of 18
Figures and figure supplements
Spatial tuning and brain state account for dorsal hippocampal CA1 activity in a
non-spatial learning task
Kevin Q Shan
et al
Shan
etal
. eLife 2016;5:e14321.
DOI: 10.7554/eLife.14321
1 of 18
RESEARCH ARTICLE
B
A
C
D
E
F
Trial #
CS-responsive cell
Animal A
B
C
Behavioral performance
CS
US
Trial delivery locations
0.5 mV
naive
trained
250 ms
1
1
4
0
50
100
Training session
CR %
0
25
Hz
250 ms
N=164
0
100
0
25
50
75
100
CS response reliability
Observed %
Expected %
CS
US
EMG
1.8 m
Figure 1.
CA1 pyramidal responses during trace eyeblink conditioning in a freely moving rat. (
A
) An eyeblink trial
is a sequence of a tone (CS), a stimulus-free period (trace interval), and a blink-inducing electrical pulse (US). Blinks
are measured on an eyelid electromyogram (EMG). (
B
) Trials are delivered randomly throughout the environment
as the rat traverses a linear track for water reward. (
C
) Eyelid EMG from early and late in learning. A conditioned
response (CR) is defined as an increase in EMG power anticipating the US onset. (
D
) Learning is apparent as an
increase in CR frequency over the course of training. (
E
) Example pyramidal cell that significantly increased its
firing rate following the CS onset. If spike counts on each trial were Poisson distributed according to this cell’s
average response (top), we would expect to observe this CS-evoked increase in 76% of trials. Instead, its spike
rasters (bottom) show that the response is much less reliable and occurs in only 32% of trials. (
F
) Observed vs.
expected CS response reliability. All 1264 recorded pyramidal cells (back dots) responded in less than half of trials.
The example from (
E
) is circled in red.
DOI:
10.7554/eLife.14321.002
Shan
etal
. eLife 2016;5:e14321.
DOI: 10.7554/eLife.14321
2 of 18
Research article
Neuroscience
A
B
DG
CA3
CA1
Sub
Post
Pre
Para
Grey: autofluorescence at 560/630 excitation/emission (nm)
Blue: nuclear stain (Hoechst)
Animal A – Right
B – Right
C – Right
C – Left
d
orsal
vent
r
a
l
a
nterior
po
sterior
Figure 1—figure supplement 1.
Location of recording sites. (
A
) Example coronal section used to reconstruct recording sites. The electrolytic lesions
used to mark the final tetrode locations can be detected as autofluorescence. This is superimposed with a nuclear stain to identify the CA1 cell layer.
Scale bar: 1 mm. (
B
) Recording sites were registered onto a brain atlas (
Paxinos and Watson, 2007
), then projected onto a flatmap of the unfolded
hippocampal formation (
Petrovich et al., 2001
). This shows only those sites from which we recorded at least one pyramidal cell.
DOI:
10.7554/eLife.14321.003
Shan
etal
. eLife 2016;5:e14321.
DOI: 10.7554/eLife.14321
3 of 18
Research article
Neuroscience
Sit
Run
Trial delivery locations
A
Animal A
Animal B
30 cm
Animal C
Trial velocities
B
Velocity (cm/s)
0.1
1
10
100
Figure 1—figure supplement 2.
Distribution of animal location and velocity during eyeblink trials. (
A
) Animal
locations where eyeblink trials were delivered. All animals received eyeblink conditioning trials at random locations
on the track. Animal C also received trials at random time intervals, producing a denser sampling of the endboxes.
(
B
) Histogram of animal velocity when eyeblink trials were delivered. The indicated thresholds were used to classify
individual trials as ’sit’ vs. ’run’ in subsequent analyses.
DOI:
10.7554/eLife.14321.004
Shan
etal
. eLife 2016;5:e14321.
DOI: 10.7554/eLife.14321
4 of 18
Research article
Neuroscience
B
A
C
D
E
F
P. field intensity
Place field intensity
Place field intensity
Trial delivery locations
Post-CS firing:
16+ spikes
6−15
1−5
0
Place field map
CS-responsive cell
2
0
0
Firing rate (Hz)
0
25
Hz
250 ms
N=164
Place field maps
N=99612
All 780 cells shown in (
A
)
N=54105
All other pyramidal cells
0
10
Hz
Within place field
(Place field intensity > 2 Hz)
0
1
Hz
Intermediate (0.1−2 Hz)
0
0.1
Hz
Out of place field (< 0.1 Hz)
250 ms
Cell-by-cell analysis
Average CS-evoked firing (Hz)
CS−Place
correlation
0.01
0.1
1
10
−0.25
0
1.00
0.1
1
10
Firing rate (Hz)
Figure 2.
Spatial tuning modulates CA1 responses to eyeblink stimuli. (
A
) Spatial firing rate maps (place fields) for the 780 cells active on the linear
track. Each row is a single cell; left and right panels show different directions of traversal. These maps are computed excluding eyeblink trials. (
B
) Place
fields predict CS responses for the example cell from
Figure 1E
. Top: Place field map. Boxes are the track endboxes, and the track itself is duplicated
to show different directions of traversal. Middle: Animal location during eyeblink trials, color-coded by CS-evoked firing. Bottom: Spike rasters ordered
by place field intensity at trial delivery locations. (
C
) Spike rasters for all cells in (
A
), ordered by place field intensity. For visualization, many rasters are
compressed onto a single row, and overlapping spikes are given warmer colors. Electrical artifacts prevent spike detection during the 10 ms US delivery
window. (
D
) Spike rasters for the remaining 484 cells not active on the linear track. (
E
) Average firing rate over all cells and trials, grouped by place field
intensity. (
F
) Cell-by-cell analysis of the correlation (Spearman’s

) between CS-evoked firing rate and place field intensity. Most cells have a large
positive correlation, especially those that appeared significantly CS-responsive (black dots). The only cells without a positive correlation are those that
fired very few spikes. The cell from (
B
) is circled in red.
DOI:
10.7554/eLife.14321.005
Shan
etal
. eLife 2016;5:e14321.
DOI: 10.7554/eLife.14321
5 of 18
Research article
Neuroscience
Trial #
Trial delivery locations
Place field map
A
0
25
Hz
Spike rasters
N=164
Trial delivery locations
Place field map
B
0
25
Hz
Spike rasters
N=164
Trial delivery locations
Place field map
C
0
25
Hz
Spike rasters
N=164
Trial delivery locations
Place field map
D
0
25
Hz
250 ms
Spike rasters
N=164
Firing rate (Hz)
0
5
10
15
20
Post-CS firing (# spikes):
16+
6−15
1−5
0
Figure 2—figure supplement 1.
Additional simultaneously-recorded cells. The example cell from
Figures 1E
and
2B
is shown in panel (
B
). The other
panels of this figure show simultaneously recorded cells from different tetrodes. As in
Figure 2B
, each panel contains a place field map, trial delivery
locations (color-coded by CS-evoked firing), and spike rasters for a single cell. Rasters are shown in chronological order (as in
Figure 1E
), so the same
row in each panel corresponds to the same trial. Note that different sets of cells fire as the animal moves around, and cells with disjoint place fields fire
on different subsets of trials. The colored bars flanking each raster show the cell’s place field intensity for each trial.
DOI:
10.7554/eLife.14321.006
Shan
etal
. eLife 2016;5:e14321.
DOI: 10.7554/eLife.14321
6 of 18
Research article
Neuroscience
Place field intensity
Location
Place field intensity
Trial #
Trial delivery locations
A
No place field
0
10
Hz
Spike rasters
N=68
Trial delivery locations
B
Endbox only
0
10
Hz
Spike rasters
N=184
Trial delivery locations
C
Track only
0
10
Hz
Spike rasters
N=85
Trial delivery locations
D
Mixed
0
10
Hz
250 ms
Spike rasters
N=169
Firing rate (Hz)
0
5
10
15
20
Post-CS firing:
16+ spikes
6−15
1−5
0
Figure 2—figure supplement 2.
Additional single-cell examples. This figure shows additional single-cell examples, presented in the same fashion as
Figure 2B
. (
A
) 484 cells (38%) did not have a place field in the environment and fired very few spikes during eyeblink trials. (
B
) 301 cells (24%) had a
place field in the endbox only. However, this count is very sensitive to the threshold on the place field’s peak firing rate. For example, increasing this
rate threshold from 2 Hz to 5 Hz would reclassify 160 of these ’endbox only’ cells as ’no place field’. A small fraction of ’endbox only’ cells (14 cells total)
had place fields in both endboxes. (
C
) 325 cells (26%) had a place field on the track proper. Most of these (188 cells) had a single uni-directional place
field. Note that non-uniform sampling of the track can cause place field traversals to appear as a CS-evoked change in firing. In this example, the
animal received eight eyeblink trials as it was exiting this cell’s place field, but only one trial as it was entering. As a result, we observe a significant
decrease in firing following the CS onset (p=0.006, Wilcoxon signed-rank test). (
D
) 154 cells (12%) had place fields on the track and in the endbox(es).
Many of these were due to a single place field that extended onto both areas, but some (like this example) had multiple distinct place fields.
DOI:
10.7554/eLife.14321.007
Shan
etal
. eLife 2016;5:e14321.
DOI: 10.7554/eLife.14321
7 of 18
Research article
Neuroscience