Allergy

Personal Genome Explorer

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Laborjournal 4/2008 reports a new software tool for DNA addicted people: the Personal Genome Explorer which is based on SNP annotation by SNPedia. So, what I tried to institutionalize on a sound level as “Genome Explained” possibly within the framework of HGVS is now being done by a street initiative fueled by early adopters like Cross, Arlington, Halamka and Smolenyak. It looks very much like an unholy alliance of profit interests and technical curiosity than good science and responsible counseling, yea, yea.
Addendum: If you believe in support vector machines, you can even let your laptop screen the medical literature for genetic associations with GAPscreener. <irony> No more lengthy training in genetics, statistics, epidemiology and bioinformatics, no more years of collecting all relevant papers & abstracts, just let your laptop score your DNA variants </irony>

 

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Genetics, Joke, Software

Our lives are unrepeatable experiments lacking a control

a prosaic quotation from the recent Nature correspondence section that highlights why genetics has been leading us into nowhere.

Our lives are unrepeatble experiments lacking a control. Myriad external factors interact with genetic and epigenetic factors and with chance to determine whether we are well or ill, smart or dull, successes or failures.

Yea, yea.

 

CC-BY-NC Science Surf accessed 30.11.2025
Allergy

Herrmann von Helmholtz on the cure of hayfever

It was difficult to find but I knew it should be there: a letter of Herrmann von Helmholtz about his private attempt to cure hay fever. Published in the increasingly important Nature magazine on May 14, 1874 von Helmholtz describes the vibrio like bodies in his own nasal fluid and the successful local treatment with quinine.

Unfortunately there is a consecutive letter that did not confirm this effect. I also do not know how this treatment would have worked. Fiction, placebo or true antiparasitic side-effect? We even know of quinine induced allergy, making even reverse causation possible.

G. Kanny, J. Flabbée, M. Morisset M, D. Moneret Vautrin. Allergy to quinine and tonic water. Eur J Intern Med 14 (2003), p. 395-396.
R. Cundall, Idiosyncrasy to quinine in bitter lemon. Br Med J 20 (1964), p. 1638.

 

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Genetics

How we are reshuffling our genome

is an exciting question that will have a large disease relevance. I think this is not so much about cytogenetic abnormalities but the general understanding which genetic modules are recombining, e.g. are compatible in terms of function, and which need to be tight together. Continue reading How we are reshuffling our genome →

 

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Philosophy

We are the model organisms

Genomeweb today reports Sidney Brenner (Nobel Prize winner 2002 and pioneer in the use of Caenorhabditis elegans as a model organism) speaking on a conference. These days he’s pushing a new model organism: humans.

“We don’t have to look for a model organism anymore,” Brenner said. “Because we are the model organisms.”

 

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Genetics, Philosophy

To be honest

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Bruce Alberts, the new editor-in-chief of Science magazine, has in his March, 21 editorial a nice comment that I would like to highlight here

Scientists share a common way of reaching conclusions that is based not only on the evidence and logic, but also requires honesty, creativity, and openess to new ideas.

Struggling in an area where no (or only seldom) conclusions ar being reached, I agree Continue reading To be honest →

 

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Allergy

Create your own Garmin vector map

It turned out to be a tricky job to move from pixel maps to a Garmin vector map; I first thought that is impossible but here is a way to do that:
1. Find the area of interest with Geocoder
2. Get digital elevation data from de Ferranti
3. Import them in 3DEM, export as GEO-TIFF, import in DEM2TOPO and export in Polish map format.
4. Finalize with Mapedit. Mapedit will read Polish format, import your already available GPS tracks or positions saved in Oziexplorer. The best Mapedit feature is certainly the Google Earth overlay. Nevertheless map editing remains a time consuming enterprise but may be the only way if there is no other map available. I wish there would be more of these maps like for Iceland or Garda Lessinia.

 

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Allergy, Vitamins

A factor in hay prevents vitamin D action

As always, a longer literature search prevents from new discoveries… Here comes a nice piece from 1952 on the antagonistic effect of LPS on vitamin D (Is that really LPS or did I interpret it wrong?). Although not included in my recent review on vitamin D and allergy – I attributed the effect to Lyakh et al. – here is the first description of this effect. Continue reading A factor in hay prevents vitamin D action →

 

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Allergy, Vitamins

Allergy starts only after birth

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Although there are numerous reports and even whole schools of thought building on a prenatal origin of allergy, a new study now clearly states that sensitization does not develop in utero. IgE traditionally measured in cord blood IgE is a contamination of maternal IgE. The authors show that there is a correlation with IgA and the “spurious specific IgE” at birth “vanishes” during the following 6 months. If you ever had a cord in hand, you will understand how easily contamination occurs.

Addendum 12/10/2008

The “prenatal origin” party doesn’t give up basically with the arguments:

  • no Ig A found that would be indicative of contamination BUT unfortunately their Ig A threshold of 32 ug/mL is not really appropriate
  • more than half of their cord blood samples have IgE negative mothers BUT unfortunately they don’t show the unclassified IgE values (is that’s just an artifact of a normal test variation?)
  • some of their cord blood samples have higher IgE levels than the mothers BUT again the same argument of an arbitrary classification applies
  • most single IgE results are not concordant between mother but they admit concordant results at least for food allergens. This may indeed been taken as an argument against simple cord blood contamination of ALL samples. As the accompanying editorial points out an in vivo translocation of immune complexes of IgG:allergen+IgE of a food allergens (that are nearly always present in contrast to some seasonal allergens) may be possible
  • the discussion ignores more or less the fact that there is definitely NO concordance with the father (as shown in table I) so leakage or contamination is likely

The authors explain the maternal/fetal association “by maternal inheritance of atopic IgE responsiveness on chromosome 11q and other gene loci” BUT unfortunately there is neither atopic IgE responsiveness on chromosome 11q nor is there any evidence of imprinting. So – according to our best evidence allergy starts only after birth. To convince me it would not need 922 neonates but 1 B cell of proven fetal origin that makes IgE – making the whole story at least a good example how insufficient methods produce doubtful conclusions, yea, yea.

 

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Joke

If pigs could fly

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is a book that I am currently reading. There is also a brief German/English account how this sentence came into life. What did you expect when reading the title??

Something like “winners don’t punish”? A smart letter in this week’s Nature with the 3 options of Cooperation(C) – Defection (D) and Punishment (P)?

"nice people"
player 1: C C C C
player 2: C C C C top payoff!
"punish and perish"
player 1: C P P P P
player 2: C D D D D extremely bad!
"turning the other cheek"
player 1: C C C C C
player 2: D D C C C payoff still positive!

we should have known this earlier…

Addendum

link to an earlier post here on “tit for tat”
link to “vengeance is ours” at Edge
link to “sermon on the mount”
link to “Prisoner’s dilemma“

 

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