RTC meeting 13 dec 2017

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Dear all, we would like to invite you all for our next RTC Bioinformatics meeting. On Dec 13th we will give you a short update on RTCB affairs, followed by a seminar by Berend Snel, professor at the Utrecht Bioinformatics Centre.
We will finish the meeting with an informal gathering and drinks.

The program can be found below. We hope you would like to attend this event and take the chance to meet your colleagues from other departments who are also working/interested in computational science and bioinformatics. We are still in the process of creating a nice mailing list for these events, so don’t hesitate to anyone else we might have missed with this email.

Hope to see many of you,
the RTCB-team

Program RTC meeting Dec 13

14:30 Welcome and RTC update

14:40 Seminar Berend Snel “How to deal with evolutionary analysis of large gene families in eukaryotes” (see abstract below)

15:10 Discussion

15:20 Drinks!

Location: Figdor Lecture Theatre, NCMLS 8th Floor


“How to deal with the evolutionary analysis of large gene families in eukaryotes?”

Kinase are hallmark signaling proteins in life. Comparative genomics is needed for many open questions concerning kinases, such as how to assign kinases in newly sequenced eukaryotic genomes to an orthologous group or how to place the ~60 unclassified human kinases into one of the seven main kinase families. However many steps in conventional phylogenetics are pivotally hampered by the massive size of the kinase family across all eukaryotes.

We here present a preliminary analysis of the pan-eukaryotic kinome that relies on a recently proposed computational approach that was developed to solve similar questions for the RAB small GTPases [1].
Although our first results suggest that the resolution for kinases is less clear than for RABs, most human kinases can now be placed next to or inside one of the kinase main families. Subsequently we project the resulting kinase orthologous groups onto a reference set of eukaryotic species. This projection reveals the fate of the ancestral eukaryotic kinase diversity across extant lineages. Some lineages such as the important model organisms Saccharomyces cerevisiae and Arabidopsis thaliana harbor relatively few ancestral kinase orthologous groups. In contrast, animals but also ciliates and especially the excavate Naegleria gruberi are most similar to LECA with respect to their kinases.

1. Sculpting the endomembrane system in deep time: high resolution phylogenetics of Rab GTPases Marek Elias, Andrew Brighouse, Carme Gabernet-Castello, Mark C. Field, Joel B. Dacks J Cell Sci 2012 125: 2500-2508; doi: 10.1242/jcs.101378

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