May 26, 2015

Tutorial: Mass spectrometry in plant science, part 3 – Calculating % atom labeling by mass spectrometry in isotopic labeling experiments



Labeling with stable isotopes is the best method for calculating the flux of metabolites through biological systems. 13C is the isotope of choice for most small organic metabolites, and labeling with 13CO2 under physiological conditions gives us the most realistic picture of how the plant's metabolism works in its natural environment. This approach is known as whole plant kinetics . In order to calculate the degree of label incorporation into the pool of metabolites following a labeling experiment, it is first necessary to extract those metabolites from labeled plant tissue and separate them by gas or liquid chromatography. We can then collect the spectra one by one as they elute from the column and enter the mass spectrometer. The resulting mass spectra tell us the pool sizes of the different isotopologs of a given metabolite (i.e. related chemical species which differ only in that they bear one or more 13C isotopes compared to the all 12C reference molecule). Depending on how the molecule fragments under a typical ionization technique like electron impact, it may be impossible to say where in the molecule these 13C isotopes are located by mass spectrometry; we can only say how many isotopic labels are present. We can however determine the relative abundances of labeled species that have 1, 2, 3, or more isotopes compared to a reference compound (usually unlabeled). But this spectral data still doesn’t tell us what we really would like to know following a labeling experiment: what percentage of the total carbon atoms in a metabolite pool are represented by 13C instead of 12C?

May 8, 2015

Pandanus candelabrum as an indicator species for diamond rich kimberlite pipes in West African jungles

There is a report this month in the journal Economic Geology on a little known tropical plant species in the Pandanaceae family. In West Africa, it apparently grows in kimberlite rich soils. Since kimberlite is a mineral which is typically rich in diamonds, this is a significant discovery in economic botany. Unfortunately, the article, a single author contribution by Stephen Haggerty, is behind a pay wall, and I have not obtained a copy yet. There is a nice summary in Science by Eric Hand that explains some of the geology behind diamond formation, deep below the surface. I did not know, for instance, that diamonds are formed hundreds of kilometers below the surface and reach the top by being pushed through pipes of kimberlite in explosive events, sometimes at speeds greater than the speed of sound.

May 1, 2015

A U.S. News and World Report article glorifies Goodall's embrace of anti-GMO nonsense

Anna Medaris Miller, writing for U. S. News and World report, gives what I hope was unintended free advertising to a dismal new book on anti-GMO quackery by Steven M. Druker ("Altered Genes, Twisted Truth"-scared yet?) and endorsed by Jane Goodall, a once great scientist currently destroying her legacy with woo. Using what is now a formulaic, emotional, fact-free, "think of the children" marketing approach to peddle absolute non-sense to a public confused over a complex scientific topic, Druker displays an intellectual honesty comparable to those who sell books on secret cures for cancer your doctor doesn't want you to know about.