Haloscan comment system closing down

 

Haloscan comment system closing down

The comment system we use for the blog, Haloscan, is closing down on the 30th December. We have exported all the comments and hope to import them into the new comment system we will use, the default system in blogger. Haloscan was never a perfect choice, but was chosen for (perceived) privacy concerns. Thank you to everyone who has posted a comment and we hope the transition to the default system goes smoothly.

Update : the blogger default comment system is now in place and seems to be functioning correctly. People can post anonymously, although all posts will be premoderated so as to avoid spam and any offence (since it's such a sensitive subject). Previously it wasn't possible to premoderate blogger comments, which is a main reason Haloscan was originally chosen.

Editor's Note (2026):

This post was originally written by blogcontributor2, one of MEBO Blog admins, in 2009, when the Haloscan commenting system was closing down. While the Haloscan name still exists in various forms today, it is no longer the same service or community platform that many blogs relied upon at the time.

Recovering this post is also a reminder of how easily knowledge disappears on the Internet. Websites close, domains change hands, commenting systems are retired, and valuable discussions quietly vanish. Patient communities are particularly vulnerable because much of their experience is shared through small websites, forums and blogs that were never archived properly.

The original MEBO website suffered a similar fate when the domain changed ownership and the blog was no longer connected, leaving years of posts effectively hidden from readers. As part of rebuilding the archive, we are restoring these articles so that the information - and the history of the TMAU community—is not lost.

Not every old idea remains current, and some scientific understanding has evolved since these posts were first published. However, preserving them provides a valuable record of how knowledge, patient experiences, and research have developed over time.

Different outcomes of TMAU urine test

 

A UK volunteer does the TMAU urine test twice and gets different outcomes

TMAU urine test results of a UK volunteer

	Jan 2009	Sep 2009	Ref. range
Urine creatinine	5.5	4.0
Trimethylamine(TMA)	56.8	32.1	2.5 - 10.9
TMA-n-Oxide	719.3	78.0	17.0 -147.0
TMA/TMA-n-Oxide	0.08	0.41	0.05-0.21

• The first sample taken in January 2009 was done with a choline food load and while directly pre-menstrual.
• The second sample taken in September 2009 was done WITHOUT a choline load and while NOT pre-menstrual.
• The tester had been following the low-choline diet between the two tests.
• The conclusions were 'secondary TMAU' in the first test, and 'primary TMAU' in the 2nd
  
• This tester is now having the gene blood test done this week. Results will be forthcoming and posted in this blog.
• Note: TMA is trimethylamine. Trimethylamine-n-oxide is the odorless metabolised end product. It is known as TMO or TMAO or TMA-n-O
  

A member of our community has kindly given permission to post her TMAU results in the blog in order to promote discussion on the current test protocol in various countries (there is no international agreed standard). These results are from the UK, and so from Sheffield Hospital, which is the only clinical tester in the UK. The parameters used were described by the tester Nigel Manning in a previous post:

TMA is regarded as normal if the concentration is below 11 micromoles per millimole of creatinine. TMA-oxide’s normal range is below 147 and the ratio of TMA to TMO is normal below 0.21.
SecondaryTMAU is a very broad term, but essentially relates to any TMAU where normal TMA oxidation appears to be indicated. Increased TMA and TMO are usually markers for TMAU2...

Nigel Manning TMAU interview

In simpler terms, Primary TMAU is a reflection of a subnormal level of conversion of TMA to TMA-n-oxide (lower than normal TMA-n-oxide production is representative of Primary TMAU). Regardless of the TMAO level, Secondary TMAU is deemed as an excessive level of TMA even if the TMA/TMAO ration is within normal limits.

In this case, while taking high choline foods, the first test shows a very high level of TMA, but her FMO3 enzyme was able to oxidize the vast majority of it, and therefore, the ratio was very low/normal. Nevertheless, the TMA present was well beyond the 'normal' range, so she was deemed as having 'Secondary TMAU' as a result.

To further confuse things, Nigel Manning mentions that he has seen cases where someone diagnosed with 'primary TMAU' (including genetic diagnosis) can later be shown to have normal levels of TMA-oxide in a later test (this should be impossible if you have genetic primary TMAU). This seems to be what is shown here. Presumably it is unknown why this is (most likely due to lack of interest from the research community)

Quote from Nigel Manning:

SecondaryTMAU is a very broad term, but essentially relates to any TMAU where normal TMA oxidation appears to be indicated. Increased TMA and TMO are usually markers for TMAU2, however we have seen TMAU1 patients (with proven FMO3 enzyme deficiency by DNA mutation analysis) whose samples also showed this pattern – albeit only temporarily. This makes the differentiation between TMAU1 and TMAU2 difficult without more than one sample to assess and without DNA analysis to confirm a mutation for the FMO3 gene.
In general – if the TMA is consistently increased the patient has TMAU.

Interestingly, in the 2nd test results where the low choline diet had been followed, the outcome diagnosis based on the 'ratio' was 'Primary and Secondary TMAU'. Her TMA level was still too high (secondary TMAU) and her TMA-oxide level was still within normal range, but according to Nigel Manning's ratio she is deemed as not converting the TMA to TMAO to a 'normal' level.

It is unclear if this particular ratio is used elsewhere. There has been mention of a different ratio used in the USA, the percentage of free TMA in regards to the whole TMA and TMAO output : TMA / TMAO + TMA.

The paper by Phillips and Shephard that is used on the NIH website describes the ratio as :

Primary TMAU parameters:

Percent of total trimethylamine (TMA) (i.e., free TMA plus the non-odorous metabolite TMA N-oxide) excreted in the urine as unmetabolized free TMA

• Severe trimethylaminuria: less than 40% of total TMA excreted as unmetabolized free TMA
• Mild trimethylaminuria: 10%-39% of total TMA excreted as unmetabolized free TMA
• Unaffected: 0%-9% of total TMA excreted as unmetabolized free TMA

NIH Trimethylaminuria explanation

It seems that whether using the percentage or Nigel Manning's ratio, both would have concluded roughly the same result here. Her percentages would have been 92.7% normal and 70.9%.

There is a pubmed paper that suggests menstruation could cause someone to be temporarily 'Primary TMAU', even if they are regarded only as a 'carrier' (of a FMO3 mutation). Perhaps the hormones have an inhibiting role on FMO3.

In comparison, three healthy control subjects that harbored heterozygous polymorphisms for [Glu158Lys; Glu308Gly] FMO3 or homozygous for wild FMO3 showed normal (> 90%) metabolic capacity, however, on days around menstruation the FMO3 metabolic capacity was decreased to ~60–70%.

Paper : Transient trimethylaminuria related to menstruation

In a citation paper done in 2008 regarding people who had been deemed 'primary TMAU' by the urine test, the citation went on to DNA test the 12 samples and only 4 were deemed 'genetically proven primary TMAU'.

In a set of our patients, two deleterious mutations were identified in 4/12 patients including a novel T237P sequence variant, while the majority of our patients (8/12) did not reveal any mutations. Some of the latter were double heterozygous for the E158K and E308G polymorphisms which could explain a mild phenotype while others had only the E158K variant which raised the question of undetected mutations. These results indicate that further experiments are needed to further delineate the full mutational spectrum of the FMO3 gene.

Genotypic spectrum and genotype-phenotype correlation of trimethylaminuria

Probably the only conclusion that can be currently made is that it is by no means a completely defined disorder and much more research is needed into trimethylaminuria. Those that can afford the test, it is perhaps best to do the urine test a few times to make sure, and the DNA test once.

Human olfactory psychophysics

 

Wednesday, June 3, 2009

Human olfactory psychophysics

This is a mainstream research paper about the sense of smell and is probably the current viewpoint of the mainstream on the olfactory system. It mentions concepts such as 'specific anosmia', 'threshold', and 'adaptation'. 'Specific anosmia' is the genetic inability to smell specific smells. Fecal body odor sufferers (or other bowel smells or other odd smells) often say they cannot smell themselves. This also seems to be the general rule for people with external body odor. However, those with fecal body odor can smell feces odor from other sources (not through human skin, it seems), so specific anosmia doesn't seem to be the reason. The same seems true for trimethylaminuria and probably other metabolic body odors, although Dr John Cashman believes that perhaps 8% cannot smell trimethylamine, although it's not known if he means only from humans or from any source. for example, most people seem to be able to smell fish. Another theory for this is 'adaptation' and desensitivity to the smell. This seems more likely than specific anosmia, however, perhaps sufferers have been in situations where a group of strangers complain of a smell but one stranger says they can't smell anything (for instance in school). Adaptation and desensitivity do not seem to account for this. At the moment it is a mystery. the most likely guess is that there is some genetic aspect, as of yet unknown.

That aside, the article is seemingly the 'latest' (2004) in olfactory perception and worth a read

Human olfactory psychophysics
Andreas Kellera and Leslie B. Vosshall 2004