castanyes blaves

Random ramblings about some random stuff, and things; but more stuff than things -- all in a mesmerizing and kaleidoscopic soapbox-like flow of words.



EMBL Postdoc retreat 2010 -- some notes

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
endoplasmic reticulum

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

Lemke Lab.

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
yeast cells

EIPOD, Huber Group Heidelberg, Knop Group, Andreas Kaufmann

Computational physics

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

msl-2. SXL

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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