A Cluster or an Ome?

August 17, 2012

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A gaggle of geese. A parliament of owls. But what do you call a group of systems biologists, asks Duncan Hall at O'Really. And he got some responses from what he dubs the "twitterome." Early votes are in for jamboree, cluster, or network, among others. Though Nathan Pearson tweets, "An ome. Duh."

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Young Investigator Profile

Sandra Pankow

Research Associate
Scripps Research Institute

The Cystic Fibrosis Interactome

Sandra Pankow is currently a research associate in John Yates' lab at Scripps Research Institute, studying protein-protein interactions involved in cystic fibrosis.

"I'm interested in trying to understand genetic diseases from a systems biology point of view," she says. "I've found that proteomics is the ideal tool for this because it gives the researcher the possibility to investigate thousands of proteins at the same time rather than just having to guess which one or two you should look at."

During her time in the Yates lab, Pankow has worked on developing a new technique for large-scale profiling of protein-protein interactions called co-purifying protein identification technology, or CoPIT. The method uses co-purification of proteins followed by mass spectrometry analysis and bioinformatic processing to identify not just primary protein-protein interactions, but second-degree and third-degree interactors as well.

With it, Pankow says, "we've reached about 30-fold to 100-fold higher sensitivity than previous methods. We're now able to profile an interactome to near completeness."
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High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates
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The University of Würzburg's Cynthia Sharma and colleagues undertook a transcriptomics-based analysis of the gastroenteritis-causing bacterial species Campylobacter jejuni. The team used its so-called differential RNA sequencing strategy to sequence and compare the transcriptomes of four C. jejuni isolates (three from humans and one from a chicken), applying a new method to automatically annotate transcription start sites in each. "Overall," they write, "our study provides new insights into strain-specific transcriptome organization and [small RNAs], and reveals genes that could modulate phenotypic variation among strains despite high conservation at the DNA level."

Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts
Hacquard, Kracher, et al. Proceedings of the National Academy of Sciences

The barley powdery mildew (Blumeria graminis f. sp. hordei) pathogen genome is comprised of chunks of sequence that are particularly rich or replete in polymorphisms, according to a study by researchers from the Max Planck Institute for Plant Breeding Research. The team sequenced the genomes of two Bgh isolates from Europe, comparing each to the barley powdery mildew reference genome. The newly sequenced isolates each contained distinct combinations of sequence blocks with high or low SNP concentrations — isolate-specific mosaic genomes that point to "exceptionally large standing genetic variation in the Bgh population," study authors say. Meanwhile, their transcriptome sequencing experiments offered a look at genes used by Bgh during attempted infiltration of barley or immunocompromised Arabidopsis.
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An international team has sequenced the genome of the carnivorous bladderwort plant, Utricularia gibba. Their findings suggest that the carnivorous plant has ditched virtually all its non-coding DNA, retaining a set of sequences that's almost exclusively genic. "What that says is that you can have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without the ['junk' DNA]," said co-corresponding author Victor Albert.
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Sponsor: EMD Millipore

GenomeWeb and EMD Millipore invite you to view an archived webinar discussing new approaches to detect RNA at the single-cell level as well as new probes for the direct quantification of circulating miRNAs. In this free online seminar, recorded April 25, 2013, our expert panel shares protocols for improved RNA and miRNA detection.

On-demand recording available here.

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