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Biophys J, July 2002, p. 161-171, Vol. 83, No. 1
School of Molecular and Microbial Biosciences, University of Sydney, New South Wales 2006, Australia
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ABSTRACT |
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The pulsed field-gradient spin-echo (PGSE) nuclear magnetic resonance (NMR) experiment, conducted on a suspension of red blood cells (RBC) in a strong magnetic field yields a q-space plot consisting of a series of maxima and minima. This is mathematically analogous to a classical optical diffraction pattern. The method provides a noninvasive and novel means of characterizing cell suspensions that is sensitive to changes in cell shape and packing density. The positions of the features in a q-space plot characterize the rate of exchange across the membrane, cell dimensions, and packing density. A diffusion tensor, containing information regarding the diffusion anisotropy of the system, can also be derived from the PGSE NMR data. In this study, we carried out Monte Carlo simulations of diffusion in suspensions of "virtual" cells that had either biconcave disc (as in RBC) or oblate spheroid geometry. The simulations were performed in a PGSE NMR context thus enabling predictions of q-space and diffusion tensor data. The simulated data were compared with those from real PGSE NMR diffusion experiments on RBC suspensions that had a range of hematocrit values. Methods that facilitate the processing of q-space data were also developed.
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INTRODUCTION |
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Pulsed magnetic field-gradients can be used in
nuclear magnetic resonance (NMR) experiments to encode spatial
information in spin-magnetization to measure positional displacement.
The analogy of the resulting spatial coherences seen in NMR data to optical diffraction was first pointed out by Mansfield and Grannell (1973)
. Cory and Garroway (1990)
showed that pulsed field-gradient spin-echo (PGSE) NMR diffusion measurements in heterogeneous systems can be used to obtain a displacement profile of molecules in a liquid,
allowing the delineation of features of compartments too small to be
observed using conventional NMR imaging. Callaghan et al. (1991)
demonstrated interference-like effects in PGSE NMR diffusion studies of
fluids in porous media and recently reviewed the spatial coherence
phenomena arising from these experiments (Callaghan et al., 1999
). We
have conducted PGSE NMR diffusion studies of red blood cell (RBC)
suspensions and showed that diffusion-diffraction and
diffusion-interference of water occurs; this was used to show the
alignment of RBC in the static magnetic field of the spectrometer and
to estimate cell dimensions, detect shape changes with time, and to
estimate membrane transport characteristics (Kuchel et al., 1997
, 2000
;
Torres et al., 1998
, 1999
). It has been independently demonstrated that
RBC align in a strong magnetic field with their disc planes parallel to
the magnetic field (Higashi et al., 1993
) so this was important in the
design of the diffusion-simulation models used herein (see Materials
and Methods).
Diffraction-like effects from PGSE NMR diffusion experiments can be
visualized by plotting the relative signal intensities as a function of
the spatial wave vector q, where q = (2
)
1
g
,
and where
is the magnetogyric ratio of the observed nucleus, g is the magnetic field gradient, and
is the duration of each of the magnetic field-gradient
pulses used in the experiment. The resulting graph (q-space
plot), from an RBC suspension consists of a series of maxima and minima
whose positions in q space can be related to average cell
dimensions and the average spacing of the extracellular cavities or
"pores" (Torres et al., 1998
, 1999
). The positions of these
features may also change when there is a change in the rate of exchange
of diffusant across the cell membrane (Kuchel et al., 1997
).
We have previously used simulations of diffusion in an RBC suspension,
in the PGSE NMR context, to aid in the assignment of q-space
features to particular modes of diffusion (Torres et al., 1999
). Here
we extend this work and demonstrate that these simulations provide
further insights that are useful for the interpretation of
q-space and diffusion tensor data from RBC suspensions.
Specifically, we show that the q-space and diffusion tensor
data contain information relating to the packing density of the cells
in a suspension and the mean cell geometry. This study, therefore,
extends the methodology and concepts used in interpreting data from
PGSE NMR diffusion experiments on RBC suspensions and potentially in
analogous cellular systems.
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MATERIALS AND METHODS |
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Simulations
Individual computer models were developed to simulate diffusion
in a suspension of biconcave discs (Program I), and to simulate diffusion in a suspension of oblate spheroids (Program II). (All programs described in this report may be obtained from DGR at d.regan{at}mmb.usyd.edu.au.) These models enable the simulation of diffusion during a standard PGSE NMR experiment (Kuchel et al., 1997
;
Torres et al., 1998
) and produce an array of signal intensities corresponding to the respective field gradient strengths specified for
a simulated experiment.
The programs use a Monte Carlo technique to simulate diffusion in a
three-dimensional (3D) hexagonal lattice of "virtual" cells (see
Fig. 1) as described previously (Lennon
and Kuchel, 1994a
,b
; Torres et al., 1998
). The uniform arrangement of
virtual cells in a hexagonal lattice, having an order parameter of
unity, is justified on the basis that real RBC align in the magnetic field, and that it was the intention to design a canonical pure system
to form the basis of the interpretation of experimental q-space data (see Discussion).
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Simulations were performed for ensembles of up to 108 noninteracting point molecules on a 64 processor SGI Origin 2400 supercomputer (APAC National Facility, Australian National Univ., Canberra, Australia). The intrinsic ensemble nature of the calculations allowed ensembles to be split into smaller "packets" of ~200,000 point-molecule trajectories, which could be distributed across multiple processors. In this way the parallel capability of the supercomputer was used. When the full complement of trajectories was completed, the results were summed and averaged.
The simulations were of diffusion in a 3D hexagonal lattice of cells
having either biconcave disc (Fig.
2 A) or oblate spheroid (Fig.
2 B) geometry. The analysis was expedited by invoking a "unit cell," consisting of a regular hexagonal prism containing a
cell, centered on the Cartesian origin, and applying periodic boundary
conditions, thereby simulating an infinite tessellation. (In all
simulations and experiments discussed in this report, a Cartesian
coordinate system was used such that the z axis was aligned
with the static magnetic field, B0, of
the NMR spectrometer.) A random number generator and a random
binary-digit generator were used to determine a random starting
position for the trajectory of each point molecule (Regan and Kuchel,
2000
). The same random number and random binary-digit generators were used to test for membrane transition and to choose random jump directions, respectively.
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The biconcave disc in Program I was represented by a degree-4 equation
in Cartesian coordinates (Kuchel and Fackerell, 1999
). The shape of the
biconcave disc (Fig. 2 A) was defined by the three
parameters: b, thickness in the dimpled region;
h, maximum thickness; and d, main diameter, whose
respective values of 1.0 × 10
6 m,
2.12 × 10
6 m, and 8.0 × 10
6 m were assigned to closely approach the
shape of human RBC and to yield the known mean volume of human RBC of
8.6 × 10
17 m3 (Dacie and Lewis, 1975
). The points of intersection of point-molecule trajectories with the biconcave disc were calculated using a
Newton-Raphson algorithm (Regan and Kuchel, 2000
).
The oblate spheroid used in Program II is described by the function
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(1) |
is a constant (Moon and Spencer,
1988
were calculated,
as functions of the specified values for the oblate spheroid semi-axes,
using the formulae
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(2) |
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(3) |
6 m, 2.0 × 10
6 m, and 8.0 × 10
6 m, respectively. These values were chosen
to match the overall dimensions of the biconcave disc but yielded a
smaller volume of 6.7 × 10
17 m3.
Another characteristic of a virtual cell that is useful for
interpreting PGSE NMR data is the mean barrier separation in the cell.
This value was calculated for both cell types in the x, z, and y directions. The calculation was
performed by assigning a random coordinate inside the cell and
calculating the length of the chord, in the relevant direction
(x, z, or y), that intersected this
point. This process was repeated for 107 random
coordinates and the average chord length calculated. The mean barrier
separation in the x, z, and y
directions for the biconcave disc and the oblate spheroid were 5.8 × 10
6 m, 5.8 × 10
6 m, and 1.8 × 10
6 m, and 6.0 × 10
6 m, 6.0 × 10
6
m, and 1.5 × 10
6 m, respectively.
For each cell type, the following simulations were performed: diffusant (water) confined by an impermeable membrane to the intracellular space; diffusant confined by an impermeable membrane to the extracellular space, and packing density or hematocrit (Ht, the volume fraction of the unit cell that is occupied by a cell) set to either 0.3, 0.4, or 0.5; and diffusant in both the intracellular and extracellular spaces and able to exchange through a semi-permeable membrane, with hematocrits (Ht) set to 0.3, 0.4, or 0.5.
Intracellular (Din) and extracellular
(Dout) diffusion coefficients were
assigned values of 1.6 × 10
9
m2s
1 and 8.0 × 10
10
m2s
1, respectively, in
accordance with preliminary estimates we have obtained experimentally
(using standard PGSE NMR methods) for water in human RBC suspensions.
The length of a jump, s, was calculated using the Einstein
diffusion equation (Tanford, 1961
),
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(4) |
5
m s
1 as has been determined experimentally for
human RBC (Benga et al., 1990We have previously demonstrated that the probability of transition
across the membrane (tp) when the membrane is intersected by
a point-molecule trajectory, in the context of the simulations described here, is related to s (jump length) and
Pd by (Regan and Kuchel, 2000
)
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(5) |
The parameter values for the simulations were chosen to be identical to
those used for the PGSE NMR experiments on RBC suspensions described in
the Results. The PGSE NMR parameters for all simulations were as
follows: field-gradient pulse duration,
= 2 ms; time interval separating field-gradient pulses,
= 20 ms; the
magnitude of the field-gradient, g, was sequentially
incremented in 96 steps from 0.0 to 9.9 T m
1;
proton magnetogyric ratio,
= 2.675 × 108 radian T
1. The phase
shifts accumulated during the total diffusion time (
+
) for all point-molecule trajectories were summed and averaged, and
the signal intensity calculated for each value of g.
It has been shown that magnetic susceptibility differences between the
interior and exterior of oxygenated or carbonmonoxygenated RBC in a
suspension are negligible (Endre et al., 1984
). Hence the model did not
incorporate differences in PGSE signal intensity that might ordinarily
be expected to occur in a system that is heterogeneous in magnetic
susceptibility and hence magnetic field.
PGSE NMR experiments
PGSE NMR diffusion experiments were conducted on RBC suspensions
having HT values of 0.2, 0.3, 0.4, 0.5, and 0.6. The general methods
(pulse sequences, etc.) used for conducting these experiments and for
preparing RBC suspensions were as described previously (Kuchel et al.,
1997
; Torres et al., 1998
, 1999
).
The experiments were conducted at 298 K on a Bruker AMX400 spectrometer
(Karlsruhe, Germany) with an Oxford Instruments 9.4 T vertical
wide-bore magnet (Oxford, UK), using a Bruker 10 T m
1, z-axis gradient-diffusion
probe. Identical pulse-sequence parameters were used for all
experiments as follows: field-gradient pulse duration,
= 2 ms; time interval separating gradient pulses,
= 20 ms; 32 transients per spectrum. The magnitude of the field-gradient was
incremented from 0.001 to 9.9 T m
1 in 32 equal
steps. (Unless the first spectrum [corresponding to the smallest field
gradient] was acquired with a small nonzero gradient, its phase was
substantially different from the rest in the series; therefore a value
close to zero (0.01 T m
1) was used.) The
gradients were calibrated using the known diffusion coefficient of
water in an isotropic and unbounded region (Mills, 1973
).
The signal intensity was measured as the integral of the water resonance after automatic phase and baseline correction. Signal intensities were normalized with respect to that of the first spectrum before q-space analysis (see Data Analysis).
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Data Analysis |
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q-Space analysis
q-Space plots were generated using both Origin (Microcal Software, Northampton, MA) and MATLAB (The Mathworks, Natick, MA) from simulated or experimental PGSE NMR data by plotting the normalized signal intensities as a function of the magnitude of q. A semi-logarithmic scale (logarithmic in the ordinate) was used to improve visualization of the features (maxima and minima) of the plots. Further enhancement was achieved by either applying a cubic spline to the data, or fitting a polynomial and interpolating points to increase their number from 96 to 1000. Simulated data invariably contained negative values at the extreme minimal intensities (see Discussion for an explanation of this phenomenon); these points could not be plotted on a logarithmic scale and thus resulted in gaps in the plots (see Figs. 3-6). A combination of methods was used to determine, as precisely as possible, the positions of maxima and minima in q-space plots (the reciprocals of which correspond to mean dynamic displacements). Maxima and minima were determined, to a first approximation, by reading the values directly from the plot using the tools available in the respective plotting programs (Origin or MATLAB). This was not possible when data points were missing in semi-logarithmic plots due to negative signal intensities. This problem was obviated by replotting the absolute values of the signal intensities, again on a semi-logarithmic scale, so that regions containing negative values appeared as inverted peaks with q values that could be readily determined. Maximum and minimum values were then more closely pinpointed by aligning the putative values with maxima and minima in the plots of the first and second derivatives of the data (generated in MATLAB). In most cases, it was possible to determine accurately the positions of at least the first two maxima and minima (see Error Analysis). This method can be applied in the analysis of q-space data for diffusion along any axis but was carried out here for diffusion in the z direction only.Diffusion tensor calculations
A program was written in MATLAB to calculate the terms of the diffusion tensor from PGSE NMR data (either real or simulated) according to the method of Kuchel et al. (2000)Fourier transform analysis
The Fourier transform of q-space data is, in most cases, approximately Gaussian (see Discussion) and thus yields an approximation of the translational displacement probability (Cory and Garroway, 1990
w1/2, of the peak in the Fourier transform plot can therefore be related to the effective root mean
square displacement (RMSD),
, by (Bailey, 1995
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Error analysis
Both linear and nonlinear regression analyses were conducted in Origin and MATLAB. Error analysis of q-space plots, as it affects the estimation of critical values of q and their uncertainty, is influenced by two factors: the intrinsic signal-to-noise of the NMR spectra, and the resolution in q that is determined by the interval between q values, that are under experimental control. This matter has been discussed previously (Torres et al., 1999| |
RESULTS |
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General
In this study, we conducted simulations of diffusion in lattices of virtual cells having either biconcave disc or oblate spheroidal geometry. Simulations were conducted under two conditions: water confined to the intra- and extracellular spaces in the absence of exchange, and water exchanging between the intra- and extracellular regions at a rate that was determined by Pd = 6.1 × 10
5 m s
1. In all
cases, except where water was confined to the intracellular region,
simulations were conducted at Ht values of 0.3, 0.4, and 0.5. In
addition, a series of PGSE NMR experiments were conducted on real RBC
suspensions at Ht values of 0.2, 0.3, 0.4, 0.5, and 0.6, at 298 K. To
facilitate comparisons with real data sets, the simulation parameters
were chosen to be identical to those used in the real experiments.
Simulations: exchange off
Intracellular diffusion
The q-space plots for simulation of diffusion of water inside biconcave discs and oblate spheroids (no exchange across the membrane) are shown in Fig. 3. Signal intensities at given values of q were initially higher for the oblate spheroid but were lower for the second and subsequent peaks. The apparent diffusion coefficients (Dapp), estimated from diffusion tensor analysis (see Table 1), were smaller for the oblate spheroid than for the biconcave disc in each of the respective x, y, and z directions. For each cell type individually, however, the apparent diffusion coefficients measured in the x and z directions were identical within the stated error range. A similar trend was observed for the RMSD calculated from the Fourier transform of the q-space data (see Table 2): RMSD values were smaller for the oblate spheroid than for the biconcave disc in their respective directions and, in each case, had virtually identical values in the x, z, and xz directions as anticipated. The smallest values of Dapp and RMSD for both cell types were observed in the y direction. The critical values in q space are given in Table 3. Although the relevant values in this case are the minima, which we have previously shown can be related to mean cell dimensions (Benga et al., 2000
1),
but there was no significant difference in the positions of the second
minimum.
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Extracellular diffusion
Figure 4 shows the q-space plots for diffusion of water in the extracellular region of suspensions of oblate spheroids (A) and biconcave discs (B) at Ht values of 0.3, 0.4, and 0.5. The figure illustrates two important features: a shift in the positions of the peaks to higher q values as Ht was increased and, with respect to the first peak, higher signal intensities as Ht was increased. Table 3 confirms the shift to higher q values (smaller dynamic displacements) as Ht is increased; in this case, the relevant values are the positions of the maxima because we have shown these to be related to the mean spacing of cells in the suspension (Torres et al., 1999
1) were
higher for the biconcave discs than for the oblate spheroids. The
apparent diffusion coefficients (Table 1) decreased as Ht was increased
and, although of similar magnitude for both cell types in the
x and z directions (when associated errors were
considered), they were larger for the biconcave discs in the
y direction. RMSD values (Table 2) were similarly decreased
with increasing Ht and were of generally larger magnitude for the
biconcave discs.
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Simulations: exchange on
The results of simulations in which water was diffusing in
both the intra- and extracellular regions and exchanging across the
membrane are shown in Fig. 5. Signal
intensities at given q values became larger as Ht was
increased, and the pore-hopping shoulder (in the region of
q = 0.75 × 105
m
1) shifted to higher q values
and became less pronounced.
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q-Space plots for the two cell types when the diffusion was
measured in the x, y, and z directions
are compared in Fig. 6. Points to note
are: 1) the overall increase in signal attenuation at given
q values for the oblate spheroid relative to the biconcave disc; 2) a shift in the positions of coherence maxima to higher q values for the oblate spheroid; 3) a much lesser degree of
signal attenuation, for a given q value, in the y
direction than in the x and z directions for both
cell types; and 4) the appearance of some additional critical points
(Fig. 6 A, q = 2.3 × 105 m
1 and 4.2 × 105 m
1, and relative to
Fig. 6 C) in the plots for the x direction, which were otherwise very similar to those for the z
direction for both cell types.
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The apparent diffusion coefficients estimated from the diffusion tensor analysis (Table 1) decreased with increasing Ht. In the x and z directions, Dapp values were virtually identical for both cell types but were larger for the biconcave disc in the y direction. In contrast, RMSD values (Table 2) were higher for the oblate spheroid than for the biconcave disc at equivalent Ht values. However, the same trend of decreasing RMSD with increasing Ht was observed for both cell types. Although no clear trend was evident in the positions of the first two diffraction minima (q1,min and q2,min) for either cell type, the positions of the pore-hopping shoulder (q1,max) corresponded to smaller dynamic displacements as Ht was increased and the respective values were smaller for the biconcave disc than for the oblate spheroid.
PGSE NMR experiments
The q-space plots of the PGSE NMR data obtained from
real RBC suspensions are shown in Fig. 7.
These plots illustrate two very clear results: signal intensities
decreased at a given q value with decreasing Ht, and the
point of inflection discernible at q = ~1.0 × 105 m
1 was more
pronounced at lower Ht.
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Note that the high-power diffusion probe used in these experiments only allowed for the application of the magnetic field gradient coaxially with the static field (i.e., in the z direction). This limitation precluded the calculation of a diffusion tensor because this requires the gradient to be applied in at least six directions. In addition, the gradient values used in the experiment were restricted to a range over which it was possible to obtain sufficient signal-to-noise. Although it was possible to observe higher-order coherences with higher gradients, estimation of displacements from the data became increasingly error prone.
Fourier transform analysis of these data (Table 2) clearly showed that
as Ht was increased the values of RMSD decreased. The relationship
between RMSD and Ht was remarkably linear as evidenced by linear
regression onto the data, which yielded the expression RMSD = (1.70 ± 0.02) × 107
((1.20 ± 0.05) × Ht), with a correlation coefficient of
0.99. However,
dynamic displacements calculated from q-space data were difficult to determine using the analytical methods that have been
developed so far, and no clear trends were apparent in the values
estimated. Although the dynamic displacements corresponding to
q1,min,
q1,max, and
q2,max were smaller than the
corresponding values for the simulated data from biconcave discs and
oblate spheroids, they were of comparable magnitude.
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DISCUSSION |
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Simulations: exchange off
We have considered two cases of simulation in which exchange across the membrane was prevented by setting Pd to zero. The first case was where the diffusant (water) inside the cells alone was studied. The second case was where the diffusant in the extracellular region alone was studied. In the latter case, simulations were conducted at three Ht values, 0.3, 0.4, and 0.5.
Intracellular diffusion
Figure 3 illustrates that overall signal attenuation (for diffusion in the z direction) for the oblate spheroid was greater than for the biconcave disc despite having a smaller volume, identical main-axis dimensions, and larger mean barrier separation in this direction. This seemingly counterintuitive result can be explained in terms of the shape of the biconcave disc. It has inward protrusions at its center that have a closest approach of 1 × 10
6 m constituting a kind of bottleneck
restriction to diffusion in the z direction. In the initial
part of the q-space curve in Fig. 3, the signal intensity is
higher for the oblate spheroid than for the biconcave disc; and it was
this region of the curve that was used for diffusion tensor analysis.
Consequently, the apparent diffusion coefficients calculated using this
method (Table 1) appear to be inconsistent with the result just
described, i.e., the Dapp values are
smaller for the oblate spheroid than for the biconcave disc. For both
cell types individually, these values were the same in the x
and z directions, reflecting the fact that, in these
directions, their dimensions are identical, and much lower in the
y direction, which is the direction in which diffusion was
most restricted. The smaller volume occupied by the oblate spheroid is
reflected in the smaller RMSD values (Table 2) with identical values
recorded for both cell types individually in the x,
z, and xz directions, in which the dimensions
were identical. The critical q values (Table 3) in this case
are the minima (q1,min and
q2,min) which are related to cell
dimensions. Although both cell types had identical dimensions in the
z direction, and the positions of
q2,min did indeed yield identical
estimates of the dynamic displacements, the positions of
q1,min were not identical and suggest
a smaller effective mean dimension in the z direction for
the oblate spheroid than for the biconcave disc. These and the RMSD
values reflect the fact that, although both cell types had identical
main dimensions in x and z directions, their
shapes and hence their mean dimensions along these axes were not identical.
Extracellular diffusion
The greater degree of signal attenuation that accompanied a decrease in Ht (see Fig. 4) was consistent with the notion that, as the compartment bounding the diffusant becomes less confining, the apparent diffusion coefficient will become larger, resulting in a more rapid attenuation of the signal in the PGSE NMR experiment. Table 1 shows that, as Ht was lowered, the apparent diffusion coefficient in the x, y, and z directions (as estimated by diffusion tensor analysis), increased for both cell types. Predictably, a decrease in Ht, and hence an increase in Dapp, gave rise to an increase in the RMSD calculated from the Fourier transform of the corresponding q-space plots (Table 2). Slightly higher values of RMSD estimated for the biconcave disc in most directions highlights the fact that, at equivalent Ht values, there was a greater volume available to the diffusant in this suspension because the volume of each biconcave disc was greater. The few exceptions to this observation, revealed by careful comparison of the data, are attributed to differences in the cell shapes that, in turn, give rise to differently shaped pores in the extracellular region. The observation that, for both biconcave discs and oblate spheroids, the signal intensity at a given q value in the second peak of the q-space plot increased as Ht was decreased (i.e., opposite to the anticipated result that is observed for the first peak) is explained as follows. The position of the second peak results from a second-order effect i.e., displacement of molecules between next-nearest neighboring pores. At lower Ht values, the RMSD is larger so there is a higher probability of displacement occurring into these pores (in the observation time of the experiment) than for a higher Ht. The number of spins giving rise to this signal at low Ht will consequently be larger than the number at a higher Ht. Thus, the resulting signal intensity will be relatively higher (i.e., relative to that at higher Ht) than for diffusion between the first coordination layer of cells. The data in Tables 1 and 2 indicate that, for the oblate spheroids, the effect of changing Ht is more dramatic for diffusion measured in the y direction than in other directions (particularly those not containing a y component). The y direction is orthogonal to the disc planes of the virtual cell and is therefore the most confining for the diffusant. Therefore, it is anticipated that relaxing the impediment to diffusion in this direction (by reducing Ht) will have a dramatic effect on the estimated apparent diffusion coefficient and thus the RMSD. This effect is less dramatic for the biconcave disc, and the reason for this can be understood as follows: The dimpled regions of the biconcave disc result in diffusion orthogonal to the disc planes being, on average, less restricted than for oblate spheroids. Hence, the effect on the RMSD of increasing the distance between the discs is less dramatic with biconcave discs. We noted above that the critical values in the q-space plots, in this case, the pore-hopping maxima q1,max and q2,max, are related to the spacing of the major extracellular pores in the array. As Ht was increased, the q values of these critical points would be expected to become larger (and their reciprocal values, the dynamic displacements, become smaller), and this was indeed the case (Table 3). A larger q value corresponds to a smaller dynamic displacement, and, as Ht was increased (i.e., the hexagonal prism containing the unit cell was made smaller), the distance between the centers of adjacent pores became smaller. The hexagonal prism enclosing the biconcave disc was larger than that for the oblate spheroid because the volume of the cell was larger. This explains the slightly larger dynamic displacements observed for the biconcave disc. For the oblate spheroid, the scaling factors relating the position of q

Simulations: exchange on
The simulations of diffusion involved identical systems to those described in the section above, but they were conducted with exchange occurring between the intra- and extracellular regions. Molecules were assigned initial coordinates either inside or outside the virtual cell in a random manner, with a distribution (inside or outside) that was determined by the Ht. One measure of the robustness, or reproducibility, of these simulations was that, at a given Ht, the final distribution of point molecules between the intra- and extracellular spaces did not change to a statistically significant extent from the initial distribution.
Relative to the simulations of diffusion in which exchange was absent, decreasing the Ht resulted in a greater degree of signal attenuation with increasing q value (Fig. 5). Again, this is attributable to the diffusant in the extracellular region being less restricted as the spacing between the cells was increased. This observation is reinforced by the estimates of the Dapp and RMSD values, which, without exception, increased with decreasing Ht (Tables 1 and 2). It is also notable that the pore-hopping shoulder was more pronounced at lower Ht values as a result of the proportionally increased contribution to the signal from the extracellular water. The additional critical points observed in Fig. 6 A arise from the fundamentally different topological arrangement of pores and cells in a hexagonal array when projected in the x and z directions.
The data in Table 2 show that RMSD values were slightly smaller for the biconcave disc than for the oblate spheroid. This result is opposite from that obtained for either intra- or extracellular diffusion in the absence of exchange. Thus the estimate of the apparent diffusion coefficient (directly related to the RMSD) in a two-compartment system with exchange is a nonlinear weighted sum of the apparent values in each compartment.
PGSE NMR experiments
The simulations described above were conducted to improve our interpretation of data obtained from PGSE NMR experiments on real cellular systems. It was shown that the biconcave disc simulations did indeed give rise to features that were seen in q-space plots from RBC suspensions.
However, as seen from (Fig. 7) and previous reports (Benga et
al., 2000
; Kuchel et al., 1997
; Torres et al., 1998
, 1999
), the various
features and critical points of the q-space plots were less
pronounced than for the simulated canonical data. This is readily
interpreted as being due to real RBC suspensions having a distribution
of cell sizes and, to a lesser extent, shapes. In addition, the cells
in a real suspension in the NMR spectrometer, although virtually
completely aligned in the z direction, will not be so
aligned in the x and y directions. Also, they
move slightly during each NMR pulse sequence and therefore will be
arranged in a continuously changing and random manner. The simulations were conducted on systems in which all cells were identical both in
size and shape, and their orientations were exactly specified with
their packing arrangement fixed and regular. Further work could entail
building in random fluctuations in cell orientation and this would lead
to a blurring of the features of q-space plots.
It is also clear from the experimental data (Fig. 7) that the extent of signal attenuation was increased at all values of q as Ht was decreased, as occurred with the simulated data. The pore-hopping shoulder was more pronounced at lower values of Ht, and this is attributed to the greater volume of water in the extracellular region resulting in its greater contribution to the overall water signal. However, had the Ht been further decreased, it is anticipated that, at some value, this feature would have become less pronounced and eventually disappeared altogether as the extracellular pores would have become ill-defined.
Also in Fig. 7, a decrease in Ht was accompanied by an increase in RMSD, reflecting the diminished restriction to diffusion in the extracellular region afforded by the lower volume occupied by the RBC. Once again, this result was observed in the simulations. The relationship between Ht and RMSD was very linear (see Results), thus suggesting a method for estimating the Ht of a sample simply by measuring the width-at-half-height of the Fourier transform of the q-space plot. The RMSD at Ht = 0.5 was considerably higher than that for the biconcave discs at the same Ht, and was closer to that for the oblate spheroids. The reason for the discrepancy lies in the values chosen for the intra- and extracellular diffusion coefficients for which only preliminary experimental values were used in the simulations.
The features of the q-space plots in Fig. 7 are not highly resolved, and, consequently, determination of the critical q-values was more difficult than for the simulated data. Nevertheless, the relationships between critical values and characteristics of the cells in the suspension at Ht = 0.5 are comparable with the simulated data at Ht = 0.5.
General points
It has been pointed out above that, in a real RBC suspension, the cells are not of identical size and are not motionless in a regular lattice. The models used in this study, in contrast, were based on an ideal and hence simplified system. The intention in the work was not merely to provide a simplification but rather to develop a canonical system that would reveal features that would be difficult to discern in a more realistic system due to the blurring effect of randomization of cell orientation.
The degree of signal attenuation in the PGSE NMR experiments on real
RBC suspensions extended to greater than 103.
Despite this high level of attenuation, we are able to ignore the
contaminating signals from other cellular metabolites or components. The concentration of water protons in the cell is 70-80 M and close to
100 M in the extracellular fluid. The concentration of nonexchangeable
glycyl protons from glutathione, the most abundant metabolite inside
the cells, is just 4 mM, a factor of 105 lower
than water. The hemoglobin concentration, although significantly higher, has a short T2 relaxation time, so, in
PGSE NMR experiments with an echo time of greater than 20 ms, the
hemoglobin makes no significant contribution to the signal in the
region of the water resonance (Kuchel and Chapman, 1991
).
A complicating factor in the analysis of simulation data has been the
appearance of negative signal values at the minima. The magnitude of
these negative echoes was, on average, of the order of
10
5 of the initial signal intensity. Although
methods have been developed to overcome this difficulty (see Materials
and Methods), considerable thought was given to the origin of this
phenomenon. At the much less than Avogadro's number of trajectories
performed for any single simulation, there will always be an excess of
displacements in the ensemble in either the positive or negative
direction along any axis. Any excess, however small, will constitute a
degree of apparent flow and will give rise to negative spin-echo signal intensities (Callaghan et al., 1999
).
q-Space data from real or simulated cell suspensions is clearly not Gaussian, and, consequently, the propagator obtained from the Fourier transform of the data is also not Gaussian. However, fitting a Gaussian to a typical q-space data set yielded a width-at-half-height of (2.27 ± 0.01) × 104 m with a correlation coefficient of 0.99. Therefore, on the basis that the propagator is approximately Gaussian, we contend that the width-at-half-height of the Fourier transform of q-space data is related to the effective RMSD (see Eq. 6).
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CONCLUSIONS |
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|
|
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We used random walk simulations of diffusion to study the
relationship between the features of NMR q-space data and
the shapes of the cells in the sample. Different cell geometries gave
rise to differences in features in the q-space plots, so
this finding will be useful in detecting pathological changes in cells
and in the identification of cell types (Torres et al., 1998
). We have
pointed out the differences that exist between the simulated and
real-cell suspensions. The ideality of the simulated systems has, in
fact, allowed us to identify features in q-space plots that
appear with lower resolution in such plots from real RBC suspensions.
Thus, we could assign these features of q-space plots to
particular modes of diffusion in an ideal setting. Two methods for
facilitating the analysis were described: first- and second-derivative analysis of q-space plots for the determination of
q values of critical points in q-space plots, and
Fourier transform analysis for calculating apparent RMSD values. The
latter method provides a quick and simple means of determining the Ht
of cell suspensions. Finally, we used diffusion tensor analysis to
estimate the apparent diffusion coefficients and to show their
dependence on direction of movement of the diffusant in a heterogeneous
system, such as a suspension of cells with only one axis of symmetry.
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ACKNOWLEDGMENTS |
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The work was supported by grants from the Australian National Health and Medical Research Council and the Australian Research Council to P.W.K., and an Australian Postgraduate Award to D.G.R.
We thank Dr. Bob Chapman and Dr. Bill Bubb for assistance with the NMR spectroscopy, and Mr. Bill Lowe for technical assistance.
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FOOTNOTES |
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Address reprint requests to Philip W. Kuchel, School of Molecular and Microbial Biosciences, Univ. of Sydney, NSW 2006, Australia. Tel.: +61-2-9351-3709; Fax: +61-2-9351-4726; E-mail: p.kuchel{at}mmb.usyd. edu.au.
Submitted January 21, 2002 and accepted for publication March 7, 2002.
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REFERENCES |
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Biophys J, July 2002, p. 161-171, Vol. 83, No. 1
© 2002 by the Biophysical Society 0006-3495/02/07/161/11 $2.00
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