The EMBL Postdoc Retreat 2010 took place in Lubeck. Here are some notes and keywords for some of the seminars:
Timothy Sauders, EMBL-Heidelberg
Dissecting a noisy subcellular gradient in fission yeast
EIPOD Timothy Saunders, collaborators Martin Howard (JIC), Eileen Furlong. Image analysis project. POM1. Agreggates. FRAP.
Kevin Knoops, EMBL-Grenoble
Utrastructural analysis of the nidovirus replication complex
reveals an unique reticulovesicular network of modified
New postdoc, presented previous project at U.Leiden (NL). EM tomography techniques. 300nM coronavirus. Vesicles connected to the rough ER.
Ciaran Carolan, EMBL-Hamburg
Combination of advanced shape description methodologies for the
identification of ligands and for drug design
Victor Lamzin, Hamburg. Gerrit Langer, Janet Thornton, Abdullarh Kahraman, Roman Laskowski. Institutions: EBI, St.Jude's Hospital, Malaria DB.
Lead generation -- bottleneck in drug design
Protein pocket -> shape -> shape features -> feature match
Surfnet program. Math descriptors, like Zernike moments, 3rd order moments. Matrix-based shape measures. Electrostatics. ATOLL database.
Daniel Fernández, EMBL-Grenoble
Structural analysis of stress tolerance proteins in plants
Jose Antonio Marquez Group - Grenoble, IBMCP - Valencia, Regina Antoni, Pedro Rodriguez
C2 Domain proteins. ABA receptor: PYR, PYL, RCARs. Humidity control device
Virginia van Delinder, EMBL-Heidelberg
Single-molecule TIRF without immobilization
FRET distance between molecules. Microfluidics. Single-molecule FRET is tough. CFP-YFP pairs: cyan+yellow = green
PDMS device (channels). Droplet generation: 8 micron deep channels. Gave up on droplets, continuous channels.
Joseph Barry, EMBL-Heidelberg
Mathematical modeling of protein aging and turnover in live
EIPOD, Huber Group Heidelberg, Knop Group, Andreas Kaufmann
Snapshot Analysis Protein Stability SAPS. Protein-mCherry-sfGFP (43min, 5min)
Colour 1 -> snapshots -> colour 2
Genome-wide library of yeast strains. One protein tagged each time. MCD1 protein-cell cycle.
R package - deSolve
Jan Medenbach, EMBL-Heidelberg
A novel and general concept for the regulation of translation by
protein-controlled upstream open reading frames (pc-uORFs)
M.Hentze lab Heidelberg
Chris Williams, EMBL-Hamburg
Insights into the regulation of an E2 enzyme by a non-
canonical binding partner
Structural Biology Unit, Matthias Wilmanns, Hamburg
Pex22 novel fold. No homologues in PDB. Y172A mutation blocks PEX4P-PEX22 binding
Pierre Khoueiry, EMBL-Heidelberg
Defining functionality and essentiality in the Drosophila
mesoderm network using inter- and intra-species comparisons
Eileen Furlong. Doing both wetlab and bioinformatics analysis
8008 CRMs mesoderm defined with about ~5 per gene -> need to purify this list
Mesoderm CRMs should be evolutionarily conserved
D.virilis ~50MYA from D.melanogaster
Compare network mel vs vir -> missing genes / new genes
Data from indels -- Jan Korbel lab
SVs/CNVs -> create regulatory changes
When we find an indel in a CRM -> might be affected by it -> redundancy -> property of CRMs
Hypothesis: developmental CRM deletions are lethal, they are supposed to avoid SVs
If one deleted, but others next to it -> still functional, redundancy in action, or not functional anymore
Andres Palencia, EMBL-Grenoble
Role of aminoacyl-tRNA synthetases in protein synthesis.
Case study: structural dynamics of the aminoacylation and proof-
reading cycle of leucyl-tRNA synthetase
Bacterial LeuRS as a model
Sebastian Glatt, EMBL-Heidelberg
"Ring"ulation of tRNA modification
Elp 4-5-6 complex. Elp 1-2-3
Rho-ssRNA, bind ssRNA, same structure as elongator. Asymmetric central cavity using heterohexameric assembly.
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