Thursday, August 10, 2006 - 07:30
It's hard sometimes when you're out of synch with the rest of the world. While my fellow ScienceBloggers have been obsessing about breasts, I've been really amused by the genetics of ear wax. Eh, what's that you say? Yes, it's true. Back in March, when Nature Genetics published this paper from Yoshiura (and friends), this bit of fun just went in one ear and out the other. But then I read this really funny blog about a person, some ear wax, and an NMR machine, and well, you guessed it, I couldn't resist. To me, it's been a jelly bean flavor that I studiously try to avoid. To several bacteria and fungi, it's home. But other famous people have found this sort of secretion interesting enough to blog about. Now I've gotten stuck in the subject, too, and had to go dig up the Nature Genetics paper to see it for myself. But first, a bit of microbiology. Perhaps it's because of the sleepless parents who've spent a night with a screaming child. Perhaps it's because of the vet bills and smelly ears from countless dogs and cats. Or maybe it's just that ears are on the outside of the body and we just can't resist digging into them. Whatever the reason, people seem to have cultured bacteria and fungi from the ear wax of a wide variety of animals, besides humans: chinchillas, gerbils, dogs, cats, elephants, horses, goats, and Swedish lynx. Looking through PubMed, it seems that an amazing number of people have been trying to grow microoganisms from mammalian ears. Mostly they get gram positive bacteria, like Staphylococci, but one group found up to 314 organisms in 48 samples of human ear wax (2). That sounds like a bad day in a pediatric ward, to me. At some point of time, someone figured out, after looking into all those ears, that all ear wax was not alike. East Asians have dry ear wax and Europeans have wet ear wax. And, now we know why. One nucleotide makes all the difference. It would have been easier to just read the paper, but I thought it would be interesting to look at the SNPs in the ABCC11 gene myself and see if I could guess which one was the culprit. First, I went to dbSNP and found the ABCC11 gene with all the SNPs marked on the map, as you can see below. Then I looked at the 8 SNPs that change the amino acid sequence (red lines on the gene map, below) and looked at the allele frequencies in different populations. dbSNP is a database at the NCBI that contains information about small scale genetic variations. These are single base subsitutions and short deletions or insertions. If you go here and look at the GeneView for the ABCC11 gene, you can see that 196 variations have been mapped to this gene. Eight of these change amino acids, one changes a splice site, and the rest are either synonymous (they change the sequence, but code for the same amino acid) or they map in an intron or the promoter. There is a table on the dbSNP page, too, with information about the mutation frequency and amount of heterozygosity. If we look at the alllele frequency for an individual SNP, we often see variation patterns like this: In the table above, all populations look about the same. We can see that many people have a T at a certain position in their DNA. In the 23 African American samples that were tested, 4 percent had a C. The allele frequency for the earwax mutation shows a much different pattern. I marked this on the image to make it easier to see. Notice, in the table below, that almost all Asians are either homozygous (two copies) for a T, or heterozygous (less than 1%). Very few are homozygous for C. Not only did the presence of this allele correlate with the type of earwax, the authors looked at changes in the function of the protein, and found that the protein behaved a bit differently, too. The authors say the advantages of either phenotype are unknown. They write about sweat and body odor. But I wonder, do Asian people get fewer ear infections? and do people with different genotypes have the different types of bacteria growing in their ears? I wish I had known about this during the many years that I taught Microbiology. All those years that we spent, with students culturing bacteria from various parts of their bodies, we could have been collecting data. References: 1. Yoshiura, K. et. al. A SNP in the ABCC11 gene is the determinant of human earwax type. Nat Genet. 2006 Mar;38(3):324-30. Epub 2006 Jan 29. 2. Stroman DW, Roland PS, Dohar J, Burt W. Microbiology of normal external auditory canal. Laryngoscope. 2001 Nov;111(11 Pt 1):2054-9.