426 9.5  Extending Length and Time Scales to Quantum and Ecological Biophysics

carbon shell provides a magnetic shield from randomized external magnetic fluctuations

due to surrounding atoms, which would otherwise result in decoherence. So, currently, one

would sensibly conclude that the speculation of quantum entanglement in cryptochrome

molecule resulting in magnetoreception is interesting; however, the jury is definitely out!

9.5.2  FROM CELLS TO TISSUES

Although the tools and techniques of biophysics have contributed to many well-​documented

studies at the level of single cells, in terms of generating significant insight into a range of

biological processes when studied at the level of single, isolated cells, there is a paucity of reli­

able experimental data, which has the equivalent quality and temporal and spatial resolutions

of isolated single cells. This is true for prokaryotic single-​celled organisms such as bacteria,

but also single-​cell eukaryotic organisms such as yeast, as well as cultured single eukaryotic

cells from multicellular organisms. The latter includes cells that often appear to operate as

a single cell, for example, white blood cells called macrophages that are part of the immune

response and operate by engulfing foreign pathogen particles. But also, for isolated cells that

would normally be expressed among a population of other neighboring cells, such as in a

tissue or organ, both in the case of normal cells and for diseases such as probing cells inside

a cancer tumor.

This tight packing of cells is very important. Not only do cells experience chemical cues

from other surrounding cells but also often very complex mechanical signals. An equally

important point to note is that this is not just true for eukaryotic cells inside tissues/​organs of

complex multicellular organisms but also for microbial organisms such as yeast and bacteria

that are described as being “unicellular.” This is because although such cells exhibit stages in

their life cycles of being essentially isolated single cells, the majority of a typical cell’s life is

actually spent in a colony of some sort, surrounded in close proximity by other cells, often of

the same type though sometimes, as is the case in many bacterial biofilms, sharing a colony

with several different bacterial species.

Investigation of cellular biophysical properties but in the context of many other

neighboring cells presents technical challenges. The key biophysical techniques to use

involve optical microscopy, typically various forms of fluorescence imaging, and mech­

anical force probing and measurement methods, such as AFM. The challenge for optical

microscopy is primarily that of light microscopy imaging in “deep tissues,” namely, a het­

erogeneous spatial distribution in refractive index and increased scatter, photodamage,

and background noise. However, as discussed previously (see Chapter 3), there are now

technical strategies that can be applied to minimize these optical imaging issues. For

example, the use of adaptive optics to counteract optical inhomogeneity, and methods

such as multiphoton excitation fluorescence microscopy and light sheet imaging to

minimize background noise and sample photodamage. Even, in fact, standard con­

focal microscopy has several merits here, though it lacks the imaging speed required to

monitor many real-​time biological processes. Similarly, one of AFM imaging’s primary

technical weaknesses was in sample damage; however, with developments in “lighter

touch” torsional AFM imaging, this problem can be minimized.

Biofilms present a particularly challenging health problem when coupled to microbial

infection, in being very persistent due to their resistance against many antiseptic measures

and antibiotic treatments. These are particularly problematic for applications of medical

prosthetics, for example, infections on the surfaces of prosthetic joints and for regions of

the body where the inside and outside world collide, for example, urinary tract infections on

catheters and periodontitis in teeth and gums. One reason for this is that cells in the center

of a biofilm are chemically protected by the neighboring outer cells and by slimy glycocalyx

structures secreted by the cells. These are known as microbial extracellular polymeric

substances (EPS), but these can also combine to form a composite gel with extracellular

biopolymers such as collagen, which are produced by the host organism. This composite coat

allows small solutes and gases to permeate but which form an effective barrier against many

detergents, antiseptics, and antibacterial toxins such as antibiotics and also to penetration