All posts by Daniel Friedman

Is your spit making you fat?

One of the central pursuits of modern human genetics is to move beyond genomic correlation. That is, to demonstrate experimentally why a specific genetic variant may be associated with a disease. New work in Nature Genetics from an international team lead by Philippe Froguel at Imperial College in London does just this – demonstrating an interesting link between saliva and obesity. Basically, all humans express amylase, a salivary enzyme that breaks down complex carbohydrates into absorbable sugars. The researchers found that people with more copies of the gene had a significantly decreased risk of developing obesity. People with fewer copies expressed less amylase, and it was hypothesized that this alteration in gastrointestinal carbohydrate metabolism affected insulin signaling, blood sugar levels, as well as the microbial community in the gut. This finding has implications for the rational design of digestive enzyme-based therapies for obesity and other metabolic disorders.

Froguel, Philippe, et al. “Low copy number of the salivary amylase gene predisposes to obesity.” Nature Genetics vol. 46, p. 492-497 (2014).

“No Ecosystem is an Island”

By Daniel Friedman, Genetics ’14

For years, ecologists have modeled the biodiversity of natural forests as if they were oceanic islands, adrift in an unlivable sea of humanity. However, research published in April in Nature by C. Mendenhall et al. suggest that this is not the most accurate or predictive way to think about these pockets of nature. By comparing bat diversity on countrysides and oceanic islands, they find that fragmented land ecosystems behave markedly different than their oceanic counterparts. They find that forest “islands” maintain species at higher overall levels of biodiversity than ocean islands, and also gain/lose species in unique patterns. This has relevance to humanity’s actions to support biodiversity on land, and suggests the need for new models, metrics, and strategies of conservation.

Mendenhall, C., Karp, D., Meyer, C., Hadly, E., Daily, G., “Predicting biodiversity change and averting collapse in agricultural landscapes”, Nature, 2014.

Image from Abu Shawka, 2009. Creative Commons.

“The Eukaryotic Ribosome”

This is a submission from UC Davis CBS Professor Sean Burgess. It comes from a future publication that relates the human quest to visualize the inner workings of the cell, molecular biology, with the quest to visualize the interior of the mind, art.

The Eukaryotic Ribosome

The basic mechanism of ribosome­based protein synthesis is conserved among all domains of life. The ribosome comes in two parts. The small subunit  interacts with the mRNA and decodes the interaction with the aminoacyl tRNAs. The large subunit contains the active site of peptidyl transferase. The two subunits together
form three pockets for three forms of tRNA. The A site is where the aminoacyl tRNA binds, the P site holds that peptidyl tRNA when the A­site is occupied. The E site contains the deacylated tRNA following peptidyl transferase. The ribosome is a huge conglomeration of RNA and proteins. The RNA appears to do all the heavy lifting for the main catalytic event of protein synthesis.  So what came first, the protein or the ribosome?
Obtaining the crystal structure of the ribosome was a tour de force effort. The Nobel Prize for solving its structure was awarded in 2009.

Top: Willi Baumeister: Mortaruru with Red Overhead (1953), The Art Book,

Phaidon Press Limited, 1994.
Bottom: The 60S (PDB: 305H) and 40S (PDB: 1S1H) subunits of the eukaryotic ribosome. Ben­Shem et al. (2010) Science, 330 (6008): 1203­1209. The image was generated by S.M.B. using MacPymol using coordinates from the Protein Databank (­bin/pdb).  MacPyMOL is product of
Schrodinger, LLC. Copyright (C) 2009­2010.