Thursday, July 23, 2020

What's on your plate - nutrition, dark matter and health

Graham Lawton at New Scientist magazine has written a nice feature on the hidden elements of human nutrition. There is so much that we do not know about the effects of thousands of molecular compounds present in the foods we eat. He explores that topic fairly well in his article.

That article mentions some software - PhyteByte - colleagues and I designed and published in BMC Bioinformatics. The software is designed to identify food compounds with potential to have pharmacological properties. I'll share details on how all that came to be in another post. As that article was wending its way through the finals stages of editorial review, I was asked to contribute a blog to accompany the PhyteByte article. You can find what I wrote on the “dark matter” of nutrition – just what are you eating here.

Tuesday, July 21, 2020

AMY1 copy number variation

Amylase comes in two forms - salivary and pancreatic - encoded by the AMY1 and AMY2 gene clusters, respectively. These genes - AMY2B, AMY2A, AMY1A, AMY1B, AMY1C - map to human chromosome 1p21.1 and form a tight five-gene group of ~206 kbp. The genes, especially the AMY1 cluster, have garnered added interest because of the findings that they show extensive copy number variation. In some studies, copy number variation (CNV) has been determined to be influenced at least in part by selection, or adaptation to available food sources.

The first step in the digestion of dietary starch and glycogen is cleavage of the 1,4-alpha-glucoside bond. This cleavage is catalyzed by amylase. Hence, this is an important enzyme for the extraction of energy from food.

Because the AMY1 gene cluster CNV mediates salivary α-amylase levels and is linked to postprandial phenotypes relevant to type 2 diabetes, we initiated a study to examine if AMY1-CNV is associated with age-mediated change in insulin resistance. We noted positive associations of insulin resistance with age among participants of two cohorts with low AMY1-copy-numbers. Type 2 diabetes was correlated with age in those with low AMY1-copy-numbers but not with high AMY1-copy-numbers.

This work recently was published in Clinical Chemistry in an article titled "Salivary AMY1 copy number variation modifies age-related type 2 diabetes risk, by Liu, et al."