270 7.3  Model Organisms

New variants of aptamers have now been developed which can directly label RNA in live

cells using a bright organic dye called (4-​((2-​hydroxyethyl)(methyl)amino)-​benzylidene)-​

cyanophenylacetonitrile (HBC) bound to the aptamer. The size of these aptamers is around

the same as that of fluorescent proteins, hence resulting in far less steric impairment of bio­

logical functional compared to antibody labeling. Aptamers can be genetically encoded into

RNA transcripts, though a weakness with the approach still is that the HBC dye must be

introduced into the cell by permeabilizing its membrane, which has some functional impair­

ment and imparts some limitation on the extent of maximum labeling possible for cel­

lular RNA.

7.3  MODEL ORGANISMS

Technical advances of light microscopy have now enabled the capability to monitor whole,

functional organisms (see Chapter 3). Biophysics here has gone full circle in this sense, from

its earlier historical conception in, in essence, physiological dissection of relatively large

masses of biological tissue. A key difference now, however, is one of enormously enhanced

spatial and temporal resolution. Also, researchers now benefit greatly from a significant

knowledge of underlying molecular biochemistry and genetics. Much progress has been

made in biophysics through the experimental use of carefully selected model organisms

that have ideal properties for light microscopy in particular; namely, they are thin and rea­

sonably optically transparent. However, model organisms are also invaluable in offering the

researcher a tractable biological system that is already well understood at a level of biochem­

istry and genetics.

7.3.1  MODEL BACTERIA AND BACTERIOPHAGES

There are a few select model bacteria species that have emerged as model organisms.

Escherichia coli (E. coli) is the best known. E. coli is a model Gram-​negative organism (see

Chapter 2) whose genome (i.e., total collection of genes in each cell) comprises only ~4000

genes. There are several genetic variants of E. coli, noting that the spontaneous mutation rate

of a nucleotide base pair in E. coli is ~10⁻⁹ per base pair per cell generation, some of which

may generate a selective advantage for that individual cell and so be propagated to subse­

quent generations through natural selection (see Chapter 2). However, there are in fact only

four key cell sources from which almost all of the variants are in use in modern microbiology

research, which are called K-​12, B, C, and W. Of these, K-​12 is mostly used, which was ori­

ginally isolated from the feces of a patient recovering from diphtheria in Stanford University

Hospital in 1922.

Gram-​positive bacteria lack a second outer cell membrane that Gram-​negative bacteria

possess. As a result, many exhibit different forms of biophysical and biochemical interactions

with the outside world, necessitating a model Gram-​positive bacterium for their study. The

most popular model Gram-​positive bacterium is currently Bacillus subtilis, which is a soil-​

dwelling bacterium. It undergoes an asymmetrical spore-​forming process as part of its normal

cell cycle, and this has been used as a mimic for biochemically triggered cell shape changes

such as those that occur in higher organisms during the development of complex tissues.

There are many viruses known to infect bacteria, known as bacteriophages. Although,

by the definition used in this book, viruses are not living as such, they are excellent model

systems for studying genes. This is because they do not possess many genes (typically only

a few tens of native genes), but rather hijack the genetic machinery of their host cell; if this

host cell itself is a model organism such as E. coli, then this can offer significant insights into

methods of gene operation/​regulation and repair, for example. The most common model

bacterium-​infecting virus is called “bacteriophage lambda” (or just lambda phage) that

infects E. coli. This has been used for many genetics investigations, and in fact since its DNA

genetic code of almost ~49,000 nucleotide base pairs is so well characterized, methods for its

reliable purification have been developed, and so there exists a readily available source of this