently study thousands of nuclei at a time, the team turned to microfluidics. Their inspiration was: Drop-Seq, a single-cell RNA-seq (scRNAseq) technique that encapsulates single cells together with DNA barcoded-beads in microdroplets to greatly accelerate expression-profiling experiments and reduce cost.

New NAS Member from Hawaii Reveals How Animals Select Good Microbes, Reject Harmful Ones

Margaret McFall-Ngai, Professor and Director of the Pacific Biosciences Research Center (PBRC), School of Ocean and Earth Science and Technology, at the University of Hawai'i (UH) at Mānoa, is the only woman at UH who is a member of the National Academy of Sciences (NAS). In her inaugural article published this week (August 28 – Seoptember 1) in PNAS commemorating her induction into one of the country's most distinguished scientific groups, she and a team of researchers reveal a newly discovered mechanism by which organisms select beneficial microbes and reject harmful ones. The internal microbial communities, or consortia, of mammals, such as humans, are complex in that they require many bacterial types for healthy function. Tissues in the respiratory system, the Fallopian tubes, and the Eustachian tubes are lined with cilia--microscopic hair-like structures that extend out from the surface of many animal cells. A central role attributed to these ciliated tissues is to effectively clear out toxic molecules and undesirable microbes; in work performed largely by Dr. Janna Nawroth (now at Emulate, Inc., Boston) and co-led by Dr. McFall-Ngai and Dr. Eva Kanso, a mathematical modeler at the University of Southern California (USC), these ciliated tissues are shown to also selectively recruit beneficial microbes, called symbionts. "A few years ago, when the biomedical community discovered that all of these surfaces of mammals have a rich co-evolved microbial consortium, a microbiome, that promotes the health of those systems, the question became: how do they do it--that is, by what mechanisms do they select the good microbes and reject the harmful ones?" explained Dr. McFall-Ngai. The ciliated tissues of most animals are inaccessible to observation and study.