Biophysical Journal Volume 110 March 2016 993–996 993

Cellular Biophysics

Rick Horwitz1,*
1
Allen Institute for Cell Science, Seattle, Washington

Cellular biophysics is the branch of biophysics that studies holds that the molecular components found periodically
cells from the perspective of a physicist or physical chemist along the muscle fiber slide to affect contraction (2).
by applying physical methods to interrogate cell structure
and function, and developing models of cells using physics
Microscopy: a major theme in cellular biophysics
and physical-chemical principles. Early on, biophysics was
usually practiced by physicists or other researchers with The organization and activities of cells are major themes in
physics-based training who had changed fields, but by the cellular biophysics, and studies have focused on observing
1960s many PhD programs in biophysics had been devel- complex structures inside cells, detecting cellular activities,
oped for undergraduate physics and physical-chemistry ma- and extending methods developed to study purified biolog-
jors wanting to study biology. ical molecules to microscope-based cellular measurements.
After World War II, biophysics in general got a lift from Microscopy, which functions across multiple scales of time
the field of radiation physics, which was trying to under- and spatial resolution, is at the center of these studies. The
stand the effects of radiation on life and genetic mutations. highly localized and often transient nature of cellular activ-
This came in the wake of H.J. Muller’s Nobel Prize studies ities is an overarching theme that has emerged from live-cell
showing that x rays induced mutations in Drosophila. microscopy and drives contemporary cellular biophysics.
Another major area of biophysics research focused on For example, some cellular receptors come together to
emerging structural methods such as x-ray diffraction, and form small bimolecular complexes when they become func-
spectroscopic methods such as fluorescence and magnetic tionally active. Analogously, many signals that regulate
resonance. This was the advent of the field of molecular cellular processes are generated from large molecular com-
biophysics, and these methods were used to determine the plexes that form transiently on scaffolds residing in specific
structures and functions of individual molecules and locations. These molecular interactions produce new struc-
contributed to the molecular biology revolution. tures that change conformations, produce new functions,
On the cellular side, however, there was great interest in or create more efficient organizations resulting in enhanced
the physiology of nerve and muscle cells, and understanding activity (3). On a larger spatial scale, cellular components
how molecular components drive cell function. Forces and are often organized into discrete, readily visible structures,
electrical activity are topics of great interest to physicists, often referred to as organelles or molecular machines. These
and biophysicists have played a major role in understanding large, identifiable molecular machines make proteins (ribo-
them in biological systems. Nerve cells propagate spikes in somes) generate energy (mitochondria), protect and regulate
electrical potential, called action potentials, across an indi- genetic material (nucleus), and cause cells to contract (acto-
vidual cell, and these signals transmit information from myosin filaments) (4). They also appear to occupy specific
one nerve cell to another nerve or muscle cell. These spikes regions and act transiently.
can be initiated by electrical or chemical stimuli and are One goal of contemporary cellular biophysics is to under-
measured using electrodes. This research culminated in a stand the molecular details of how cellular components
Nobel Prize to Alan Hodgkin, Andrew Huxley, and John organize to generate and regulate specific activities. Another
Eccles in 1963 (1). goal is to determine how all of these diverse cellular activ-
Muscles generate force through a mechanism involving ities and structures work together to produce characteristic
contraction of individual muscle cells. Our understanding and specialized cellular behaviors. Biophysicists are also
of this process has been greatly enhanced by detailed struc- developing mathematical and computational models that
tural studies of the organization of muscle cells using describe these cellular functions.
electron and light microscopy. Muscle cells form highly At present, microscopy is at center stage in the world
organized repetitive filamentous structures, and changes in of cellular biophysics, driven by the development of new
the spacing of these repetitive structures during contraction microscopic methods and fluorescence reagents specialized
form the basis of the sliding-filament hypothesis, which for cellular imaging. Recent advances in light microscopy
now allow us to view structures at previously unattainable
spatial and temporal resolutions, image live cells in tissues
Submitted November 4, 2015, and accepted for publication January 15, and animals, and visualize many colors (and thus different
2016. molecules) in the same measurement. Amazingly, new
*Correspondence: [email protected]
Ó 2016 by the Biophysical Society
0006-3495/16/03/0993/4 http://dx.doi.org/10.1016/j.bpj.2016.02.002
994 Horwitz

highly sensitive cameras even allow for the visualization of into the mechanisms of specific cellular processes, such as
individual molecules (5–9). Similar to advances in light cargo transport along microtubules (18). One goal is to
microscopy, improvements in electron microscope tomog- develop mathematical or computational models for indi-
raphy now allow us to see the molecular architecture of vidual cellular processes. These models could be based on
organelles in cells at a higher level of detail (10). Finally, detailed physical-chemical principles, as has been done
measurements can be made in living cells of molecular for some highly complex and integrated processes, such as
attributes, including concentration, binding affinities, and membrane protrusion and cytokinesis in vitro (19). They
diffusion and flow, which were previously studied by using could also be integrated whole-cell models, such as that
purified components in test tubes (11). All of these mea- described for the life cycle of a bacterium (20). The promise
surements provide data that can be used to develop and is that new methods in quantitative microscopy will provide
test theories and mathematical models for complex cellular better data, leading to models that are increasingly realistic
phenomena. and predictive.
New fluorescence reagents complement advances in The complexity of cells in terms of the numbers of
microscopy. They include genetically encoded tags that different molecular machines and regulatory complexes,
can be attached to biological molecules, as well as dyes and the numbers of molecules that comprise them, has
and other fluorescence reagents that localize to specific forced us to look at cells from the point of view of a single
cellular structures or sense biological activities, telling not or small group of molecules at a time. This approach has
only where a molecule or organelle is but also what it is do- been enormously productive, as each protein and complex
ing at that time. These reagents allow us to localize and of proteins becomes a source of fascinating new informa-
measure the positions and dynamics of molecules and the tion as we learn more. However, each molecular machine
complexes in which they reside, as well as when and where or complex is comprised of many molecules, each cell
cellular activities occur. has many different organelles and complexes, and there
Biosensors are another useful tool that was developed are many different kinds of cells, each exhibiting special-
to measure alterations driven by cellular processes. Fluores- ized behavior. In addition, tissues are comprised of many
cence changes are induced in biosensors when molecules different cell types working together. This integrative
come into close proximity or undergo a conformational behavior of cells is highly challenging and therefore
change (12,13). Similarly, optogenetic reagents allow per- largely uncharted territory.
turbations of cellular function with great spatial and tempo- The ever-growing complexity of understanding how cells
ral resolution (14). In contrast, other microscopic methods work at a molecular level is driving researchers to work more
probe the interaction of the cell with its exterior, sensing collaboratively and form multidisciplinary teams. Many
the forces that cells exert though their contacts with other areas of specialization are needed to understand cellular
cells or connective tissue components (15). functions and how they are altered by genetic and environ-
mental factors. New multidisciplinary groups and institutes
are being formed, and arguably the largest effort along this
Looking ahead
line is the Allen Institute for Cell Science, cofounded and
These are exciting times in cellular biophysics, and this era supported by Paul Allen, the cofounder of Microsoft.
of breathtaking progress and newly developed technologies The Allen Institute aims to develop predictive computa-
points to a bright future for the field. We now have tools to tional models of cell behaviors and how they respond to envi-
address questions that have lingered for decades, and recent ronmental and genetic alterations. In its initial project, the
findings are raising new questions that are moving science Institute is focusing on live-cell imaging and using genome
down important and unexpected paths. Imaging in particular editing of induced pluripotent stem cells (iPSCs) to measure
has benefited from significant advances, and our under- the locations and relative organization of cellular machinery,
standing of cellular organization and activities is becoming regulatory complexes, and activities, as well as the concen-
ever more refined and providing new insights into cellular trations and dynamics of key molecules. iPSCs proliferate
processes such as cell differentiation. The development of and can be induced to differentiate into different kinds of
biosensors that report the activities of various cellular ma- cells, including muscle, nerve, gut, and skin (Fig. 1). Using
chines and processes is still young, but these devices have genome editing, investigators can inactivate a gene or change
already revealed how the machinery of the cell is integrated, it by inserting either a mutation that mimics a disease or a
coordinated, and regulated (16). New genome-editing tech- fluorescence protein tag, which allows quantitative estimates
nologies are being used to introduce genetic tags to specific of molecular number. Once developed and characterized,
proteins using the cell’s own genome and regulatory appa- these cells will become a launch pad for the study of many
ratus, enabling researchers to obtain highly quantitative different cell types by members of the Institute and the
measurements regarding the numbers of proteins and organ- greater scientific community, to whom they will be distrib-
elles (17) present in a cell. Our ability to detect single uted freely. The goal is to measure the changes that occur
molecules has already provided highly detailed insights when cells execute their various activities, as well as when

Biophysical Journal 110(5) 993–996

Cellular Biophysics 995

FIGURE 1 A systems approach to meso- and nanoscale imaging and modeling. To see this figure in color, go online.

they differentiate into specialized cells and respond to ge- include the use of large-scale and integrative approaches,
netic and environmental alterations, including drug interven- such as looking at effects on several cellular components
tion. Investigators could then combine these measurements rather than a specialized one. The Institute will share data,
with other cellular data to develop computational models reagents, models, and tools openly with the community,
that predict cellular states and behaviors during homeostasis, and will focus on interdisciplinary team science with clear
regeneration, and disease. objectives and milestones.
To execute this program, the Institute will foster multidis- Cellular biophysicists are working toward understanding
ciplinary research, with a strong focus on physical methods cells as individuals and collectives, and how this drives
and approaches. This research will have a major biological tissue, organ, and organism functions. Such knowledge
component that includes the processing, genome editing, would help satisfy our innate human curiosity about
and differentiation of iPSCs. These cells will be used to un- how life works, and would also contribute significantly
derstand different cell states and how these states change as to regenerative medicine and disease therapies by eluci-
the cells execute their characteristic behaviors and respond dating tissue formation and identifying new therapeutic
to different environments. The Institute will incorporate en- targets.
gineering aspects by bringing its activities to large-scale, Cellular biophysics also drives innovation and economic
automating, and integrating methodologies, and undertak- growth. Efforts to understand the biology of the cell have
ing systems-level approaches. Physical science approaches driven the development of new technologies, including
will take center stage in the state-of-the-art microscopic two-photon, confocal, light-sheet, and superresolution
methods and biosensors that will be employed. Computa- microscopies. These technologies will greatly impact the
tional and mathematical modeling will benefit from theoret- pharmaceutical industry by advancing drug discovery and
ical physics, computer science, and applied math and improving diagnostic methodologies. Finally, the ability to
engineering approaches, as both systems- and physicochem- model the cell and its regulatory pathways, connecting
ical-level models will be employed. A novel product of the genomic, epigenetic, environmental, and other data with
project, an animated cell, will be a visual output designed to quantitative cellular data of the kind discussed here, holds
integrate image data and existing structural data, and will enormous predictive promise, leading to a computational
show the dynamic inner organization and workings of a ‘‘cell clinic’’ where one can query what the effects of
cell in unprecedented detail. It is also designed to integrate different alterations will be on cell and tissue function,
quantitative data on subcellular structures that can be visu- building on the premise that most disease originates from
alized together, allowing the viewer to see, both en groupe alterations in cell function.
and selectively, the relative positions of cellular structures
and activities.
ACKNOWLEDGMENTS
The Institute’s model for research is defined by attributes
that can be applied to similar ventures. These characteristics The author thanks Paul Allen for his vision and support.

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996 Horwitz

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