Category Archives: Genetics

All humans, and two ancestors?

Daily Mail reports a study in Human Evolution with comments at phys.org

A scientific study has prompted speculation that all modern humans could have descended from a solitary pair who lived 100,000 to 200,000 years ago.
Scientists surveyed the genetic ‘bar codes’ of five million animals – including humans – from 100,000 different species and the results have prompted speculation that we sprang from a single pair of adults after a catastrophic event almost wiped out the human race.
These bar codes, or snippets of DNA that reside outside the nuclei of living cells, suggest that it’s not just people who could have come from a single pair of beings, but nine out of every 10 animal species, too.

I have heard that before.

 

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How does the soma to germline transfer work?

I never had problems to understand environmental induced sperm methylation as spermatozoa of animals are produced continuously by meiotic division.  But I learned that in humans all ova are produced before birth, so how could these ever be influenced by an environmental exposure? It seems that the dogma of prefabricated eggs is wrong as described already in 2012.

Rare mitotically active cells have a gene expression profile that is consistent with primitive germ cells. Once established in vitro, these cells can be expanded for months and can spontaneously generate 35- to 50-μm oocytes

So there is a lifelong chance that environmental exposures both in fathers and mothers can be transmitted to the offspring “fat eggs, fat offspring” – there is no Weismann Barrier. (This remains also an important question as somatic gegen therapy could accidentally introduced germline changes – at least in theory).

But how does any soma to germline transfer work? A new paper examined this  in more detail. They found that the negative regulator of sperm activation in C elegans, SWM-1, is produced in body wall muscle, then secreted into the body cavity. Whenever it enters the gonad it finds it target TRY-5, a spermiogenesis activator, that influences sperm success.

So to the more conventional soma to germline theories of persistent methylation changes or RNA fragments ( as described in a recent review) there maybe more possibilities like microbiome transfer.

 

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Der chinesische Menschenversuch

This content has restricted access, please email me for the password.


 

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No eternal life

Seven years ago we published a 15% heritability of life span from data in South Tyrol. The heritability of longevity increased from 0.20 to 0.35 as the longevity threshold increased.

A new study now finds that we have been exaggerating

true heritability of human longevity for birth cohorts across the 1800s and early 1900s was well below 10%, and that it has been generally overestimated due to the effect of assortative mating. … Spouse life spans correlate as much or more than those of genetic relatives, raising the possibility that correlated environments and/or assortative mating have confounded those estimates.

I think there is a misunderstanding of assortative mating (AM). AM is a form of sexual selection in which individuals with similar phenotypes mate with one another more frequently than would be expected under chance conditions. BUT the phenotype longevity is not known to anyone at mating. Instead there seems to be a simple “environmental” interaction: We know that elderly couples frequently die together, also known as broken hearts phenomenon.

Adjusting any regression model for any AM will therefore seriously reduces the heritability of longevity, which is exactly what the authors describe in their new paper.

Spousal correlation is expected on two grounds: shared-household environment during adulthood and/or assortative mating. The two can be distinguished by definition: the effects of shared-household environment are nontransferable through inheritance, whereas the factors correlated by assortative mating are transferable, allowing them to also generate correlations with family members of the spouse

This is not very convincing as A) shared-household environment can be transmitted by epigenetic factors and B) it is a myth there is any AM for lifespan.

 

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Cell life span in the human body: 7 years?

Karel & Iris Schrijver “Living with the starts” have an intestine chapter “Dying to Live” that is about the cell turn over

Take the skin, for example: a Iiving, breathing, regenerating tissue that is the largest organ of the body and that acts as a barrier between the internal organs and the environment. In adults, it encompasses about 22 square feet (2 m2) and weighs around eight pounds (4 kg). It protects the interior of the body from injury, from harmful effects of microorganisms, and from the damaging ultraviolet rays of the Sun. It plays a role in the body’s thermal regulation through the constriction or dilatation of small blood vessels, it contains nerve endings that allow us to feel touch, temperature, pain, pressure, and vibration, and it slows the loss of fluids from the body. The skin also shelters the hair follicles, which produce the hairs that cover most of the body’s surface, and it provides storage for a variety of substances. The skin, composed of several layers, ages quickly but is remarkably effective at renewing itself. In the top layer, the epidermis, most cells eventually reach the surface as the outermost layers at cells wear off. They are replaced in a time frame of roughly a month or two, in a continuous process that culminates in the loss of approximately 30,000 cells every minute throughout our lives. This translates into roughly eight pounds (4 kg) of dead material per year. Some features of our skin are, of course, more lasting. For example, we may have seemingly permanent moles and we may have scars that persist for years. These tissues, however, are not really skin. Moles are embedded within our skin but they are in fact benign growths that are typically composed of pigmented cells that do not follow the same lifecycle as true skin cells. Likewise, scars are repairs of deep cuts in our skin.

Unfortunately they do not give any reference there. Data should have been produced by carbon 14 dating. And yes, there are references

Radioactive carbon decays slowly, such that a given amount of carbon-14 halves every 6,000 years. So detecting the subtle change in the ratio of normal to naturally occurring radioactive carbon over just a few years is incredibly hard.
But Jonas Frisén of the Karolinska Institute in Stockholm, Sweden, says it can be done if one takes advantage of the signal left by nuclear testing, which spewed high levels of carbon-14 into the air during the Cold War.
By the time a halt was called to aboveground nuclear testing in 1963, levels of carbon-14 in the atmosphere had doubled beyond natural background levels, says Frisén. Since the halt, this has halved every 11 years. By taking this into account, one can see detectable changes in levels of carbon-14 in modern DNA, he says.
“Most molecules of the cell will turn over all the time. But DNA is a material that does not exchange carbon after cell division, so it serves as a time capsule for carbon,” Frisén says.

basically referring to a Cell 2005 paper

We therefore modified established DNA-extraction protocols to minimize the risk of carbon contamination (see Experimental Procedures). DNA samples were analyzed for purity in several ways; in addition to spectrophotometric analysis, the contents of all samples were analyzed by HPLC and the amount of total carbon (12C, 13C, and 14C) was determined during graphite preparation for isotope analysis by accelerator mass spectrometry.

They needed a minimum of 15 million cells for 14C analysis with the current sensitivity of accelerator mass spectrometry while it would be  interesting to repeat this study with single cell genome sequencing.

 

CC-BY-NC Science Surf accessed 05.11.2025

Purifying selection affect as much as 95% of the variants

New research shows that most genetic variants in the human genome are affected by purifying selection, so there is no “neutral” variant anymore.

Pouyet, Aeschbacher et al. created a measure of genetic diversity that is only affected by selection or transmission bias. The results showed that negative selection influences as much as 85 percent of our genome, whereas transmission bias affects a majority of the rest of the genome. After removing these two biases, less than 5 percent of the human genome is found to evolve by chance. This suggests that while most of our genetic material is formed of non-functional sequences, the vast majority of it evolves indirectly under some type of selection.

 

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Finding the allergy cause

Genomics did not really help to explain allergic mechanisms beyond IL33. But combining  now stem cell & immune cell Identity tracking looks like a promising strategy for identifying initial disease events. At least colleagues at the MDC  think so.

LifeTime – ein visionärer Vorschlag für ein EU-Flagschiff. Zuverlässig vorherzusagen, wann eine Krankheit ausbricht oder wie sie verläuft, erscheint wie ein Traum. Ein europäisches Konsortium will ihn Wirklichkeit werden lassen und dabei vor allem neue Technologien der Einzelzellbiologie nutzen. Führende Forscherinnen und Forscher haben daher einen Antrag für ein FET-Flagschiff mit dem Namen LifeTime eingereicht.

 

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New insights by single-cell genomics

Congress report Annual AGD Meeting 2018, Potsdam Oct. 5–6

Welcome and Opening of Symposium by  Peter Nürnberg, President of the AGD and Joachim L. Schultze, Chair of the Program Committee.

Joachim L. Schultze
Peter Nürnberg

The AGD meeting was interesting and a great primer for all of us who are not directly working with single cells.

Maybe it is an unusual research field – dissecting single cells in the first stage is not a trivial task. And single cell  means single cell experiment that can be replicated only in other cells. The current readout is  RNA content at a given time while genomics and proteomics still need to be integrated. Experiments cover mainly abundant RNAs and for cost reasons only the 3′ ends. The statistical analysis usually is a 2 dimensional PCA (known to overfit noise) so this not a trivial approach at all. Newly identified cell cluster need careful confirmation as addressed in the talk of Andreas Schlitzer.

Continue reading New insights by single-cell genomics

 

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What could be done – single cell birth dating

The famous Spalding paper 2005 used an interesting approach

We show that the level of 14C in genomic DNA closely parallels atmospheric levels and can be used to establish the time point when the DNA was synthesized and cells were born… Retrospective birth dating is a generally applicable strategy that can be used to measure cell turn-over in man under physiological and pathological conditions.

I was more in favor of calculating mutation rates, S. Horvath suggested methylation changes. Maybe lineage tracking will be the next big thing in single cell analysis and the human cell atlas?

 

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Der Vitamin D Lobbyist Achim Zittermann und seine erfundene Heidi Geschichte

Es ist schon kurios, was das Web manchmal zu Tage fördert.

Zum Beispiel den Vortrag des Vitamin D Experten Prof.  Dr. oec. troph. Achim Zittermann ( zuletzt Bad Oeynhausen ), der Clara Sesemann aus dem Heidi Roman eine Rachitis andichtet.

 

 

Im Original bei Johanna Spyri kann man aber nachlesen, dass Clara regelmässig “Fischthran” bekommt, also hochdosiert Vitamin  D (und A).

 

 

Wenn Claras Symptome also wirklich auf eine endokrine Störung zurückzuführen wären, dann müsste es sich um eine Vitamin-D resistente Rachitis Typ I oder II sein.

Beide Formen reagieren aber leider nicht auf zusätzliche Sonneneinstrahlung in den Bergen.

Die Heidi Geschichte des Vitamin D Experten ist also genauso Unsinn wie seine 18300 Toten durch Vitamin D Mangel.

 

CC-BY-NC Science Surf accessed 05.11.2025

Froome, salbutamol and the WADA

Many professional cyclists are suffering from “asthma”, a diagnosis that can be easily used like “headache” if you know how to blow a typical lung function test. You are then prescribed beta2 agonists and a get the diagnosis excercise induced asthma.

For good reasons, salbutamol is prohibited by the WADA, the world anti-doping agency. So, I would expected asthmatic patients to take part in activities like the paralympics for simple reasons:  High-tech prostheses could give runners an unfair advantage and high tech drugs opening the airways of cyclists will lead to an increased air exchange with less efforts.

Nevertheless the WADA allows exceptions by providing “TUEs” until 2009, since 2009 a declaration of use:

The highest risk for developing asthmatic symptoms is found in endurance athletes and swimmers. … Asthmatic athletes commonly use inhaled ß2-agonists to prevent and treat asthmatic symptoms. However, ß2-agonists are prohibited according to the Prohibited List of the World Anti-Doping Agency (WADA). An exception can be made only for the substances salbuterol and salmeterol by inhalation, as long as a so called “therapeutic use exemption” (TUE) has been applied for and was granted by the relevant Anti-Doping authorities, and for salbutamol and salmeterol by inhalation. Since the beginning of 2011 for the latter two substances neither a TUE nor a Declaration of Use (DoU) is required as it is for formoterol from beginning of 2012).

Rules were quite clear in the past: Alessandro Petacchi was banned from November 2007 to August 2008 for salbutamol overdosing;  Diego Ulissi received a nine-month suspension ending in March 2015 after having found almost twice the permitted concentration of salbutamol in his urine.

The most recent 2 July 2018 decision of the WADA right before the start of the Tour de France 2018 was unexpected for denying any Adverse Analytical Finding (AAF) in the Froome case.

Whatever we believe is being correct, it  shows at least the inability of the WADA to reach at any conclusion within a reasonable time period. Froome was already tested positive for excessive salbutamol on 7 Sept 2017.

The WADA’s announcement follows that of the UCI earlier today, which announced that the anti-doping proceedings involving Mr. Froome have now been closed. Based on careful consideration of the facts, the Agency accepts that the analytical result of Mr. Froome’s sample from 7 September 2017 during the Vuelta a España, which identified the prohibited substance Salbutamol at a concentration in excess of the decision limit of 1200 ng/mL(1), did not constitute an Adverse Analytical Finding (AAF).

Unfortunately neither the ASO (the Tour organization) nor cycling fans wanted Christopher Froome to participate in the 2018 Tour de France. I largely agree with Velonews

At present we condemn dopers because our concept of fairness is treated as absolute and clear, but the truth is that the world is far more complex than right or wrong. It’s worth bearing in mind that what is seen as ‘unfair’ competition is not set in stone.

Tom Fordyce of the BBC was given exclusive access to data behind Chris Froome’s 2018 Grand Tour victory at the Giro d’Italia, another exceptional ride of Froome (as in the Vuelta 2017 where he was tested positive).  Fordyce published, however, only unimportant calorie intakes and irrelevant WhatsApp messages. No “fake news” as Richie Porte said, but “fog news”.
What I am interested in, is the number of hubs Froome is taking from the inhaler, his inhalation technique, any short- and longterm effects on heart rate, power output, VO2max and maybe even more. Michael Hutchinson makes the point

The problem with this kind of data is that while it is very nice and we assume it’s accurate, it needs context to make sense of it. It makes perfect internal sense. You need external data. If we knew the power output of every rider in that lead group over the hills towards the end of this stage, if there was anything that didn’t match we’d spot it.

Maybe we even need more than the WADA ever requested from Team Sky?

Chris Froome may have some unusual beta2 receptor variants as we described it as already as 2000 (amino acid positions 16, 27 and 164). Maybe a similar condition as with the Pechstein case / hereditary spherocytosis? Any increased smooth muscle relaxation profile,  more coronary artery dilation or boostered glycogenolysis? The only way to find out more, would be DNA testing, performance and excretion studies with and without beta2 agonists. From the literature I would NOT expect so much benefit of salbutamol on gas exchange but in rare and exceptional cases like Froome, there could be a fair (or unfai)r advantage: ß2-receptor variants improve the metabolic profile, they increase glucose tolerance and decrease leptin resistance, with the Arg16Gly polymorphism giving even a better endurance performance. So Froome might have indeed performance benefits from overdosing salbutamol. Did the WADA ever discussed that? It seems that the Guardian has been arguing in the same way

It had been expected that the Briton would have to undergo a controlled pharmacokinetic study, which would have attempted to replicate the “unique circumstances” that may have caused the abnormal levels of salbutamol in his body. However, in a statement, Wada accepted this was not “practicable”.

Just in the own interest of Froome and Team Sky but also in the interest of the WADA and the “post-doping” cycling era

  • Team Sky should release the 1,500 page report.
  • WADA can not refer to unpublished salbutamol studies or explain that they have only partially involved in the UCI decision. Salbutamol is a forbidden drug as it is increasing performance  (otherwise Froome would not take it).
  • WADA need to explain in detail why they are making an exception for Froome but not for Petacchi  and Ulissi.
  • I think WADA need to sponsor pharmacogenetic studies that exclude any performance enhancing effects in the therapeutic range.

11 July 2018 WADA publishes a clarification

It was accepted by the UCI, however, that in this case such a study would not have provided reliable evidence as it would be impossible to adequately recreate similar conditions to when Mr. Froome was subjected to the test, taking into account his physical condition, which included an illness, exacerbated asthmatic symptoms, dose escalation over a short period of time, dehydration and the fact that he was midway through a multi-day road cycling race.

Recreating specific conditions is never possible, so it is a weak argument. What is interesting is the detailed statistics about salbutamol use that we did not know before

From the data available to WADA in the Anti-Doping Administration and Management System (ADAMS), of the 41 completed cases that involved salbutamol as the only substance: 20% (eight out of 41 cases) resulted in acquittal. […] In the same time period, 57 cases contained salbutamol, either on its own (see above) or in combination with other prohibited substances, and of those: 14% (eight out of 57 cases) resulted in acquittal.

So 16% acquittal only… And well, no further criteria for acquittal or suspensions…

15 July 2018

Former pro rider Jens Voigt believes that money rules – the UCI fears the damage they have to pay if they are loosing a lawsuit against Froome/Sky (Katrin Krabbe received 1.2 millions).

And again the Guardian

Wada’s director general, Olivier Niggli, also raised the possibility of Wada lowering the dosage for which a TUE for salbutamol would be required. […] Niggli rejected accusations. “Maybe the finger is being pointed in the wrong direction – and maybe what needs to be done is to point the finger at how much we allow athletes to take and maybe be more restrictive. Maybe the weakness in the system is that we are being too nice,” he added. “Maybe we need to be tougher and say: ‘You are going to have to take less, otherwise you need a TUE.’”

Looks a bit like a bazaar now.

Niggli also insisted that the fact Froome was not sanctioned was not unusual for salbutamol cases and that 20% of such cases have a similar result. “These cases are not black and white, which means they require a process,” he said. “I know a lot of people would love it if it was positive or negative, but it is not the case. So until we have a different test, or the science evolves, we will have to deal with it.”

Olivier Rabin, the World Anti-Doping Agency’s director of science, is quoted as

Under current rules athletes are allowed a maximum of 1600 micograms of salbutamol over 24 hours, with no more than 800mg taken in a 12-hour period. But Wada’s director of science, Dr Olivier Rabin, suggested those limits could potentially be cut by between a quarter and a half […]
Froome provided a number of elements, some of which were specific to his case, such as the increase in concentration [compared to the tests undertaken in the preceding days], for example. There was, it seems, a worsening in his asthma due to an infection […] He took a certain number of medicines to treat it and other elements linked to his diet were also taken into account, as were dietary supplements. And other things too.

Froome seriously ill on that day? Finishing as 23rd rider of 162??

I can’t see any major illness and agree with  Bradley Wiggins who describes Chris Froome salbutamol affair as ‘a mess’ and claims Wada need more investment.

Something needs reviewing massively. I don’t think WADA have a massive amount of money, they need more investment. They were set up 20 years ago and their rules were probably written then, so perhaps they need to be re-written. But to really combat doping in sport and the more secret ways people are finding to dope in sport they need more money and funding.

And who has finally cleared the case – the WADA or the UCI?

 

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An explanation of heredity

An explanation of heredity can be found at the Wired interview of Carl Zimmer.

People have been trying to use genetics as a form of identification for a very long time. Of course they didn’t always call it that. DNA is just a modern substitute for the old idea of blood. But in many ways it hasn’t evolved much from the time we thought of ancestry as a pure substance. We still say “I’ve got some Irish blood in me,” but it’s not like you can take out just the Irish blood and fill a cup with it. It’s the same with the bits of DNA in your genome that came from people that once lived in that part of the world. We’re all an amalgam of fragments that have all traveled different paths and each only influences us in very subtle ways. What we really want from heredity is an explanation of why we are the way we are, and genes alone can’t give us that. There are other things we inherit that matter just as much—like the chemical modifications to our DNA that turn genes on and off or the microbes that abound in our bodies or the human-made environments we’re born into. We literally pass down the whole world to our children, and right now our children are inheriting climate change.

This is clearly an argument against the European genetic exceptionalism. But even accepting that argument to a large extent, I do not understand why Zimmer uploaded now the genomes of his children Charlotte and Veronica for public viewing? Because it is largely irrelevant?

 

CC-BY-NC Science Surf accessed 05.11.2025

How does vitamin D imprinting work?

I have  predicted an epigenetic regulation of vitamin D converting enzymes in 2010 to explain the programming effect of vitamin D supplements on later allergy.
Last week, a first study examining vitamin D supplement effects in newborns has been published. They compare 400IU versus 3800IU while I am already convinced that 400 IU has some measureable effect.

 

table 2 screenshot of selected rows

 

So maybe I was wrong with my prediction of a differential CYP24A1 methylation, as the authors now describe CYP7B1. CYP7B1 encodes for 25-hydroxycholesterol 7-alpha-hydroxylase which is more upstream in the  synthesis of cholesterol.

 

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Where have all the flowers gone?

Here is some background information of my forthcoming talk.

Congress: European Academy of Allergy and Clinical Immunology
Congress: 2018 Munich
Session number: OAS 03
Session title: Pan-omics in respiratory and skin disorders
Session date: Sunday, 27 May 2018
Session time: 10:30 – 12:00
Session room: Hall C
Abstract number: 0012

 

Background: In the pre-GWAS era (1993-2007) numerous association studies have been published in renowned journals including The Lancet, New England Journal of Medicine, Nature, Nature Genetics, Nature Immunology, Science and Human Molecular Genetics. They all showed an association of allergy related traits while these results have not been systematically matched with results from current GWAS studies.
Method: We are now following up several prominent associations by comparing the previously published results with currently deposited data at the NHGRI-EBI Catalog of published genome-wide association studies http://www.ebi.ac.uk/gwas NHGRI-EBI listed phenotypes were only selected if they are not suffering themselves from serious problems like unstandardized outcomes. Also the SNP marker set should have a good coverage of the region of interest.
Results: In total 26 allergy associated genes could be reanalyzed. The initial association could not be confirmed for CD14, ADRB2, TNF, MS4A2, ADAM33, GSTM1, IL10, CTLA4, SPINK5, LTC4S, LTA, NPSR1, NOD1, SCGB1A1, GSTP1, NOS1, CCL5, TBXA2R, and TGFB1. Some genes showed borderline significant results like IL4 and IL4R while only IL13, HLA-DRB1, HLA-DQB1, IL1 cluster and STAT6 were clearly associated also in recent GWAS studies.
Conclusion: Most of the early SNP association studies could not be replicated which has also been described in other disease areas (“non- replication crisis”). Assumed reasons range from insuffficient editorial oversight, poor review, phenotyping or genotyping errors, selective reporting or intentional fraud. In addition there are numerous study inherent problems like population stratification or wrong significance thresholds that may have led to largely irreproducible results.

 

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Hyperkalzämie durch Überdosierung mit Vitamin D

Die Arzneimittelkommission der deutschen Ärzteschaft warnt

Eine 78-jährige Patientin (A) und ein 60-jähriger Patient (B) hatten sich eigenständig Vitamin-D-haltige Präparate besorgt und täglich hohe Dosen (A: Vitamin D3 10.000 IE/d; B: „Vitamin D“ 50.000 IE/d) eingenommen. Beide entwickelten ein akutes Nierenversagen bei ausgeprägter Hyperkalzämie (A: 3,42 mmol/l; Referenzbereich: 2,15–2,58 mmol/l; für B liegt genauer Wert nicht vor). Hinweise auf alternative Ursachen wie primären Hyperparathyreoidismus, Sarkoidose oder Tumorerkrankung gab es nicht. Der Zustand der Patientin A besserte sich unter forcierter diuretischer Therapie und peroraler Kortisongabe. Patient B entwickelte schwere Komplikationen und hat eine dialysepflichtige Niereninsuffizienz davongetragen (Nierenbiospie: schwerer tubulärer Schaden mit Mikroverkalkungen, passend zu hyperkalzämischer Schädigung).

Damit also Warnung vor Coimbra Protokoll und vor vitamind.net (David Rotter, Jörg Schweikart, u.a.). Eine Hochdosistherapie ist nur bei nachgewiesenem genetischen Defekt der Vitamin D Konversionsenzyme indiziert.

 

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