Category Archives: Allergy

Allergy GWAS hits in VDR binding sites

It seems that I missed an interesting 2017 paper that looked for disease-associated SNPs in canonical DR3 motifs. Only 7 out of 211 traits showed significant hits, one of these was self-reported allergy. When annotating these SNPs, there are only two genes: LINC00299 and TLR1

hg38 position
rs10174949 2:8302018 LINC00299
rs10178845 2:8303773 LINC00299
rs5743566 4:38804221 TLR1
rs2101521 4:38809830 TLR1
rs5743565 4:38804262 TLR1
rs45588337 4:38805607 TLR1
rs55830619 4:38805643 TLR1

So are TLR1 & LINC00299 variant carriers more susceptible to vitamin D induced allergy?

LINC00299 (Long Intergenic Non-Protein Coding RNA 299) is a RNA Gene of largely unknown function, associated so far with allergy only on a genetic level in Framingham,  href=”https://pubmed.ncbi.nlm.nih.gov/23817569/”>23andme and other studies. We don’t know so much here, the function of the long non coding RNAs

depends on subcellular localization. Depending on their niche, they specifically interact with DNA, RNA, and proteins and modify chromatin function, regulate transcription at various stages, forms nuclear condensation bodies and nucleolar organization. lncRNAs may also change the stability and translation of cytoplasmic mRNAs and hamper signaling pathways. Thus, lncRNAs affect the physio-pathological states and lead to the development of various disorders, immune responses, and cancer.

The TLR1 genetic association is found by many genetic studies, while the clinical association is probably more by an infectious origin. TLR1 is a pattern recognition receptor with a specificity for gram-positive bacteria and also included in my forthcoming exome paper as a protective factor for asthma/allergy.  And we are also close to  my earlier review of vitamin D, the microbiome and allergy…

Does any co-infection response during first vitamin D exposure influence allergic sensitisation? There are indeed some hints of an short-lived effect of lung group 2 innate lymphoid cells (ILC2s)

Laboratory mice cohoused for 2 weeks had impaired ILC2 responses and reduced lung eosinophilia to intranasal allergens, whereas these responses were restored in mice cohoused for ≥2 months. … These findings suggest that ILC2s respond dynamically to environmental cues and that microbial exposures do not control long-term desensitization of innate type 2 responses to allergens.

 

 

 

 

Rotten Baby Milk

I have criticized in the past the milk industry sponsored research that is now operating at a similar scale like research funded by cigarette industry [1]. And well, it seems that I am not alone here when reading a new CEA paper “Are paediatric allergy services promoting or harming public health?”

There were increasing and excessive sales of specialized formula designed for infants with milk allergy—either extensively hydrolysed or amino acid formula. These represented 7.6% of formula sold in 2019 … Although pediatric allergy services cannot be held solely to blame for whole population trends, there is evidence that the clinical guidance used in pediatric allergy clinics might promote or exacerbate these trends. Moreover, many allergy, gastroenterology and pediatric societies and professionals routinely flaunt public health guidance from the World Health Organization by continuing to accept funding from formula companies, despite World Health Assembly resolutions that such conflictive relationships should be avoided.

 

So many asthma papers under fire

As an avid PubPeer reader, I found a  new  entry  by Elisabeth Bik recently about Andreas Pahl of Heidelberg Pharma who has already one retracted and several more papers under scrutiny.

Unfortunately there are now also many asthma trash papers from paper mills. Another example was identified by @gcabanac, distributed by @deevybee and published at Pubpeer.

In total there are 386 asthma entries at PubPeer. What is  really happening in this field? When I started the field there was just one misconduct case – Ranjit Kumar Chandra. That’s an increase from 1 to 386…

What makes it even more complicated that there is no border anymore to predatory journals if also respected scientists drop their names at predatory journals.  Only recently I received an email addressed to one of my former technical assistants as “professor” inviting her to send a paper…

 

Eine Fußnote zu Fußnoten

https://twitter.com/hekabeohnename/status/1559795108400201728

Schön jedenfalls die vielen juristischen und historischen Einordnungen in diesem Twitter Thread. Es fehlt dabei nur Grafton

Die Fußnote, besonders die deutsche, wird oft für den Inbegriff langweiliger Wissenschaft, für einen Geheim-Code trockener akademischer Gelehrsamkeit gehalten. Doch das heißt, sie als Tummelplatz der Leidenschaften, als Schlachtfeld intellektueller Kämpfe zu verkennen. Anthony Grafton ist es unter Einsatz von zahlreichen Fußnoten gelungen, neues Licht auf ihr Schattendasein zu werfen und ihre dramatische Bandbreite darzulegen.

und die FAZ Fußnote zu Grafton

Geisteswissenschaftler lächeln gerne über den vermeintlich naiven Objektivismus der Naturwissenschaftler. Dabei ist die Geschichte der Naturwissenschaft der geisteswissenschaftlichen Konkurrenz in der Kritik der wissenschaftlichen Denkformen weit voraus. Thomas Kuhn regte Chemiker und Physiker an, nach der Geschichte von Versuchsanordnungen und Beweisverfahren zu fragen.

Hygiene hypothesis hyperbole

Having written about the hygiene hypothesis, I missed a PNAS News feature even some years ago.

Again: The hygiene hypothesis was not born by David Strachan and well, there are more cracks of the hygiene hypothesis.

“The trouble is, as soon as you use the words ‘hygiene hypothesis,’ the word hygiene prejudges what the cause is,” says Bloomfield. To the public, “hygiene” is interpreted as personal cleanliness: washing hands, keeping food clean and fresh, sanitizing the home. However, because the hypothesis has been largely uncoupled from infections, the idea that we need to be less hygienic is wrong. Relaxing hygiene standards would not reverse the trend but only serve to increase the risks of infectious disease, says Bloomfield. The term “hygiene hypothesis” also fails to incorporate all of the other factors now linked to the increase in immunoregulatory diseases.

I expect that five years after mandating “super hygiene” during COVID-19 we can finally bury the hygiene hypothesis.

Not too bad: Citation Gecko

Just tried citationgecko.com on a topic that I have been working on for 2 decades. It will find rather quickly the source  paper, much faster than reading through all of it. Unfortunately reviews are rated to be more influential than original data as Citation Gecko picks articles with many references.

This error does not affect the results or conclusions

Please see also an earlier comment on image duplications: While results do not change if authors are repeating images of the same object without notice, this is not providing independent evidence and  therefore affecting the conclusions.

JACI – retractions overdue

JACI is the journal with the poorest experience  that I ever encountered as an author and  as a reviewer.  The editors never adequately responded to numerous errors in an earlier paper where I sent a long letter describing all details.

And it is a nightmare – even now with more than 100 corrigenda in this journal – as the editorial office  even modified correctly submitted images.  Yes, the JACI editor published also falsified data.

Only recently I also found another strange retraction note

The Publisher regrets that this article is an accidental duplication of an article that has already been published in J Allergy Clin Immunol

while the link of this retraction note goes to https://pubmed.ncbi.nlm.nih.gov/24892183 which is, however, a different paper.

It seem that the journal already lost the overview…

Parental allergy history at farms

A recent paper on the bias of farming studies did not discuss a  healthy worker although this is being a reasonable explanation.

So let’s have a more detailed look here at farm parents. It is an important question if parents are also “protected” (or if some affected parents just moved away).

AFAIK there are 7 studies dealing with this question. Continue reading Parental allergy history at farms

Every morning he begins his work with hope, and every evening he ends in despair

Bertrand Russell about Ludwig Wittgenstein…

His disposition is that of an artist, intuitive and moody. He says every morning he begins his work with hope, and every evening he ends in despair.

–more–

 

Allergy research – waste of time?

A waste of time – has been said about other fields but applies to allergy research also when reading the review request of “Allergy” today. I have to keep the content confidential but not the comment of  AI expert Jeremy Howard

It’s a problem in science in general. Scientists need to be published which means they need to work on things that their peers are extremely familiar with and can recognize an advance in that area. So, that means that they all need to work on the same thing. The thing they work on… there’s nothing to encourage them to work on things that are practically useful so you get just a whole lot of research which is minor advances and stuff that’s been very highly studied and has no significant practical impact.

Eine Insel der Vernunft

 

https://www.blaetter.de/ausgabe/2022/juni

Jens Kersten. Die dritte Revolution. Plädoyer für ein ökologisches Grundgesetz.

Für die notwendige ökologische Transformation unserer Gesellschaft genügt es jedoch nicht, neue ökologische Grundrechte zu schaffen und die Rechte der Natur anzuerkennen. Damit die ökologischen Rechte im politischen Prozess auch aktiv wahrgenommen und effektiv umgesetzt werden, ist es notwendig, auch die zweite Ebene des Grundgesetzes ökologisch auszugestalten – das Staatsorganisationsrecht. Das klingt zwar technisch, ist aber politisch von zentraler Bedeutung. Denn nur wenn das parlamentarische Regierungssystem für ökologische Rechte sensibilisiert ist, werden diese nicht schlicht in den weiten gesetzgeberischen Abwägungsspielräumen „verpuffen“.

Um die ökologische Sensibilität unseres Staatsorganisationsrechts zu erhöhen, muss zunächst die Ökologie als Staatsfundamentalnorm in Art. 20 Abs. 1 GG verankert werden: Die Bundesrepublik Deutschland ist ein demokratischer, sozialer und ökologischer Bundesstaat.[22] Damit gehört die Ökologie zur verfassungsrechtlichen DNA unserer Staatsorganisation, sodass sie die Arbeit der drei demokratischen Gewalten – Legislative, Exekutive und Judikative – bestimmt.

 

Real collaborations

I have taken part in so many collaborations – on institute level, on a national and on EU level. But usually these collaborations are mainly there on getting monies not in getting any real progress.

So I am very much intrigued by a project in a completely different area – sound localization in the brain – that is simply based on common interest. It includes a great description including a video, Python notebook, discussion forum and is open to everybody who wants to contribute. I wish this would have been possible also in allergy research (where not even published data of the consortium are available for reanalysis).

https://twitter.com/neuralreckoning/status/1536297590618193921