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Allergy, Vitamins

Hans Selye: Ancestor of the allergy vitamin hypothesis

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I spent a lot of time in libraries verifying bibliographic lists as I expected that somebody else could have had the idea of allergy induction by vitamin D before — in particular when being closer to the introduction of vitamin D supplements. Fortunately Science Magazine now offers a fulltext search of their archives (what is currently not possible with old Nature volumes). I could locate about 70% of the computer hits when searching manually the Science index for vitamin and hayfever. The loss of about one third could be mainly attributed to the fact that extra supplement pages have only occasionally preserved in the libraries that I have visited for this project (Marburg, Berlin, München STABI + TUM, Garching). Text recognition is also limited, so my results may be preliminary.

What I found this afternoon in the library at TUM Garching Continue reading Hans Selye: Ancestor of the allergy vitamin hypothesis →

 

CC-BY-NC Science Surf accessed 15.01.2026
Genetics, Software

Annotation of regulatory sequences is largely insufficient

Of a proven set of regulatory regions in zebrafish, computer programs find only between 29% and 61% of the true motifs. This does not come very much unexpected given the vast array of data shown by the Encode project. It even relates to the most basic question: What is a gene?

The more expert scientists become in molecular genetics, the less easy it is to be sure about what, if anything, a gene actually is.

iwith at least 5772 21U-RNAs? So – if I am sitting on the other side of the table when you are being examined don’t talk about junk DNA anymore, yea, yea.

 

CC-BY-NC Science Surf accessed 15.01.2026
Genetics, Software

Anonymizing genetic data

I have currently a paper under submission at the EJHG that covers ethical issues of genetic testing. One of the key messages is that genetic data are not anonymous if having simply stripped of names.
A story in a completely different field confirms my fears. According to a NYT article

Last October, Netflix, the online movie rental service, announced that it would award $1 million to the first person or team who can devise a system that is 10 percent more accurate than the company’s current system for recommending movies that customers would like.

but things turned worse by an article of Narayanan und Shmatikov Continue reading Anonymizing genetic data →

 

CC-BY-NC Science Surf accessed 15.01.2026
Genetics, Software

Genome explained

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You may want to read the full story at Public Rambling (fiction), the NYT article of Amy Harmon (fact) or the “Peepshow” article of Marco Evers (fact) and come back here afterwards.
The recent advances in genome sequencing (and typing) has left us with an enormous amount of data. Although technology has been available for a couple of years knowledge exploded only recently, where people now may decide to participate in a genome study or even have their genes tested on their own costs at DeCodeMe, 23andme, Navigenics or other personal genome service provider.
The main question is, what do these data really mean for us? Should we start an Open Source Project Genome Explained to collect the necessary annotation rules and provide a platform to apply these rules to local data? The data mode may be quite simple: Continue reading Genome explained →

 

CC-BY-NC Science Surf accessed 15.01.2026
Philosophy

The only point of contact

Steven Pinker complains in this week Nature about the recent review of his book “Stuff of Thought“.

The fact that I (like most cognitive psychologists) have not signed up to these views is the only point of contact between my book and her review.

While Pinker could have got at least his opinion through, my comments on ORMDL3 remained stuck although I also claimed that the authors of this paper

free-associate to her own beliefs.

Yea, yea.

 

CC-BY-NC Science Surf accessed 15.01.2026
Allergy

Endocrine disruptors

This is a topic occasionally popping up (frequently after some spectacular press article) but there doesn´t seem so much systematic research. Only recently I came across an article on plastic additives and surfactants (alkylphenols) that can suppress Th1 development – so is plastic the “Western life style factor”? The only other study that I have heard before is about benzophenone, octylphenol, and tributyltin chloride (TBT).

 

CC-BY-NC Science Surf accessed 15.01.2026
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 15.01.2026
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 15.01.2026