Seminar III: Applied Visualization

An Opportunity in Agriculture

Problem Background

Drosophila suzukii is a fruit fly species that is capable of infesting fruit during the ripening stage unlike its more familiar relatives that infest fruit typically only when fruits begin to decompose.

Methyl benzoate is an organic compound with a pleasing aroma and is produced in some plants such as Antirrhinum majus commonly known as the snapdragon. In a paper titled “Developmental Regulation of Methyl Benzoate Biosynthesis and Emission in Snapdragon Flowers”, Natalia Dudareva of Purdue University describes the temporal and spatial aspects of how snapdragon flowers synthesize this scented compound from the precursor benzoic acid.

In the paper titled "A Floral Fragrance, Methyl Benzoate, is An Efficient Green Pesticide, Yan Feng & Aijun Zhang describe how this compound may be useful in mitigating the effects of common crop pests such as Drosophila suzukii.

All of this information leads to an idea: might we be able to use bioengineering methods to boost crop tolerance of pest species through the internal production of methyl benzoate?

Activity

What questions should we ask in order to prepare to design such a system?

Promoter Strength Testing

Assume we have constructed a bacterial system to produce methyl benzoate but we think the system could be optimized to produce a greater volume through the use of a carefully selected promoter. A team has designed a series of five promoters (pA, pB, pC, pD, pE) and has tested each with two different chassis (chassis 1 and 2) producing the dataset contained in promoters.csv. We will use the dataset to decide which promoters should be selected for use in additional in vivo trials with three commercial cultivars of Solanum lycopersicum (tomato): Trust, Blitz, and Match.

Separation Chamber Testing

Assume you have selected a single promoter pX to be used in live plant material and have successfully transformed plant tissues of all three cultivars to carry and express this construct. A separation chamber experiment has been designed and run to test the extent to which flies in each of the chambers (control,test) will die following exposure to fruit over a period of time. The treatment chamber contains fruit from a transformed apple which produces methyl benzoate in the fruit tissues. The data represent a count of fruit flies.

Additional Testing

What additional tests might be needed to more fully investigate this system?

Making Sense of Data

This activity has three parts: we’ll first examine and plot data from a promoter strength assessment and then we will compare results from a separation chamber experiment. Lastly, we will attempt to improve a box plot that describes the data from the separation chamber experiment.

Please open RStudio Cloud and navigate to the materials for Seminar 3. We will work through these activities together.