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Journal of Biotechnology 71 (1999) 225 – 228

Short communication

Single-cell models: promise and limitations
M.L. Shuler *
School of Chemical Engineering, Cornell Uni6ersity, Ithaca, NY 14853 -5201, USA
Received 11 October 1996; accepted 10 November 1998

This article describes the development of single-cell models, their uses and accomplishments, the barriers to the
greater adoption, and a perspective on challenges to the biochemical engineering community where the single-cell
model approach may be used advantageously. In particular, it may become an important tool in relating genomic
information to cellular regulation and dynamics. © 1999 Elsevier Science B.V. All rights reserved.
Keywords: Biochemical engineering; Cellular regulation; Genomic information; Single-cell models

1. Why single-cell models?
The cell, itself, is the biochemical reactor. The
engineer often faces the challenge of designing
macroscopic bioreactors, operating polices and
control strategies for the macroscopic reactor.
However, the engineer must recognize that the
macroscopic reactor only ‘houses’ the cellular
bioreactors; the reactions take place under the
control of the cell’s own internal regulatory system. Thus, the design of the macroscopic reactor
and its operating policy requires a quantitative
and explicit linkage between the abiotic and biotic
environment; between the macroscopic control
policy and the cellular regulatory system.
* Tel.: +1-607-255-7577; fax: + 1-607-255-1136.
E-mail address: (M.L. Shuler)

The development of a single-cell model is a
logical consequence of this perspective since it
allows the development of this linkage. The kernel
of the idea to formulate a single-cell model developed while I was a graduate student at Minnesota
from conversations with Arnie Fredrickson, John
Jost, Fred Bader, and Jim Drake. Many of these
conversations came from Arnie’s recognition of
the importance of structure in models.
Our first public discussion of the single-cell
model was in 1978 at an Engineering Foundation
Conference (see Shuler et al., 1979). Although a
number of attempts at single cells had been made
previously, ours was the first to explicitly link the
extracellular (abiotic) compartment with the cellular (biotic) compartment.
Single-cell models (Shuler, 1985) offer advantages due to:

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M.L. Shuler / Journal of Biotechnology 71 (1999) 225–228

(1) Explicit accounting for temporal events such
as cell cycle changes. Much of the cell’s regulatory
machinery must interact with the cell cycle engine.
(2) Explicit accounting of cell size and shape
which is related to physiological state; this feature
is particularly important during transient or unbalanced growth conditions.
(3) Explicit recognition of intracellular spatial
organization which is important when the rate of
transport between organelles is potentially ratelimiting.
(4) Providing a basis for non-segregated and
segregated models. If an ‘average cell’ can represent the whole population, then results of a SCM
run coupled with an idealized size distribution will
predict the population-average response. If we
need to explicitly consider the distribution of
properties among individuals (e.g. plasmid content), then we can use a finite-representation technique (Domach and Shuler, 1984b; Kim and
Shuler, 1990a). The use of a SCM coupled with a
finite-representation approach circumvents the
computational difficulties associated with the integral-differential equations resulting from population balance models with structured models of the
biotic phase.
Overall, the SCM approach is a very effective
tool to relate hypotheses about molecular level
mechanisms to whole cell and population response to changes in the local environment.

2. Some applications of the SCM approach
Listed below are some of the applications of the
SCM approach that have been pursued at
(1) Predicted cell geometry as function of
growth rate and limiting nutrient — confirmed afterward by experiments (Domach et al., 1984).
(2) Related molecular level stochastic changes
to imprecisions in cell cycle parameters and predicted correctly the relation of the cell cycle
parameters in progeny to parental cell cycle fluctuations (Domach and Shuler, 1984a).
(3) Predicted switching in metabolism/growth
rate to change from aerobic to anaerobic
metabolism (Ataai and Shuler, 1985a).

(4) Predicted, without adjustable parameters,
transient response of a population to changes in
flow rate or glucose levels in a chemostat (Ataai
and Shuler, 1985b).
(5) Predicted switching in growth-rate limiting
nutrient (glucose/NH4+ ) as dilution rate changed
(Lee et al., 1984).
(6) Simulated replication of ColE1 plasmids—
changes in copy number due to mutations or
changes in growth rate (Ataai and Shuler, 1986,
1987; Kim et al., 1987; Kim and Shuler, 1990a,b).
(7) Predicted under what circumstances plasmid
multimerization would alter genetic stability of a
construct (Kim and Shuler, 1991).
(8) Predicted that multiple steady states could
occur in NH4+ limited chemostats (Shu et al.,
(9) Predicted transient response in genetic stability to changes in flow rates in CFSTR (Kim
and Shuler, 1990a).
(10) Predicted that amino acid supplementation
would alter plasmid stability and that this effect
was not a growth rate effect (Shu and Shuler,
1991, 1992).
(11) Predicted effects of different mutations in
lac-type promoters (Laffend and Shuler, 1994b).
(12) Predicted ribosomal protein limitations in
r-protein synthesis—predicts observed maximum
in ribosomes/cell with intermediate plasmid copy
number (Laffend and Shuler, 1994a).
(13) Used S. cere6isiae model to design operating strategy for multimembrane reactor (Steinmeyer and Shuler, 1989, 1990).
(14) Predicted for CHO cells the glucose/glutamine usage and waste product formation (Wu et
al., 1992, 1993).
(15) Predicted transient response of CHO physiology to acid and alkaline loads (Wu et al.,
In addition, others have made use of SCM.
These include SCM for E. coli (Peretti and Bailey,
1986, 1987; Joshi and Palsson, 1987; Bentley and
Kompala, 1989), Bacillus sp. (Jeong and Ataai,
1990; Jeong et al., 1990), and non-CHO animal
cells (Batt and Kompala, 1989; Lee and Palsson,
1990); this list is not exhaustive. More recently
there has been a trend to build partial SCM that
incorporate in detail part of the intracellular

M.L. Shuler / Journal of Biotechnology 71 (1999) 225–228

metabolism (e.g. cell cycle machine without other
metabolic details or metabolic pathways without a
cell cycle engine). However, we and others have
found the SCM approach useful for engineering
design and/or insight into cellular mechanisms.
3. Limitations of the SCM approach
In spite of this record of accomplishment the
use of SCM has been limited. Such models are
complicated and must mirror the underlying biology faithfully. Typically one must understand the
biology at least one level deeper than the level in
the model, so that the modeler can logically make
the appropriate assumptions. In many cases a lack
of more detailed biological knowledge on the part
of the modeler is the barrier. In such cases close
collaboration of the modeler with a biologist is
essential to overcome the barrier.
The inherent complexity of a SCM also is inhibiting because the process of independently estimating model parameters is often time-consuming
and labor intensive. Here, advances in instrumentation (flow cytometry, HPLC, 2-D electrophoresis, NMR, etc.) may assist in providing
simultaneously measurements of ‘all’ intracellular
concentrations of interest under known culture
conditions. Measurements under at least two
growth conditions would provide the basis for
estimating most parameters.
Another consequence of complexity is that
SCM (especially population models using the
finite-representation technique) are computationally intensive. The models are too slow for some
applications, such as on-line control. However,
the rapid increase in availability of inexpensive
computing power will increasingly reduce the seriousness of this barrier.
Another barrier is often lack of familiarity and
comfort with the technique. Although students
are often exposed to the existence of the SCM
approach, it is usually too complex for serious use
by students. Dr Gary Stanlake worked with us to
develop a classroom version (Stanlake and Shuler,
1996) to be used for instructional purposes by
biology students. There is likely an opportunity
for its use in the instruction of biochemical engineering students.


4. Some challenges/opportunities
The tools of genome analysis are making available to us the full genetic sequence of an increasingly large number of organisms. A philosophy of
‘genetic determinism’ has developed where ‘if you
know the gene, all else follows’. Yet, cells exist
with hierarchical regulatory systems that can often compensate for genetic deletions or miscues.
The interaction of this epigenetic, or regulatory
network, with the genome is not understood. The
interaction must be quantitative and involves interlocking, non-linear systems. Could SCM be
used in developing techniques to relate genetic
knowledge into physiology (e.g. functional genetics)? Would it be worth building a ‘complete’ E.
coli model as a prototype of an approach to the
problem of relating the genome to cell physiology? These are challenging problems, but it is
difficult to imagine a more important problem for
modelers. A successful project responsive to these
challenges would be a fitting successor and tribute
to the work of Arnie Fredrickson.

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M.L. Shuler / Journal of Biotechnology 71 (1999) 225–228

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