The 'evolution' of a PhD project—from jumping genes to biochemical pathways

Traffic, Jan, 2007 by Henry Chung

In this essay, I describe how my PhD project 'evolved' from the study of jumping genes and regulation of a single gene, Cyp6g1, to the expressional characterisation of the entire family of genes of which Cyp6g1 is a member. Furthermore, I describe how an early single control experiment led to the identification of an elusive gene in a biochemical pathway for the synthesis of juvenile hormone, a key hormone in insect development.

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'Nothing in biology makes sense except in the light of evolution.'

Evolutionary biologist, Theodosius Dobzhansky (1)

The term 'evolution' has always been historically associated with biology, describing how diverse forms of life have come about from ancient and primitive origins. However, the meaning of the term 'evolution' itself has evolved. 'Evolution' often now means simply the change that occurs as time passes, presumably due to natural processes and events which take place. Indeed, the University of Melbourne proudly displays a big banner proclaiming 'The Evolution Starts Here' in front of the John Medley Building as it launches its Melbourne Model of new generation degrees. Using evolution as a theme for this essay, I describe my PhD project as having 'evolved', from the beginning to now, almost the end. However, I shall not take evolution's name in vain, as I will describe how it (in its biological sense) forms the basis of my project, and eventually led to the evolution of my project.

AN HISTORICAL GENETIC QUESTION

Evolution by natural selection is probably one of the most, if not the most, important concept in biology. Natural selection describes how heritable traits that have selective advantages to an organism increase in frequency over generations in a population of reproducing organisms, whereas traits that decrease the fitness of the organism decrease in frequency. An organism's ability to survive in a changing environment depends on its ability to evolve and adapt. The lack of the ability to evolve in response to environmental changes will likely lead to the extinction of the species. (2)

Around the time of the Second World War, insecticides such as dichloro-diphenyl-trichloroethane (DDT) were widely used to kill insect pests such as mosquitoes that carry the deadly vector which causes malaria. The use of DDT was also extended to agriculture and used against insect pests, to increase food production. Although the use of DDT contributed to the eradication of malaria from Europe and North America in the 1960s, resistance to this insecticide has evolved in many insects exposed to this chemical, rendering it ineffective. One such example is the 'star' of this essay, the fruitfly Drosophila melanogaster, a human commensal that owes its current cosmopolitan distribution largely to human activity. (3)

The fruitfly has been the workhorse of genetics since the early 20th century, leading to many important scientific discoveries, such as how genes are arranged on chromosomes and how genes organise the development of an embryo--both discoveries leading to Nobel prizes. In recent years, many researchers have made the fruitfly their choice organism and they have made major discoveries in the understanding of human diseases such as cancer (4) and neurodegenerative diseases. (5) Research on the fruitfly has also led to landmark findings on the study of its behaviour. (6)

Because of the genetic tools available to study the fruitfly, researchers used it to study the mechanisms of how resistance to insecticides such as DDT can evolve. The earliest published study is by Professor James Crow from the University of Wisconsin-Madison in 1954, in which he concluded that resistance to DDT is a genetic trait (i.e. heritable) and involves many different factors on different chromosomes. Later work by many other researchers showed that DDT resistance maps to a single locus (named DDT-R) on the right arm of the second chromosome in some fruitfly populations. The DDT-R locus has become almost 'mythical' as researchers over the years associated numerous traits with it, such as susceptibility to the chemical phenylthiourea and resistance to other insecticides (organophosphates and carbamates). Due to the lack of molecular tools at the time, the identity of DDT-R remained unknown for the next fifty years. (7)

MAPPED

In 2000 Celera Genomics (the company that tried to sequence and patent the human genome), in collaboration with researchers from University of California, Berkeley, sequenced the fruitfly's genome (the organism's entire DNA sequence). This means that almost every single DNA base in the fruitfly is now known. This sequenced genome makes it possible to now hunt for the identity of DDT-R. Several groups were in the race to map and identify this gene, including the Berkeley team which sequenced the genome. The complexity of mapping an insecticide resistance trait made this task extremely difficult. However, using a rigorous mapping scheme involving a combination of resistance testing and molecular markers, the gene was eventually mapped by an international group of scientists from the University of Melbourne as well as universities and research institutes in the US, UK and France. Leading the study, which was published in the prestigious journal Science, was Dr Phil Daborn, a PhD graduate from the University of Melbourne and his mentor, Associate Professor Phil Batterham.