Allergy, Genetics

Best allergy paper 2007

The end of the year 2007 is approaching very fast. I can already vote for the best allergy paper in 2007 – it is a paper from Vienna by Victoria Leb about the molecular and functional analysis of the Ambrosia antigen T cell receptor. They have been able to isolate and transfer alpha (TRAV17-TRAJ45) and beta chain (TRBV18,TRBD1 and TRBJ2-7) TCR chains into Jurkat cells and even other human blood lymphocytes with convicing evidence that the infected cells were Ambrosia Art V1 reactive.
This opens brand new perspectives for developing a truely allergic TCR transgenic mouse that can be easily challenged and desensitized. It may even allow immediate testing of a variety of substance (and constructs) to ultimately cure allergy. My favorite is to feed DCs with antigen coupled to a T cell suicide program on succesfull antigen presentation.

 

CC-BY-NC Science Surf accessed 30.11.2025
Genetics

How to get closer to the target

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Attending last week another Illumina sequencer course, I still have the question how to enrich the target sequence. A colleague calling me this morning (thanks TB!) had a pointer to a new nature methods editorial covering three different methods- a 100-mer capture probe for each exon sized segment with the need of extremely deep resequencing and two other methods using direct hybridization of segments onto commercially oligo arrays. Aren´t there any other protocols?

 

CC-BY-NC Science Surf accessed 30.11.2025
Philosophy

We need INDEPENDENT replication

We always need replication in scientific studies. I therefore can´t understand why there is now such a fuzz in Nature as they

… took the unusual step of soliciting an independent verification of the paper during the process of peer review. This is the first time that Nature has obtained second-party replication ahead of publication.

this could have saved thousands of dollars if it would have been also applied to other studies before, yea, yea.

 

CC-BY-NC Science Surf accessed 30.11.2025
Genetics, Philosophy

Barbara you are my nemesis

The former nature genetics editor has been recently here in Munich giving a talk on Open Access. Chatting after her talk, she told us that on another occasion a guy was yelling at her “you are my nemesis” because she once declined to publish his paper. We laughed but there is some serious background – journals editors often decide on careers of young people.
From my recent experience Continue reading Barbara you are my nemesis →

 

CC-BY-NC Science Surf accessed 30.11.2025
Genetics

Monorail

X chromosomal inactivation is difficult enough to understand – there are now some more data on autosomal monoallelic expression (editorial & paper). Up to 10% of 4,000 genes in clonal cell lines were found to be monoallelic expressed (and up to 20% in some B cell clones). Only odorant and T cell receptors are selectively expressed while all other genes are thought to be randomly silenced.
I wonder how any transmission disequilibrium test makes sense if a variant is only transmitted to a silent chromosome? Possibly there are also epigenetic feedback loops where proteins can remodel chromatin and induce epigenetic marks ultimately silencing a chromosomal region. In any case, a fundamental paper, yea, yea!

 

CC-BY-NC Science Surf accessed 30.11.2025
Genetics

My second paper

isn´t my second paper as this NEJM letter was sent out without me. Authorship rules are less well defined than generally assumed. Why counting impact points from publication lists if these do not reflect your previous work?

 

CC-BY-NC Science Surf accessed 30.11.2025
Software

Personal digital right management

is a serious issue as personal data in the internet grow exponentially. I have just recently completed a paper on informed consent in medical studies but think now it will not go far enough. In accordance with recent proposals at the Internet Governance Forum of the United Nations we might need a system that allows a personal digital right management where a server runs a checksum or does a reverse lookup before transmitting personal data – otherwise data tranfer should be aborted. See more at the EU funded project PRIME – I fear that people will no more participate in our studies if we can´t guarantee them confidentiality.

 

CC-BY-NC Science Surf accessed 30.11.2025
Software

Move your PC

Did you ever move a windows system to another computer? Reinstalling Office and R libraries, ODBC data sources, paths, skins, shortcuts? All your emails and other data? It takes me 2 days … Fortunately there is some software that can help.
mover.png

 

CC-BY-NC Science Surf accessed 30.11.2025
Allergy, Genetics

Finally the ß2 receptor

The full crystal structure of the ß2 receptor is now clear after many attempts for its low natural abundance – with the extracellular domain still difficult to resolve (more on the relevance of the mutations depicted in Fig.1 in my recent Lancet editorial). Interesting: the effects of mutations on distant sites by breaking off van der Waals interactions like I135 that disrupt a ionic lock simply by a more loosely packed molecule.

 

CC-BY-NC Science Surf accessed 30.11.2025