#rhodamine

Red River

It’s not often that a river totally changes color for fairly benign reasons, but that’s exactly what this shot of the Missouri River in late June captures.

These scientists from the USGS are trying to understand the environment of the Pallid Sturgeon, an endangered species found in the Missouri and Mississippi River basins. The larvae of this fish move downstream with the current, so measuring how quickly water from one site disperses and moves down stream will help scientists know how the offspring of this sturgeon move as well.

To measure that dispersion they’ve added a dye called Rhodamine-WT to the water. That dye has a bright red color when it is concentrated and even when it has become too dilute to see the red color its presence can be measured because it fluoresces when exposed to certain wavelengths of light. The dye is also, importantly, non-toxic and breaks down into simple organic compounds with time, making it a useful compound for measurements of how waters disperse, which is often particularly important for tracking environmental pollutants.

-JBB

Image credit: USGS https://flic.kr/p/JtwXjm

This interview was based on an in-class interview with Jessica, who is a doctoral student in molecular toxicology and is studying the effects of an herbicide, Acetochlor, on mice; and also uses “click chemistry” to study the structure and constituents of biomolecules.

As an herbicide, Acetochlor is used primarily on corn, but also soy and peanuts, and less often on other crops. The world divides into Acetachlor “targets,” which are unwanted plants--weeds--that compete with marketable crops farmers are growing.  Any non-target organism, plant or animal, is referred to as an “off-target” organism. 

Little is known about the long-term effects of Acetochlor on off-target organisms, such as human beings. We do know that Acetachlor preferentially binds to cysteine, one of the twenty amino acids that are the building blocks of proteins.  A common experiment is to inject mice with Acetochlor and after four hours, add a molecular probe, which binds with reactive cysteine so that the effects of the Acetochlor may be studied.

Not all cysteines are reactive, but many are.  The effect of large doses of Acetochlor is to render metabolic pathways nonfunctional if enough Acetochlor binds to reactive cysteine.  Pathways may also become nonfunctional if the dose of Acetochlor is lower but there are more reactive cysteines.

Acetochlor has affinity for enzymes that are involved in fatty acid oxidation, the process by which animals metabolize fatty acids for energy when glucose is unavailable.  Thus, the adverse effects of Acetochlor become apparent when animals rely on fatty acids for essential metabolic energy. 

Click chemistry is a method for analyzing the composition of biomolecules and depends on the use of probes.  Probe molecules have two active regions at opposing ends:  1) the warhead, which is the binding site of the probe; and 2) the alkyne, which is a nitrogen triple bond, N≡N. 

If we bind rhodamine with a probe to a biomolecule of interest, we can learn about its composition by pulling it through a gel to which we apply an electric current.  The current separates the components of the molecule on the basis of its weight as done in gel electrophoresis.