Chapter 7 – Complementary Experimental Tools  273

methods using an invaluable technique of optogenetics, which can use light to control the

expression of genes (see later in this chapter). At the time of writing, C. elegans is the only

organism for which the connectome (the wiring diagram of all nerve cells in an organism) has

been determined.

The relative optical transparency of these organisms allows standard bright-​field light

microscopy to be performed, a caveat being that adult zebrafish grow pigmented stripes

on their skin, hence their name, which can impair the passage of visible light photons.

However, mutated variants of zebrafish have now been produced in which the adult is

colorless.

Among invertebrate organisms, that is, those lacking an internal skeleton, Drosophila

melanogaster (the common fruit fly) is the best studied. Fruit flies are relatively easy to culti­

vate in the laboratory and breed rapidly with relatively short life cycles. They also possess

relatively few chromosomes and so have formed the basis of several genetics studies, with

light microscopy techniques used to identify positions of specifically labeled genes on isolated

chromosomes.

For studying more complex biological processes in animals, rodents, in particular

mice, have been an invaluable model organism. Mice have been used in several biophys­

ical investigations involving deep tissue imaging in particular. Biological questions involving

practical human biomedicine issues, for example, the development of new drugs and/​or

investigating specific effects of human disease that affects multiple cell types and/​or multiply

connected cells in tissues, ultimately involve larger animals of greater similarity to humans,

culminating in the use of primates. The use of primates in scientific research is clearly a chal­

lenging issue for many, though such investigations require significant oversight before being

granted approval from ethical review committees that are independent from the researchers

performing the investigations.

KEY POINT 7.3

A “model organism,” in terms of the requirements for biologists, is selected on it

being genetically and phenotypically/​behaviorally very well characterized from pre­

vious experimental studies and also possesses biological features that at some level

are “generic” in allowing us to gain insight into a biological process common to many

organisms (especially true for biological processes in humans, since these give us

potential biomedical insight). For the biophysicist, these organisms must also satisfy an

essential condition of being experimentally very tractable. For animal tissue research,

this includes the use of thin, optically transparent organisms for light microscopy. One

must always bear in mind that some of the results from model organisms may differ

in important ways from other specific organisms that possess equivalent biological

processes under study.

7.4  MOLECULAR CLONING

The ability to sequence and then controllably modify the DNA genetic code of cells has

complemented experimental biophysical techniques enormously. These genetic technologies

enable the controlled expression of specific proteins for purification and subsequent in vitro

experimentation as well as enable the study of the function of specific genes by modifying

them through controlled mutation or deleting them entirely, such that the biological function

might be characterized using a range of biophysical tools discussed in the previous experi­

mental chapters of this book. One of the most beneficial aspects of this modern molecular

biology technology has been the ability to engineer specific biophysical labels at the level of

the genetic code, through incorporation either of label binding sites or of fluorescent protein

sequences directly.

KEY BIOLOGICAL

APPLICATIONS: MODEL

ORGANISMS

Multiple biophysical

investigations requiring tractable,

well-​characterized organism

systems to study a range of bio­

logical processes.