The German Ärzteblatt reports that Medecins Sans Frontières is facing enormous problems in Congo. Besides this humanitarian problem there is virtually no research for neglected diseases.
“The situation for patients has not changed and the future is bleak,” said Dr Rowan Gillies, President of the MSF International Council. The website shows how to donate. Yea, yea.
A hitch in the glitch of the switch
The CD14 / allergy story never ends – after many years and numerous contradictory reports. A new comment in the AJRCCM concludes that “further research is required” – at this time “research into the area of gene-by-environment interaction where large-scale studies, advanced assessment of environmental exposure of and experimental investigations of interactions are needed”. Is there any sense with neverending loops (except playground for hamster)? Nay, nay.
Scholarship, academic libraries, and publication
First Monday has an interesting article of Paul N. Courant about “scholarship, academic libraries, and publication”. There is a risk with all these websites that academically valuable material will become invisible some time. I also have frequent problems to locate 5 year old online supplements. Yea, yea.
Resurrection or reanimation of old myth?
JCI has a paper about resurrection of vitamin D deficiency (more about the author at 1, 2 and 3). The author uses references 46-59 to underpin his opinion that rickets has again become an epidemic. These references are from 1992, 1984, 2005, 2000, 1987, 1987, 1989, 1994, 1989, 2001, 1998, 2001, 1987, 2006. So nothing really new – no prospective study, no systematic survey, just a few isolated reports. Sure, that there might be a rickets problem in a selected areas or in minority groups, but there is no world-wide epidemic. He argues also that many (if not all) studies show “low” serum 25-OH-D3 values. Is this chasing a phantom? A more systematic study concludes that rickets in Africa is more a disease of calcium deficiency. The JCI article is particular poorly written when it comes to immunological effects; asthma is misquoted from the Camargo study (which is subject of my review at Pediatric Allergy. Nay, nay.
Gastric Acid
German news magazine SPIEGEL ONLINE writes of an ongoing trial in Berlin where 1 to 6 month year old newborns are given some kind of “oral LPS vaccination”. You might know my opinion about LPS and will therefore understand my hope that newborn gastric acid pH will prevent them from any LPS side effect. Yea, yea.
Happy Birthday WWW
Slashdot Accommodate Students writes “The BBC is amongst those reporting that the World Wide Web has turned fifteen. However, 6 August 1991 is not the only date claimed as the ‘birthday of the intern.” There is nothing to compare with that scientific evolution. Did Herrmann Hesse think of the internet when writing his “Glasperlenspiel”? Yea, yea.
PLoS ONE – a wikipedia like publishing system?
PLoS ONE may revolutionize science communication. Have a first look at www.plosone.org. As they write: “Be one of the first to appear in this new Open Access 2.0 online forum—and qualify for a great low pre-launch price. We’ll peer review your work and publish it online as soon as possible so that it can start a conversation within the community that will enhance scientific progress.” Will it still be traditional, 1:1 translated publishing system? Or can we even edit any text? What about lists of open questions? And a true synopsis – like the one theologians use to compare the four canonical gospels? Yea, yea.
How deep is deep enough?
In case that the common disease / common variant is leading to nirvana, we urgently need to resequence common genes in large populations. 2kb long CRP is a particular good candidate which might be a reason why Crawford from Uwash resequenced ~500 individuals. They found indeed potentially relevant codings SNPs – of course rare (<1%) but they are there! There is a greater number in African-Americans than other populations and more than half are private to a single population (BTW more than half in dbSNP can not be validated). Of course tag SNPs would not discover them. Yea, yea.
Nothing but skin and bone…
… was the title of a recent editorial in JCI. Clearly that’s not true for vitamin D as you may know of the many immunological functions. A new study now shows, that mice get atopic dermatitis by applying vitamin D ointment. A EJCN paper published on the same day concludes that “the national fortification of fluid milks and margarines with vitamin D safely improved the vitamin D status of children”. Nay, nay.
Exact tests for R
If you are looking for exact tests, I have some links: an unbiased allelic test dedicated to case-control association studies and another for testing Hardy Weinberg equilibrium. Yea, yea.
At-Home Genetic Tests
FTC now warns that a healthy dose of skepticism may be the best prescription: Having also reviewed many sites that are offering genetic testing either for health outcome or genealogy I could not find anything that is worth the money. Do you believe in horoscopes? Nay, nay.
Where we recombine
Finally, and long awaited, there is a first detailed analysis of mutational hotspots in the human genome by Myers from the McVean group in Oxford. There are roughly 1k-2k hotspots per chromosome, each 1kb-2kb long while there are no 200 kb without apparent recombination. Recombination avoids repeats, exons and L1 elements but likes GC as well as the THE1A/B 7mer CCT.CCC.T and the 8mer CCA.CGT.GG. As rec laways needs double strand breaks, are these also the first cancer motifs found? Yea, yea.
Looking for 100 year old DNA
You can probably find hundreds of times the argument in the medical literature that the main cause of asthma is the environment – as genes can not spread within 1 or 2 generations. While this might be true for de novo mutations it is certainly not true with pre-existing variations and recent population dynamics. In a review how asthma came into live, I argued that introduction of antibiotics and improved child care extremely shaped our genome by suppressing purifying selection. In developing countries respiratory infections are among the main killers. Who can help with 1,000 unbiased 100 year old DNA samples to prove this hypothesis? I have an excellent dentist to punch holes in bones.
Again paranormal inheritance?
Following the exciting Lolle paper, now again non-chromosomal transfer of genetic information in a new study of Mary Alleman. Yes, of course, humans inherit mito DNa, there is imprinting, but also siRNA (not found in maize) or RNA polymerases (found!)? BTW much fuss of maternal imprinting in genetic epidemiology is simply preferential maternal reporting.
Addendum
Pollen contamination may have been the reason for the Lolle/Pruitt results.
Once in a lifetime
You may think twice about participating in a genetic study. Science magazine makes the point: If you have been ever been profiled by a SNP scan that is now (even anonymous) in the public domain, every further study (or anyone else who has access to trace amounts of your DNA) can re-identify you by 20 – 70 characteristic SNPs. This is even problematic as likelihoods for your disease risk can be calculated from SNP arrays of distant relatives, yea, yea.