A Fix for Expression Analyses

December 2012/January 2013

By Ben Butkus

Underlying many gene expression studies is the assumption that all cells produce similar levels of messenger RNA, a notion that may not hold true.

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Ben Butkus is senior editor of GenomeWeb's premium content and the editor of PCR Insider. He covers technologies and trends in PCR, qPCR, nucleic acid amplification, and sample prep. E-mail Ben Butkus or follow his GenomeWeb Twitter account at @PCRInsider.

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Advances in Single-Cell Genomics: Live Cell RNA and Circulating miRNA Detection

Sponsor: EMD Millipore

Data presented in this webinar illustrates the value of live cell analysis at the single-cell level to identify differences in expression levels across populations of cells. The cells remain intact for downstream analysis. Our experts also discuss the use of SmartFlare RNA detection probes for the direct quantification of circulating miRNAs with rapid processing of blood plasma/serum, which is done without the use of enzymes. Using circulating miRNAs with established roles in cancer and quality control, we can accurately detect these miRNAs in plasma using a microplate fluorometer within an hour after plasma preparation.

On-demand recording is available here.

Optimization of NGS Library Preparation: Low Inputs and Fast, Streamlined Workflows

Sponsor: New England Biolabs

Library preparation methods continue to be challenged by the requirement for faster and more efficient protocols, using lower input amounts. In this online seminar, recorded Feb. 7, 2013, experts discuss new approaches to tackle these challenges, particularly for bacterial and exome sequencing.

Available here.
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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Papers of Note

Variation and genetic control of protein abundance in humans
Wu, Candille, et al. Nature

Stanford University scientists publish a study demonstrating high-throughput human proteome quantification, and its combination with DNA variation and transcriptome information to add a "new dimension" to the characterization of gene expression regulation. The investigators used isobaric tag-based quantitative mass spectrometry to determine relative protein levels of 5,953 genes in lymphoblastoid cell lines from 95 diverse individuals genotyped in the HapMap Project. They found that protein levels are heritable molecular phenotypes and have considerable variation between individuals, populations, and sexes. Additionally, the investigators found protein quantitative trait loci, including variants not detected by previous transcriptome studies.

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies
Supple, Hines, et al. Genome Research

A group from the US, UK, and Colombia describes findings from a comparative genomics-based study on a form of adaptive variation in butterflies known as mimetic wing coloring. By sequencing co-mimicking Heliconius butterflies from two species and a handful of hybrid zones, researchers narrowed in on a color pattern-associated site near a gene already implicated in red color variation — an apparent regulatory region suspected of evolving by convergence in the two species distantly related species. "Using a combination of next-generation sequencing analyses, we have refined our understanding of the genetic architecture of wing pattern variation in Heliconius," they write, "and gained important insights into the evolution of novel adaptive phenotypes in natural populations."
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Gina Costa is now senior director of genomic applications at Illumina. She joins Illumina from Life Technologies, where she was senior director of genetic analysis, working on development of the Ion Torrent and SOLiD sequencing technologies. She has also held positions at Agencourt Bioscience and Roche's 454 Life Sciences.

Bioinformatics firm Golden Helix has hired Andreas Scherer to be its new president and CEO. Scherer has managed large global software services businesses, and he started his executive career at AOL/Netscape. He will replace Former CEO Christophe Lambert, who will take on the new role of company chairman.
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Jun 8-11 / Paris
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Jun 9-13 / Minneapolis
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Science
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.
Business
Agilent Technologies announced a restructuring program expected to reduce its headcount by about 450 employees and save the company $50 million annually in operating expenses. CEO Bill Sullivan said that the focus of the restructuring will be on Agilent's Electronic Measurement Group and that the company will explore opportunities "to streamline our organization around the world." The firm also announced that its Q2 revenues were flat year over year.
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The US Department of Energy's Joint Genome Institute has funded six new initiatives to develop technologies that will help JGI and its users conduct their research efforts into microbiology, metagenomics, and plant genomics. The projects will be supported under the Emerging Technologies Opportunity Program with a total of around $3.5 million over the next two years. Among the researchers receiving funding are Stephen Quake and Jay Shendure.
GenomeWebinars
GenomeWebinar: Advances in Single-Cell Genomics: Live Cell RNA and Circulating miRNA Detection

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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