Just in time for SCP2019, we have a new preprint led by Harrison Specht released on bioRxiv titled ‘High-throughput single-cell proteomics reveals the emergence of macrophage heterogeneity’. In this manuscript we describe the various sample processing and computational advances that have come together to form our next-generation method for single-cell proteomics: SCoPE2. We were able to apply this method to the study of monocyte cells differentiating to macrophages. We showed that the macrophages had increased heterogeneity over the monocytes, and that this heterogeneity included reciprocal expression of genes known to be unregulated in M1 or M2-polarised macrophages. The paper can be read here.Read More →

SCP2018 Attendees

Its not long until SCP2019 begins at Northeastern University in Boston, featuring talks from a range of international speakers on single-cell and low abundance proteomics, and single-cell studies. As part of SCP2019, Ed, along with others from the Slavov lab will be delivering a workshop on how to perform the labs SCoPE-MS method for multiplexed, quantitative single cell proteomics. Eds workshop will cover ‘Sample preparation for single-cell MS analysis’, alongside other workshop sessions on experimental design, optimising system performance, and data analysis. The full program can be found here.Read More →

A new preprint in collaboration with the Sweeney lab is now out: Ifit1 regulates norovirus infection and enhances the interferon response in murine macrophage-like cells. In this work we show that murine norovirus mRNA with the viral VPg protein attached to its 5′ is resistant to the translation inhibition effects of Ifit1 and is not bound, whereas in vitro transcribed norovirus mRNA bearing a 5′ Cap is inhibited. However we showed Ifit1 knockout lines show enhanced norovirus replication, and observe these lines show diminished interferon signaling upon stimulation of cytoplasmic RNA sensing. The preprint is available here.Read More →

New preprint from Ed’s previous postdoc, from lead authors Myra Hosmillo and Jia Lu on how noroviruses use the cellular factor G3BP for viral translation is now on bioRxiv. In this work we used multiple proteomic and CRISPR-based approaches to identify cellular factors critical for norovirus replication. G3BP1 was identified as such, and subsequent cellular and in vitro assays confirmed a role in viral protein synthesis. The preprint can be read here.Read More →

Together with five other eLife ambassadors, Ed published a perspective on the value of preprinting for early career researchers in PLoS Biology. All six authors are ECR’s themselves, based across the USA, Argentina, Australia and Portugal. We describe some of the positive benefits of preprinting for ECRs and science in general, and discuss some of the perceived concerns ECRs have on preprints. The article can be found here, and was itself a preprint, available on PeerJ Preprints.Read More →

Together with Marko Jovanovic and Nikolai Slavov, Ed was invited to contribute to Trends in Biochemical Sciences new ‘Technology of the Month’ format, now  published in TiBS. This article provides an outline of some of the mass spectrometry-based and sequencing approaches to study ribosome specialization and is a companion to our earlier ‘Ribosome Stoichiometry: From Form to Function’ article. You can read the new article here.Read More →

Ed’s last first-author manuscript from his time in the Goodfellow lab: ‘Polyprotein processing and intermolecular interactions within the viral replication complex spatially and temporally control norovirus protease activity’,  is now accepted in the Journal of Biological Chemistry. In it, we looked at the roles of different forms of the norovirus protease, how they accumulate throughout infection, and how these forms vary in their localization, interactions and ability to cleave different substrates. Link    Read More →

Ed has a new first author review – ‘Ribosome heterogeneity: from form to function‘ published with co-authors Marko Jovanovic (Columbia U.) and Nikolai Slavov in Trends in Biochemical Sciences. In it we review the evidence in favor of the existence of functionally specialized ribosomes, and discuss the approaches and tests that will allow confirmation of the specialized ribosome hypothesis. The review was previously made available as a preprint.Read More →

Anna has two new parainfluenza virus type 3 papers now out. In the first paper she looked at the sequences of parainfluenza virus type 3 strains circulating in the UK. In her second, she used this data to develop a new diagnostic PCR and track a previously undetected PIV3 outbreak that occurred on a pediatric oncology ward. The papers can be found on Wellcome Open Research. Paper 1: Sequencing of PIV3 strains circulating in the UK Paper 2: Unrecognised outbreak of PIV3 on a pediatric oncology wardRead More →