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Article
Intact-Brain Analyses Reveal Distinct Information
Carried by SNc Dopamine SubcircuitsGraphical Abstract
Highlights
d Intact, inclusive approaches to classifying neuronal cell
types
d Differential brain-wide circuit incorporation of SNc dopamine
neuron subpopulations
d Opposite valence encoding of shock by projection target-
defined SNc neurons
d Independently controlled information streams from the SNc
to the DMS and DLS
Lerner et al., 2015, Cell 162, 635–647July 30, 2015 ª2015 Elsevier Inc.http://dx.doi.org/10.1016/j.cell.2015.07.014
Authors
TaliaN. Lerner,CarrieShilyansky, Thomas
J. Davidson, ..., Liqun Luo, Raju Tomer,
Karl Deisseroth
In Brief
Exploring the mammalian brain with an
array of intact-brain circuit interrogation
tools—including CLARITY, COLM,
optogenetics, viral tracing, and fiber
photometry—reveals that neurons in the
SNc region present different biophysical
properties, wiring of inputs and outputs,
and activity during behavior, despite
signaling through the same
neurotransmitter.
Article
Intact-Brain Analyses Reveal Distinct InformationCarried by SNc Dopamine SubcircuitsTalia N. Lerner,1,2 Carrie Shilyansky,3 Thomas J. Davidson,1,2 Kathryn E. Evans,4 Kevin T. Beier,3,4,5,6
Kelly A. Zalocusky,1,2,7 Ailey K. Crow,2 Robert C. Malenka,3,5 Liqun Luo,4,6 Raju Tomer,1,2 and Karl Deisseroth1,2,3,6,*1Department of Bioengineering2CNC Program3Department of Psychiatry and Behavioral Sciences4Department of Biology5Nancy Pritzker Laboratory6Howard Hughes Medical Institute7Neuroscience Program
Stanford University, Stanford, CA 94305, USA
*Correspondence: [email protected]
http://dx.doi.org/10.1016/j.cell.2015.07.014
SUMMARY
Recent progress in understanding the diversity ofmidbrain dopamine neurons has highlighted theimportance—and the challenges—of defining mam-malian neuronal cell types. Although neurons maybe best categorized using inclusive criteria spanningbiophysical properties, wiring of inputs, wiring ofoutputs, and activity during behavior, linking all ofthese measurements to cell types within the intactbrains of living mammals has been difficult. Here,using an array of intact-brain circuit interrogationtools, including CLARITY, COLM, optogenetics, viraltracing, and fiber photometry, we explore the diver-sity of dopamine neurons within the substantia nigrapars compacta (SNc).We identify two parallel nigros-triatal dopamine neuron subpopulations differing inbiophysical properties, input wiring, output wiringto dorsomedial striatum (DMS) versus dorsolateralstriatum (DLS), and natural activity patterns duringfree behavior. Our results reveal independently oper-ating nigrostriatal information streams, with implica-tions for understanding the logic of dopaminergicfeedback circuits and the diversity of mammalianneuronal cell types.
INTRODUCTION
Dopamine (DA) is a neurotransmitter that is crucial for many bio-
logical processes relevant to health and disease and is thought
to regulate (among other behaviors) voluntary movement, rein-
forcement learning, and motivation (Bromberg-Martin et al.,
2010). Seminal early studies into the information encoded by
midbrain DA neurons suggested that a key function of DA is
to transmit reward prediction error signals (Mirenowicz and
Schultz, 1996; Schultz et al., 1997; Waelti et al., 2001), a hypo-
thesis concordant with temporal difference learning models
(Montague et al., 1996, 2004; Steinberg et al., 2013; Sutton,
1988). However, not all midbrain DA neurons appear to encode
similar information in their activity patterns (Bromberg-Martin
et al., 2010; Lammel et al., 2014; Roeper, 2013). For example,
DA neurons have been observed that differ in their responses
to aversive stimuli, leading to the hypothesis that the DA neu-
rons, which increase their firing in response to these stimuli,
may signal salience rather than value (Brischoux et al., 2009;
Bromberg-Martin et al., 2010; Matsumoto and Hikosaka,
2009), though controversy on this point remains (Cohen et al.,
2012; Fiorillo et al., 2013, 2013; Ungless et al., 2004).
The concept that there are diverse subsets of midbrain DA
neurons transmitting distinct signals naturally leads to the ques-
tion of whether these subsets are functionally incorporated into
different circuits with different roles in the brain. Explorations of
DA neurons in the ventral tegmental area (VTA) have revealed
that these neurons can be divided into distinct categories based
on their projection targets, which include the prefrontal cortex,
nucleus accumbens (NAc) core, NAc medial shell, NAc lateral
shell, and amygdala. When divided by projection target, different
VTA DA neuron classes express varying levels of the DA trans-
porter (DAT), DA D2 autoreceptors, GIRK channels, and HCN
channels mediating the Ih current (Lammel et al., 2008, 2011;
Margolis et al., 2008), all of which could affect the dynamics of
signals represented and transmitted. Furthermore, projection
target-defined subpopulations are located in different subre-
gions of the VTA, their excitatory synapses are differentially
modulated by rewarding and aversive stimuli, and they receive
distinct inputs, which can elicit opposite behaviors when selec-
tively recruited (Lammel et al., 2008, 2011, 2012).
Distinctions among DA neurons have also increasingly been
drawn between DA neurons within the VTA and those within
the substantia nigra pars compacta (SNc). For example, a recent
viral circuit tracing study showed that VTA and SNc DA neurons
receive different proportions of inputs from key brain regions
(Watabe-Uchida et al., 2012). In particular, this study noted
that SNc neurons receive a large proportion of their inputs
from the dorsal striatum. In contrast, studies attempting to func-
tionally characterize direct striatal projections to midbrain DA
neurons using optogenetics and slice recordings that have failed
Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc. 635
DM
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Other)
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eeks
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Figure 1. Whole-Brain Mapping of Inputs to DMS-Projecting and DLS-Projecting SNc DA Neurons
(A) Viral injection strategy for whole-brain input mapping based on output (TRIO). CAV-cre is injected into the striatum (DMS or DLS), and AAVs expressing cre-
dependent TC and G are injected into the SNc. Two weeks later, RVdG-GFP is injected into the SNc, where it infects TC-expressing cells and spreads one
synapse upstream from G-expressing cells.
(legend continued on next page)
636 Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc.
to identify such connections (Chuhma et al., 2011; Xia et al.,
2011) or found them to be very weak (Bocklisch et al., 2013).
The functional connectivity from striatum to SNc thus remains
an open question.
In addition to differences from VTA neurons, there are hints in
the literature that SNc DA neurons alone could be further divis-
ible into functionally distinct subsets. One pioneering study
demonstrated that DA neurons located more medially within
the SNc express higher levels of K-ATP channels, whichmediate
burst firing (Schiemann et al., 2012). Another study used record-
ings in awake monkeys to demonstrate a correlation between
the depth at which a DA neuron was recorded along the elec-
trode (indicating a more ventromedial location in the midbrain)
and the likelihood that it would decrease rather than increase
its firing in response to an aversive cue (Matsumoto and Hiko-
saka, 2009).
How might such differences among SNc DA neurons relate to
circuit wiring and function? One intriguing hypothesis is that
distinct locations within the SNc give rise to projections targeting
distinct locations within the dorsal striatum, such as dorsomedial
striatum (DMS) and dorsolateral striatum (DLS); distinct SNc
subfields could furthermore be set up to receive, process, and
transmit functionally distinct streams of information from else-
where in the brain. Such circuit organizationwould have powerful
implications. For example, given the highmedial SNc expression
of K-ATP channels that enable bursting, the prediction could be
made that the striatal target field of themedial SNcwould receive
strong novelty-driven bursts of DA during exploratory behavior
that the striatal target field of the lateral SNc could not receive.
However, other lines of research suggest that DAergic projec-
tions to the DMS and DLS carry similar information streams
because restriction of DA signaling to either subregion has
similar effects (Darvas and Palmiter, 2009, 2010). In fact, SNc
DA neurons could in principle even be similar to VTA DA neurons
in terms of the valence of information represented because mice
will self-stimulate for SNc DA neuron activity just as for VTA DA
neuron activity (Ilango et al., 2014; Rossi et al., 2013).
In the end, though this is clearly a question of great potential
significance, it remains unknown whether different SNc DA
neuron populations are fundamentally distinct in their projection
targets in striatum, in the types of information represented in their
electrical activity, or in the sources of their incoming information
across the brain. Here, using an array of intact-brain circuit
interrogation tools, including CLARITY, COLM, optogenetics,
viral tracing, and fiber photometry during behavior, we explore
this issue and find that all three conjectures regarding the
(B) Low-magnification (53) images of DMS- and DLS-projecting SNc ‘‘starter cells
shows TC expression, and blue shows (TH) immunostaining.
(C) Quantification of the percentage of starter cells that were TH+. Error bars are
(D) High-magnification (403) images from the sections shown in (B).
(E) Examples of GFP labeling of ipsilateral inputs to DMS- and DLS-projecting S
nucleus accumbens; DS, dorsal striatum; BNST, bed nucleus of the stria termin
amygdala; LHb, lateral habenula; DR, dorsal raphe; MRN, midbrain reticular nuc
(F) Quantification of ipsilaterally labeled inputs to DMS- and DLS-projecting SNc D
***p < 0.001 and ****p < 0.0001. Other abbreviations: motor cortex (M1/2), somat
limb of the anterior commissure (FS/IPAC), substantia innominata/ventral pallidu
compacta (SNc), substantia nigra pars reticulata (SNr), ventral tegmental area (V
See also Figure S1 and Table S1.
complexity of SNc functional wiring are borne out, with substan-
tial implications for understanding the logic of DAergic signaling
to striatum.
RESULTS
Unbiased Brain-wide Mapping of Inputs to StriatumSubfield-Projecting SNc NeuronsTo directly explore the hypothesis that distinct SNc neuron pop-
ulations receive and deliver separable information streams, we
began with an unbiased approach for globally mapping the
input/output relationships of SNc neurons. We mapped inputs
onto two subpopulations of SNc DA neurons defined by their
outputs to the DMS and DLS. These regions of the dorsal stria-
tum have been functionally distinguished by previous studies
(Castane et al., 2010; Faure et al., 2005; Featherstone and
McDonald, 2004; Yin and Knowlton, 2004; Yin et al., 2004,
2005a, 2009, 2005b), leading us to hypothesize that SNc projec-
tions to these areas might also participate in separable circuits.
We achieved unbiased global visualization of SNc inputs and
outputs using a combination of CLARITY and CLARITY-opti-
mized light-sheet microscopy (COLM) (Chung et al., 2013;
Tomer et al., 2014), along with a variation of rabies-based circuit
mapping (Schwarz et al., 2015); the lattermethod (TRIO) operates
similarly to previously published rabies-based circuit mapping
technologies, utilizing a GFP-expressing rabies virus (RVdG-
GFP) that both lacks the glycoprotein needed to spread trans-
synaptically and is pseudotyped with EnvA (so that it can infect
only neurons expressing TVA, an avian receptor protein normally
absent in mammalian cells [Wickersham et al., 2007]).Glycopro-
tein andTVAcan thenbeexpressedusingcre-dependent vectors
to direct the rabies virus to infect and spread to connected inputs
from a cre-defined subset of neurons. In TRIO, cre is delivered
from the retrograde CAV-cre virus (Hnasko et al., 2006; Soudais
et al., 2001), which transduces axon terminals and thereby de-
fines ‘‘starter cells’’ (fromwhich rabies tracingwill occur) by virtue
of their projection target. We injected CAV-cre into either the
DMS or DLS and then injected AAVs expressing cre-dependent
rabies glycoprotein (G) and TC, a high efficiency version of the
TVA receptor fused to mCherry (Miyamichi et al., 2013), into the
SNc. Two weeks later, we injected RVdG-GFP into the SNc (Fig-
ure 1A). Control experiments revealed that resulting putative
starter cells in the SNc, as defined by neurons that expressed
both RVdG-GFP and TC, were predominantly DAergic (TH+;
96% ± 3% after CAV-cre injection into the DMS, n = 4 mice;
98% ± 2% after CAV-cre injection into the DLS, n = 4 mice;
,’’ fromwhich tracing likely occurred. Green shows RVdG-GFP expression, red
SEM.
Nc DA neurons from various brain regions. S1, somatosensory cortex; NAc,
alis; GPe, globus pallidus external segment; HY, hypothalamus; CeA, central
leus; PAG, periaqueductal gray.
A neurons, shown as a percentage of all ipsilateral inputs. Error bars are SEM.
osensory cortex (S1), fundus of the striatum/interstitial nucleus of the posterior
m (SI/VP), superior colliculus (SC), inferior colliculus (IC), substantia nigra pars
TA), pedunculopontine nucleus (PPN), and parabrachial nucleus (PB).
Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc. 637
Figures 1B–1D). Additional controls demonstrated that the
RVdG-GFPwasproperly EnvA-pseudotypedand that long-range
tracing of inputs was cre dependent (Figures S1A and S1B).
We began our analysis of GFP-labeled inputs to DMS- and
DLS-projecting SNc DA neurons by optically clarifying the
labeled brains (Chung et al., 2013; Tomer et al., 2014) and visu-
alizing using COLM (Tomer et al., 2014). We reasoned that,
although thin sectioning approaches used for analysis of
anatomical tracing have yielded important insights, these are
not ideal for visualization of brain-wide patterns. Thin sectioning
results in particular caveats for the interpretation of negative
results: slices may tear, fragment, or otherwise be damaged or
lost, and strategies to minimize overcounting of somata split
across adjacent sections (such as counting only separated sec-
tions—e.g., every third or sixth) may underestimate cell counts,
particularly in small brain regions. Whole-brain CLARITY/
COLM circumvents these difficulties, allowing an intact global
overview of brain-wide structural patterns.
Using CLARITY/COLM, we noted an interesting GFP expres-
sion pattern in the striatum (Movies S1, S2, S3, and S4). When
inputs to DMS-projecting SNc DA neurons were labeled, we
observed relatively strong labeling in the NAc and DMS (Movies
S1 and S2) in comparison to the DLS, whereas when inputs to
DLS-projecting SNcDA neurons were labeled, we observed rela-
tively strong labeling in the DLS, particularly in the caudal tail of
the striatum (Movies S3 and S4) in comparison to the DMS and
NAc. Moreover, fine details of local neuronal architecture in
GFP-labeled neurons could be observed in higher-resolution vol-
ume renderings (Movie S5).
To quantify these divergent input patterns to SNc subfields de-
pending on their projection target, we followed up with detailed
targeted slicing approaches and quantified the inputs from
each brain region to DMS- and DLS-projecting SNc DA neurons
as a proportion of the total inputs observed (Figures 1E and 1F
and Table S1). Existing atlases used to define major brain re-
gions were further refined to define the boundaries of the DMS
and DLS (Figures S1C and S1D). Because the inputs to SNc
DA neurons are almost entirely ipsilateral (DMS-proj 96.4% ±
0.9%, n = 4; DLS-proj 96.5% ± 0.8%, n = 4, p = 0.91), we focused
on the injected hemisphere (contralateral inputs were examined
separately; Figures S1E and S1F and Table S1), noting first that
brain-wide inputs to SNc DA neurons, regardless of projection
target, broadly matched those observed by Watabe-Uchida
et al. (2012) using RVdG-GFP tracing from the SNc of DAT-cre
mice. However, despite gross similarities between groups, a
two-way ANOVA revealed a significant interaction between
starter cell projection target and input area (p < 0.001). Multiple
comparisons revealed significant differences in inputs from the
DMS (p < 0.001) and the DLS (p < 0.0001; Figure 1F), indicating
a marked preferential reciprocal connectivity of dorsal striatal
subregions to their specific DAergic SNc input subregions.
Injections in D1-tomato bacterial artificial chromosome (BAC)
transgenic mice further revealed that striatal inputs to SNc DA
neurons arise from DA D1 receptor-expressing neurons (Fig-
ure S1G; 92/97 DMS-projecting neurons and 210/214 DLS-
projecting neurons), consistent with the idea that D1 (but not
D2) striatal neurons project directly to the midbrain and with
hypotheses regarding the patch/matrix organization of striatum
638 Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc.
(Crittenden and Graybiel, 2011). These anatomical studies
suggested a fundamental distinction in circuit incorporation for
projection-defined SNc subregions and provided a roadmap
for a more detailed investigation of the circuit.
Organization of SNc DA Neurons Projecting to DistinctRegions of Dorsal StriatumTo quantify the spatial patterns of cre expression following injec-
tions of CAV-cre into the striatum, we injected CAV-cre into
the DMS or DLS of Ai9 tdTomato cre reporter mice (Figure 2A).
Viral spread in the striatum was contained within the targeted
subregion (Figure S2A). In the SNc, two key observations
were made. First, cre expression was largely restricted to DA
neurons, identified by tyrosine hydroxylase (TH) immunostaining,
following injection in both the DMS (344/360 neurons) and the
DLS (722/772 neurons). Although a few scattered TH+ cells
were labeled in the VTA in both groups, adjacent non-DAergic re-
gions did not contain cre-expressing cells (Figure 2B). Second,
the patterns of cre expression following DMS and DLS injection
differed. DMS-projecting neurons were observed in the medial
SNc, whereas DLS-projecting neurons were observed in the
lateral SNc. This differing anatomical localization of DMS- and
DLS-projecting SNc DA neurons supports the idea of parallel
nigrostriatal subcircuits within the SNc.
We next asked whether DMS- and DLS-projecting SNc DA
neurons projected only to the DMS or DLS, or instead collateral-
ized substantially. To visualize the boundaries of SNc DA neuron
axonal arborizations in the striatum, we injected CAV-cre into the
striatum and an adeno-associated virus (AAV) for cre-dependent
expression of membrane-bound GFP (mGFP) and synaptophy-
sin-mRuby (SYP-mRuby) into the SNc (Beier et al., 2015 [in this
issue ofCell]; Figure 2C). With this approach, axons were labeled
in green, and putative presynaptic sites were labeled in red. In
the SNc, both green and red labeling were visible as anticipated
(Figure 2D). The areas of highest fluorescence colocalized with
TH in a pattern concordant with the locations of DMS- and
DLS-projectingSNcDAneuronsobserved inAi9mice (Figure 2B).
In the striatum, axons of DMS-projecting SNc DA neurons
remained within the DMS, and axons of DLS-projecting SNc
DA neurons remained within the DLS (Figures 2E–2G and S2B).
To quantify this differential axon distribution, we acquired a
systematic image series from each mouse corresponding to
the full anterior-posterior span of the striatum (Figure S2B). Pro-
jection fraction was calculated as the axonal coverage area in
one region (DMS or DLS) divided by the total area covered
across the entire striatum (Figure 2H). The entire striatum was
defined to include the NAc, but we observed negligible contribu-
tions of projections to any of the NAc subregions across all con-
ditions (Figure S2C). NoGFP-labeled axonswere observed in the
prefrontal cortex or amygdala (Figure S2D). In dorsal striatum, an
overwhelming fraction of DMS-projecting axons was localized
within the bounds of the DMS (DMS 0.98 ± 0.01, n = 2, versus
DLS 0.02 ± 0.01, n = 2; two-way ANOVA, brain area3 projection
target interaction, p < 0.0001; post hoc Tukey’smultiple compar-
isons, p < 0.0001); similarly, DLS-projecting axons were local-
ized largely within the bounds of the DLS (DMS 0.14 ± 0.02,
n = 2, versus DLS 0.86 ± 0.02, n = 2; post hoc Tukey’s multiple
comparisons, p < 0.0001). These data confirmed that the SNc
SNr
SNc
PBP
IPN
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THcre DLS-projecting
SNr
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344/360 ≈ 96% TH+ 722/772 ≈ 94% TH+
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Figure 2. Medial-Lateral Distribution of SNc DA Neurons Projecting to Medial and Lateral Subregions of Dorsal Striatum
(A) CAV-cre was injected into the striatum of Ai9 td-Tomato cre reporter mice, labeling SNc neurons projecting to the injected region in red.
(B) DMS- and DLS-projecting SNc neurons are labeled with td-Tomato (red). Blue shows TH+ neurons. Both DMS- and DLS-projecting SNc neurons were found
to be predominantly DAergic. Scale bars are 0.5 mm.
(C) To map the outputs of DMS- and DLS-projecting SNc DA neurons, CAV-cre was injected into the striatum (DMS or DLS) of wild-type mice. Cre was then used
to direct the expression of mGFP-T2A-SYP-mRuby, labeling processes in green and presynaptic sites in red.
(D) DMS- and DLS-projecting SNc DA neurons expressing mGFP and SYP-mRuby. Staining for TH (blue) shows overlap with DA neuron cell bodies. Scale bars
are 0.5 mm.
(E) Example images (53) of patterns of mGFP expression in the striatal projections of DMS- or DLS-projecting DA neurons. Ctx, cortex; Str, striatum; V, ventricle.
(F) Example images (403) of regions of interest (DMS, DLS) in mice expressing mGFP and SYP-mRuby in DMS- and DLS-projecting SNc DA neurons. Scale bars
are 50 mm.
(G) Projection fraction of DMS- and DLS-projecting SNc DA neurons in DMS and DLS. Error bars are SEM. ****p < 0.0001.
See also Figure S2.
projections to the DMS and DLS are largely parallel, defining
separable nigrostriatal subcircuits with the potential to convey
distinct and independent signals to the DMS and DLS.
Distinct Properties of SNc DA Neurons Dependingupon Projection TargetWe next explored whether projection-defined SNc DA neurons
could be distinguished by intrinsic electrophysiological proper-
ties. To mark neurons for recording, we injected red-fluorescent
retrobeads into the DMS or DLS of TH-GFP mice. Retrobead-
labeled SNc neurons were also primarily GFP+ (Figure 3C;
509/515 DMS-projecting neurons and 526/542 DLS-projecting
neurons). Although the specificity of the TH-GFP line has been
questioned (Lammel et al., 2015), we found that GFP expression
is specific for TH+ neurons in the SNc (Figure S3). Retrobead in-
jections remained well localized to the injection site (Figure 3A)
and retrobead-containing neurons within the SNc were readily
identifiable for patching (Figure 3B).
Whole-cell patch-clamp analysis of retrobead+ andGFP+ SNc
neurons revealed similar membrane capacitance, resistance,
Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc. 639
DMS-projectingDLS-projecting
DMS-proj DLS-proj0
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eigh
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509/515 ≈ 99%
526/542 ≈ 97%
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mIPSCs
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alf-w
idth
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K
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s
10 mV
**** ****
Figure 3. Intrinsic Properties of DMS-Projecting and DLS-Projecting SNc DA Neurons
(A) Retrobeads (red) injected into the striatum of TH-GFP mice. Ctx, cortex; Str, striatum. Scale bars are 0.5 mm.
(B) DIC and red fluorescent images of a patched retrobead-containing neuron. Dotted lines highlight the position of the recording electrode. Scale bars are 10 mm.
(C) Colocalization of retrobead-containing neurons (red) with TH-GFP-labeled neurons (green) in the SNc. Colocalization rates were �99% and �97% in DMS-
and DLS-projecting neurons, respectively.
(D) Membrane capacitance (Cm) of DMS- and DLS-projecting SNc DA neurons. Error bars are SEM.
(E) Membrane resistance (Rm) of DMS- and DLS-projecting SNc DA neurons. Error bars are SEM.
(F) Left, example responses of DMS-projecting SNc neurons (orange) and DLS-projecting SNc neurons (blue) to a hyperpolarizing current injection. Right,
Ih and Ileak current measurements in response to hyperpolarizing current injection from DMS- and DLS-projecting SNc DA neurons. Error bars are SEM.
**p < 0.01.
(G) Average action potential waveforms from DMS- and DLS-projecting SNc DA neurons. Area of light shading is SEM.
(H) Phase plots of average action potential waveforms from DMS- and DLS-projecting SNc DA neurons. Area of light shading is SEM.
(I) Average action potential height from DMS- and DLS-projecting SNc DA neurons. Error bars are SEM.
(J) Average action potential half widths from DMS- and DLS-projecting SNc DA neurons. Error bars are SEM. *p < 0.05.
(legend continued on next page)
640 Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc.
and leak currents of DMS-projecting and DLS-projecting DA
neurons (Figures 3D and 3E; Cm, DMS-proj 69.24 ± 3.589 pF,
n = 21 versus DLS-proj 71.94 ± 4.563 pF, n = 16, p = 0.64; Rm,
DMS-proj 384.7 ± 41.09 MU, n = 21 versus DLS-proj 327.4 ±
30.03 MU, n = 16, p = 0.30; Ileak, DMS-proj 317.1 ± 25.51 pA,
n = 21 versus DLS-proj 345.6 ± 35.81 pA, n = 16, p = 0.51). How-
ever, we identified distinctly larger Ih currents in DLS-projecting
DA neurons (Figure 3F; Ih, DMS-proj 296.2 ± 29.25 pA, n = 21
versus DLS-proj 460.8 ± 49.69 pA, n = 16, p < 0.01). All recorded
neurons displayed significant Ih currents and broad action
potential waveforms consistent with reliable identification of DA
neurons across groups. A small but significant difference was
observed in action potential half-width of DMS- versus DLS-pro-
jecting neurons (Figures 3G–3J; AP heights, DMS-proj 63.34 ±
1.901 mV, n = 21 versus DLS-proj 59.95 ± 2.395 mV, n = 16,
p = 0.27; AP half widths, DMS-proj 1.152 ± 0.06ms, n = 21 versus
DLS-proj 0.9938 ± 0.03 ms, n = 16, p < 0.05).
SNc DA Neurons Are Embedded within a LargelyInhibitory NetworkProjection-defined SNc DA neurons exhibit different intrinsic
properties, project to non-overlapping striatal subregions, and
receive differential inputs, together suggesting fundamentally
different roles in the circuit. However, since the nature of the
signals carried by the differing afferents remained unclear, we
next functionally investigated these afferents using slice electro-
physiology. As a first assessment of global functional afferent
input, we recorded miniature excitatory and inhibitory postsyn-
aptic currents (mEPSCs and mIPSCs) (Figure 3K). Although
no significant differences were observed between DMS- and
DLS-projecting SNc DA neurons, both the amplitudes and
frequencies of mIPSCs were higher than for mEPSCs across
both groups (Figures 3L and 3M; mEPSC amplitude, DMS-proj
�15.27 ± 0.50 pA, n = 15 versus DLS-proj �15.79 ± 0.68 pA,
n = 15; mIPSC amplitude, DMS-proj �29.69 ± 2.23 pA, n = 15
versus DLS-proj �26.71 ± 2.13 pA, n = 15; two-way ANOVA, ef-
fect of mEPSCs versus mIPSCs, p < 0.0001; mEPSC frequency
DMS-proj 0.49 ± 0.16 Hz, n = 15 versus DLS-proj 0.27 ± 0.10 Hz,
n = 15;mIPSC frequency, DMS-proj 7.11± 1.86Hz, n = 15 versus
DLS-proj 15.07 ± 4.29 pA, n = 15; two-way ANOVA, effect of
mEPSCs versus mIPSCs, p < 0.0001). This finding indicates
that SNc DA neurons in general are embedded within a largely
inhibitory network, in agreement with our findings and the find-
ings of Watabe-Uchida et al. (2012) that SNc DA neurons receive
afferents from many areas known to have GABAergic projection
neurons, including the striatum.
Functional Optogenetic Characterization of DorsalStriatal Inputs to DMS- versus DLS-ProjectingSNc DA NeuronsTo extend these findings, we employed targeted optogenetics to
test the functionality of synapses from dorsal striatum to SNc,
(K) Example traces of excitatory (top) and inhibitory (bottom) miniature postsyna
neurons.
(L) Amplitudes of mEPSCs and mIPSCs recorded from DMS-projecting and DLS
(M) Frequencies of mEPSCs and mIPSCs from recorded DMS-projecting and DL
See also Figure S3.
where we had specifically observed differences in inputs onto
projection-defined SNc neurons using TRIO (Figure 1F). First,
we expressed ChR2-eYFP in either DMS or DLS. Then, we in-
jected retrobeads into one of these regions to enable patching
of projection-defined SNc neurons. Blue light pulses stimulated
inputs specifically from the striatal subregion expressing ChR2
(Figure 4A). Examples of injection sites for ChR2 and retrobeads
are shown in Figure 4B, along with the resulting distributions of
red and green fluorescence in SNc (green fibers were observed
both in the SNc and in the underlying SNr, where many direct
pathway striatal neurons project).
Because striatal projection neurons are GABAergic, the gluta-
mate receptor antagonists NBQX (5 mM) and APV (50 mM) were
included in the extracellular solution to isolate inhibitory postsyn-
aptic currents (IPSCs), and a high-chloride internal solution was
used to facilitate event detection. We also included the voltage-
gated sodium channel antagonist TTX (1 mM) and potassium
channel antagonist 4-AP (100 mM) to isolate monosynaptic in-
puts by preventing disynaptic disinhibitory responses through
the GABAergic cells of the SNr (with TTX) while enabling ChR2
to drive neurotransmitter release in the absence of action poten-
tials (with 4-AP) (Petreanu et al., 2009). In all mice, recorded neu-
rons were identified that directly responded to blue light stimula-
tion, with response rates varying by condition. Connections from
DMS to DMS-projecting SNc DA neurons and connections from
DLS to DLS-projecting SNc DA neurons were clearly favored
(Figure 4C; X2 p < 0.0001), mirroring our TRIO results (Figure 1)
and functionally confirming a striking reciprocal connectivity
between dorsal striatal subregions and their DAergic inputs.
DLS Inputs to SNc DA Neurons Are Strongerthan DMS InputsBroad anatomical methods, while useful, cannot resolve key
aspects of function, such as distinguishing very strong from
very weak connections. In contrast, targeted optogenetic exper-
iments can provide information not only about connection
probabilities, but also about input strength. We next found, via
IPSC amplitude quantification for SNc neurons that responded
to stimulation of striatal afferents, that responses detected in
both DMS- and DLS-projecting SNc neurons were much larger
when DLS inputs were stimulated (Figure 4D; ChR2 DMS/
DMS-proj �205.27 ± 146.09 pA, n = 13; ChR2 DMS/DLS-proj
�96.23 ± 69.28 pA, n = 3; ChR2 DLS/DMS-proj �1193.10 ±
324.30 pA, n = 22; ChR2 DLS/DLS-proj �2737.96 ± 369.82 pA,
n = 38; two-way ANOVA, effect of ChR2 injection site, p <
0.01). Additionally, DLS-projecting SNc neurons had larger
responses to DLS stimulation than did DMS-projecting SNc
neurons (Tukey’s multiple comparisons, p < 0.05).
The observed differences in IPSC amplitudes between SNc
neurons receiving inputs from the DMS and DLS were not fully
explained by differences in the numbers of inputs arising from
the two striatal subregions (Figures 1 and 4C), suggesting
ptic currents from DMS-projecting (orange) and DLS-projecting (blue) SNc DA
-projecting SNc DA neurons. Error bars are SEM. ****p < 0.0001.
S-projecting SNc DA neurons. Error bars are SEM. ****p < 0.0001.
Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc. 641
ChR2-eYFPretrobeads
record
o-stim
ChR2 DMS ChR2 DLS0
20
40
60
80
% re
spon
ding
DMS-projectingDLS-projecting
38/49
22/39
3/28
13/32
A B
C D
ChR2 DMS ChR2 DLS
-4000
-3000
-2000
-1000
0
IPSC
am
plitu
de (p
A)
**
*
n.s.
Stri
atum
SN
cChR2 DMS
ChR2 DLS
20 ms500
pA
20 ms50 p
A
TTX4-AP
M LV
D
ChR2retrobeads
ChR2retrobeads
TH
50 ms50 p
A
ChR2 DMS
ChR2 DLS
ChR2 DMS ChR2 DLS
-50
-40
-30
-20
-10
0
qIPS
C a
mpl
itude
(pA)
DMS-projectingDLS-projecting
*
E
Figure 4. Optogenetic Mapping of Dorsal Striatal Inputs to DMS- and DLS-Projecting SNc DA Neurons: Reciprocal Connectivity Bias
and Divergent Strength
(A) ChR2-eYFP was expressed in either the DMS or the DLS. Red retrobeads labeled inputs to either the DMS or the DLS. Retrobead-containing cells in the SNc
were patched, and blue light was flashed to activate ChR2-expressing terminals nearby. Responses were recorded in the presence of TTX (1 mM) and 4-AP
(100 mM) to isolate monosynaptic inputs.
(B) Example images of striatal injection sites in the four experimental groups (top row) and of retrobead and ChR2 expression in the SNc (bottom row). Blue shows
TH immunostaining. Images are of slices used for recordings. Scale bars are 0.5 mm.
(C) Percentage of patched neurons responding to ChR2 stimulation of striatal terminals in the four experimental groups.
(D) IPSC amplitudes of responding neurons from (C). Example traces from each group are shown on the right. The blue bar indicates the time of blue light
stimulation. Error bars are SEM. **p < 0.01 and ****p < 0.0001.
(E) Quantification of the quantal IPSC (qIPSC) amplitude observed in DMS- and DLS-projecting SNc DA neurons in response to stimulation of DMS or DLS ChR2-
expressing terminals. Example traces of evoked asynchronous IPSCs are shown on the right, with the period of qIPSC event collection highlighted in a pop out
box. The blue bar indicates the time of stimulation. Error bars are SEM. *p < 0.05.
additional possible differences in quantal IPSC amplitude, the
number of synapses per input cell, and/or release probability.
To test for differences in quantal amplitude, we replaced calcium
642 Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc.
in the extracellular recording solution with strontium to induce
asynchronous release and found that the average quantal
IPSC amplitude was larger for inputs arising from the DLS versus
the DMS (Figure 4E; ChR2 DMS/DMS-proj �28.86 ± 3.48 pA,
n = 10; ChR2 DMS/DLS-proj �26.77 ± 2.75 pA, n = 8; ChR2
DLS/DMS-proj �36.64 ± 3.77 pA, n = 11; ChR2 DLS/DLS-proj
�40.60 ± 4.94 pA, n = 10, two-way ANOVA, effect of ChR2 injec-
tion site, p < 0.05), providing an additional partial explanation for
the observed differences in IPSC amplitude.
Selective Opposite-Valence Encoding of AversiveStimuli by DMS- versus DLS-Projecting SNc DA NeuronsParallel nigrostriatal SNc DA subcircuits clearly have the
potential to deliver different kinds of information to the DMS
and DLS. To formally test this intriguing possibility, we moni-
tored activity from projection-defined SNc DA neurons during
behavior using fiber photometry, a method for collecting popu-
lation intracellular [Ca2+] fluorescent signals from a genetically
encoded Ca2+ indicator such as GCaMP through a single
chronic fiber optic implant (Gunaydin et al., 2014). We ex-
pressed GCaMP6f (Chen et al., 2013) in DMS- or DLS-projec-
ting SNc DA neurons by injecting CAV-cre into the DMS
or the DLS, followed by injection of a cre-dependent GCaMP6f
construct into the SNc. Through a fiber optic implanted into
SNc at the GCaMP6f injection site (Figure 5A), we delivered
excitation light at 490 nm to stimulate GCaMP6f fluorescence
in a Ca2+-dependent manner and at 405 nm, an excitation
isosbestic wavelength for GCaMP6f that allowed us to perform
ratiometric measurements of GCaMP6f activity, thereby
correcting for bleaching and artifactual signal fluctuations
(Figures S4A–S4D).
We recorded the activity of DMS- or DLS-projecting SNc
DA neurons following either appetitive or aversive stimuli. To
record appetitive signals, we trained mice to lever press for
a sucrose reward retrieved from a reward port. Each press
had a 10% chance of delivering reward, a contingency that
allowed us to record during both rewarded and unrewarded
port entries within the same behavioral session for comparison.
DMS- and DLS-projecting SNc DA neurons reacted similarly
to rewarding outcomes (Figures 5C–5E); a similar peak DF/F
was observed on rewarded port entries for both sets of mice
(DMS-proj 2.164 ± 0.549%, n = 7 versus DLS-proj 1.753 ±
0.247%, n = 9, p = 0.47). Peaks were not observed for non-
rewarded port entries (Figures 5C, 5D, and 5F; DMS-proj
0.043 ± 0.195%, n = 7 versus DLS-proj �0.274 ± 0.083%,
n = 9, p = 0.13).
To record responses to aversive stimuli, we subjected the
same set of GCaMP6f-expressing mice to mild, unpredicted
electrical shocks. Strikingly, DMS- and DLS-projecting SNc
DA neurons responded oppositely to this aversive stimulus.
DMS-projecting neurons showed a marked dip in activity at the
time of shock, whereas DLS-projecting neurons showed an
increase (Figures 5G–5I; peak DF/F i.e., positive or negative
extreme during shock, DMS-proj�2.628 ± 0.513%, n = 8 versus
DLS-proj 1.527 ± 0.358%, n = 9, p < 0.0001). Additionally,
DLS-projecting neurons were returned immediately to baseline,
whereas more persistent changes were observed in DMS-pro-
jecting neurons (Figure 5J; mean DF/F between seconds 1 and
5, DMS-proj 2.403 ± 0.525%, n = 8 versus DLS-proj �0.3146 ±
0.176%, n = 9, p < 0.001). Post hoc histology revealed that
GCaMP6f-expressing axons were located in the DMS or DLS
as expected, that fiber optic implants were placed appropriately
in the SNc relative to GCaMP6f-expressing cell bodies, and that
GCaMP6f-expressing cell bodies were TH+ (Figure S4E). We
also verified that differences in movement between groups
during the reward and shock sessions could not account for
the observed differences in the photometry signal (Figures
S4F–S4K). Together, these results suggest that the projections
from subsets of SNc DA neurons to subregions of the dorsal
striatum are set up so that the DMS and DLS receive fundamen-
tally different signals; the DMS may receive a value signal
(DAergic population firing signals the valence of the outcome),
whereas the DLS may receive a salience signal (DAergic firing
alerts the system to adaptation-relevant events, whether appeti-
tive or aversive).
DISCUSSION
Here, we have developed and applied anatomical and functional
methodologies to provide a deeper understanding of striatoni-
grostriatal circuitry. We began by demonstrating that novel cir-
cuit-tracing and -recording methodologies can be effectively
combined with whole-brain CLARITY/COLM imaging (Chung
et al., 2013; Tomer et al., 2014) to provide a uniquely informative
overview of richly defined cell types and their global connectivity
motifs within the intact experimental subject brain. Further
development of high-throughput processing of these whole-
brain datasets will be needed (Chung and Deisseroth, 2013;
Kim et al., 2013, 2015) to fully capitalize on this opportunity for
the rapid advancement of understanding structure-function
relationships in the brain. For example, looking to the future, it
will be vital to increase experimental-subject group sizes despite
the immensely large datasets acquired for each experimental
subject. Although our current methods successfully captured
the large though complex connectivity differences observed
here, larger group sizes would broaden the potential to identify
biologically and potentially clinically important differences with
smaller effect sizes, including, perhaps, effects of age, gender,
and life experience.
Additionally, we have shown that, despite the utility of
anatomical tracing techniques such as TRIO, following up find-
ings from their use with other experimental modalities examining
the functionality of identified connections is essential. By stimu-
lating inputs from the striatum to SNc DA neurons optogeneti-
cally, we discovered that DLS inputs are an order of magnitude
stronger than DMS inputs, a finding that could not have been
predicted anatomically but is nevertheless likely to be crucial
in thinking about SNc circuit function. Our observations of
unequivocal inputs from the dorsal striatum to the SNc contrast
with certain earlier reports, which failed to find connections
using similar techniques (Chuhma et al., 2011; Xia et al., 2011).
Although it is often difficult to explain negative findings, these
previous studies used younger animals than did this study,
which is consistent with a possible role of age- or experience-
dependent plasticity; moreover, we have shown that striatal
projections to DA neurons may be very difficult to find if the
subregions of the striatum and the SNc are not well matched
(highlighting the value of the CLARITY/COLM/TRIO approach).
For example, if ChR2 expression were predominantly in DMS
Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc. 643
Photoreceiver
DichroicGFP
excitationfilter
Dichroic
Focusing lens
Realtime Modulation and Demodulation
GFP emission filter
405nm LED
490nm LED
405 bandpass filter
MultimodeOptical Fiber
Time (s)-5 0 5 10
ΔF
/F (
%)
-6
-4
-2
0
2
4
6
DMS-projecting
CAV-cre AAV
pA
GCaMP6f
fiber optic implant
A B
G H
Time (s)-5 0 5 10
ΔF
/F (
%)
-2
-1
0
1
2
3
4
DLS-projecting
****
Time (s)-5 0 5 10
ΔF
/F (
%)
-2
0
2
4
6rewardno reward
DMS-projectingC D
Time (s)-5 0 5 10
ΔF
/F (
%)
-2
0
2
4
6rewardno reward
DLS-projecting
E F
I J ***
Figure 5. DMS- and DLS-Projecting SNc DA
Neurons Respond Similarly to Appetitive but
Differentially to Aversive Stimulation
(A) CAV-cre was injected into either the DMS or
DLS. An AAV expressing cre-dependent GCaMP6f
was injected into the SNc. A 400 mm fiber optic
implant was placed in the SNc.
(B) Fiber photometry rig schematic. See Experi-
mental Procedures for amore detailed description.
(C) Example of responses to reward observed in a
mouse expressing GCaMP6f in DMS-projecting
SNc DA neurons. Time 0 is aligned to either re-
warded or non-rewarded port entries in an operant
chamber. Arrow is placed at time 0. Area of light
shading is SEM.
(D) Example of responses to reward observed in a
mouse expressing GCaMP6f in DLS-projecting
SNc DA neurons.
(E) Quantification of the peak DF/F observed in
response to reward in mice expressing GCaMP6f
in DMS-projecting SNc DA neurons or in mice
expressing GCaMP6f in DLS-projecting SNc DA
neurons.
(F) Quantification of the DF/F observed at time 0 in
response to a non-rewarded port entry in mice
expressing GCaMP6f in DMS-projecting SNc
DA neurons or in mice expressing GCaMP6f in
DLS-projecting SNc DA neurons.
(G) Example of responses to shock observed in
a mouse expressing GCaMP6f in DMS-projec-
ting SNc DA neurons. Yellow bar indicates the
time of the shock (0–0.5 s). Area of light shading
is SEM.
(H) Example of responses to shock observed in a
mouse expressing GCaMP6f in DLS-projecting
SNc DA neurons.
(I) Quantification of the peak (extreme, whether
negative or positive) DF/F observed during the
shock in mice expressing GCaMP6f in DMS-pro-
jecting SNc DA neurons or in mice expressing
GCaMP6f in DLS-projecting SNc DA neurons.
****p < 0.0001.
(J) Quantification of the mean DF/F observed 1–5 s
post-shock in mice expressing GCaMP6f in DMS-
projecting SNc DA neurons or in mice expressing
GCaMP6f in DLS-projecting SNc DA neurons.
***p < 0.001. The same mice are shown in (C)–(J).
See also Figure S4.
and laterally located (DLS-projecting) DA neurons were being
patched, we would expect connections to be extremely sparse,
small and difficult to detect.
644 Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc.
Our result regarding the in vivo activity
of DMS- and DLS-projecting SNc DA
neurons is concordant with the hypothe-
sis put forward by Matsumoto and Hiko-
saka (2009) that DA neurons located
more ventrolaterally within the midbrain
increase firing in response to aversive
stimuli. By targeting SNc DA neurons
for observation based on their striatal
projection target, we directly tested and
substantially extended this hypothesis, demonstrating that the
differences in the representation of aversive stimuli among sub-
sets of SNc DA neurons relate to projection target. Additionally,
we observed a sustained activity increase in DMS-projecting
SNc DA neurons following shock. We speculate that this popula-
tion of DA neurons may also encode for a heightened sensitivity
or motivational state following an unfamiliar outcome (unlike the
reward stimulus, the mice had no previous experience of shock
prior to test day) in order to promote future action-outcome
learning.
Regarding anatomy of efferents alone, our finding that the
projections from SNc DA neurons to the DMS and DLS arise
from distinct locations within the SNc is not inconsistent
with several previous findings. For example, in rats that had
the DA neuron toxin 6-OHDA injected into the DLS, degenera-
tion of DA neurons was observed primarily in the lateral SNc
(Faure et al., 2005). Similarly, for mice in which DA neuron
TH expression was restricted to neurons projecting to either
the DLS or the ventromedial striatum (VMS), DLS-projecting
neurons were located more laterally than VMS-projecting neu-
rons (Darvas and Palmiter, 2009; 2010; see also Schiemann
et al., 2012).
Information transmitted along these separable activity
streams will depend on intrinsic properties of the DA neurons
and on their afferents. Indeed, combined with other recent lines
of evidence (Lammel et al., 2008, 2011; Margolis et al., 2008),
we have found that projection-defined subpopulations of DA
neurons display different intrinsic properties. For example,
increasing-amplitude Ih currents are observed progressing
medially to laterally within the midbrain DA system; DA neurons
in the medial paranigral nucleus of the VTA express little to no Ihcurrent (Lammel et al., 2011), whereas DA neurons in the lateral
SNc express the largest Ih currents. Differences in Ih currents are
strongly correlated with action potential rebound delays and can
influence pacemaking activity (Neuhoff et al., 2002), particularly
in the case of calbindin-negative SNc DA neurons (which consti-
tute the majority of the SNc DA neuron population).
Afferents to projection-defined SNc DA neurons also differ; in
particular, we here identify new principles of afferent-projection
complexity in SNc subcircuits (see Beier et al., 2015 for addi-
tional illuminating information regarding VTA subcircuits). A
prominent finding is that the DMS and DLS are preferentially
reciprocally connected with the very same DA neurons that
project back to these areas. This information notably enriches
the ascending spiral model proposed by Haber et al. (2000),
which could not make definitive statements about striatal inputs
onto DAergic versus non-DAergic midbrain cells. We also
observed strong DLS projections to DMS-projecting DA neu-
rons; this finding implies a novel route of lateral to medial infor-
mation flow.
In summary, our identification of two distinct nigrostriatal
DA circuits—differing in inputs, outputs, biophysical properties,
and environmental information representations—both reveals
independently controlled information representations streaming
through SNc and provides a generalizable framework for
brain-wide mapping of diverse populations of neurons defined
by multiple independent types of features. Particularly in the
case of DA neurons, this type of approach may improve our un-
derstanding of the circuit mechanisms underlying normal brain
function, as well as diseases such as depression, addiction,
and schizophrenia.
EXPERIMENTAL PROCEDURES
Animals
All experiments were approved by the Stanford University IACUC committee,
protocol 10747. All mice (Ai9, TH-GFP, D1-tdTomato, and wild-type) were on a
C57BL6/6J background and were 2–4 months old.
Stereotaxic Injections
Viruses and retrobeads were injected and optical implants placed at the
following coordinates, relative to bregma: DMS +0.75 AP, 1.5 ML, �2.8 DV;
DLS +0.25 AP, 2.5 ML, �3.4 DV; medial SNc �3.1, 0.8 ML, �4.7 DV; lateral
SNc �3.1, 1.3 ML, �4.2 DV.
Histology
TH staining was done with 1:500 primary antibody overnight at 4�C and 1:500
secondary antibody coupled to Alexa Fluor 647 for 2–3 hr at room temperature.
GFP staining was done with 1:500 primary antibody coupled directly to either
Alexa Fluor 488 or Alexa Fluor 647 overnight at 4�C. Counterstaining was done
with Neurotrace 435/455 Blue Fluorescent Nissl Stain (1:500) and/or DAPI
(300 nM).
CLARITY
Brains were perfused and incubated with CLARITYmonomer solution contain-
ing 1% acrylamide, 0.0125% bis-acrylamide, and 4% PFA and then polymer-
ized at 37�C for 6–7 hr. Brains were passively cleared in SDS Borate Buffer
(pH 8.5) at 37�C for 4–5 weeks, equilibrated in Focusclear for imaging and
imaged using COLM methods (Tomer et al., 2014).
Slice Electrophysiology
300 mm coronal sections were prepared in an NMDG-based solution at room
temperature. Striatal slices were fixed in 4% PFA and saved for verification
of injection sites. Whole-cell recordings were performed in standard aCSF at
30–32�C. Where indicated, TTX (1 mm), 4-AP (100 mM), NBQX (5 mM), APV
(50 mM), and picrotoxin (50 mM) were added. In some experiments, extracel-
lular Ca2+ was replaced with Sr2+ to induce asynchronous release. K-gluco-
nate internal was used for recording action potentials and Ih currents. EPSCs
were recorded using CeMeSO3 internal and IPSCs were recorded using high
chloride CsCl internal. 5 ms blue light pulses (475 nm, �10 mW/mm2) were
used to stimulate ChR2.
Reward Behavior
Mice were trained to lever press for 20% sucrose reward on an RR10
schedule, earning a maximum of 40 25 ml rewards in a 1 hr session.
Shock Behavior
Mice received 15 mild foot shocks (0.4 mA, 0.5 s) on an RI60 schedule.
Fiber Photometry
A 490 nm LED was sinusoidally modulated at 211 Hz and passed through a
GFP excitation filter. A 405 nm LED was modulated at 531 Hz and passed
through a 405 nm bandpass filter. Both light streams were coupled to a high
NA (0.48), large core (400 mm) optical fiber patch cord, which was mated
to a matching brain implant in each mouse. GCaMP6f fluorescence was
collected by the same fiber, passed through aGFP emission filter, and focused
onto a photoreceiver. Custom software running on a real-time signal processor
controlled the LEDs and independently demodulated the fluorescence bright-
ness due to 405 nm and 490 nm excitation. The timing of behavioral variables
was recorded by the same system. To calculate DF/F, a least-squares linear fit
was applied to the 405 nm signal to align it to the 490 nm signal, producing a
fitted 405 nm signal that was used to normalize the 490 nm as follows: DF/F =
(490 nm signal � fitted 405 nm signal)/fitted 405 nm signal.
Statistics
Unpaired t tests were used for comparisons between two groups (DMS- and
DLS-projecting SNc DA neurons). Two-way ANOVAs were used to assess
how the properties or responses of DMS- and DLS-projecting SNcDA neurons
were affected by other factors (e.g., input area). When a statistically significant
Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc. 645
effect was observed using a two-way ANOVA, post hoc testing with correction
for multiple comparisons was performed using Tukey’s or Sidak’s multiple
comparisons test.
SUPPLEMENTAL INFORMATION
Supplemental Information includes Supplemental Experimental Procedures,
four figures, one table, and fivemovies and can be found with this article online
at http://dx.doi.org/10.1016/j.cell.2015.07.014.
AUTHOR CONTRIBUTIONS
T.N.L. and K.D. designed experiments, with input from L.L. and K.T.B on viral
tracing and with input from R.T. on CLARITY and COLM implementation. L.L.
and K.T.B. provided unpublished TRIO procedures. T.N.L. performed and
analyzed all experiments with contributions from K.T.B. on viral tracing, contri-
butions from R.T. and A.K.C. on whole-brain COLM imaging experiments and
related image analysis, contributions from K.E.E. on image quantification, and
contributions from C.S., T.J.D., and K.A.Z. on fiber photometry methods
development, implementation, and combination with freely moving behavior.
T.N.L. and K.D. wrote the paper with editorial input from all authors. K.D. su-
pervised all aspects of the work.
ACKNOWLEDGMENTS
We thank L. Ye and K. Engberg for advice on CLARITY; C. Ramakrishnan, S.
Pak, A. Shi On Hong, A. Wang, A. Lei, and H. Swanson for assistance with
animal husbandry and reagent production and acquisition; P. Rothwell and
L. Steinberg for advice and sharing of transgenic mouse lines; E. Callaway
for advice on rabies tracing; and the entire K.D. and L.L. labs for invaluable dis-
cussion. We also thank E. Kremer (IGMM) for supplying CAV-cre, M. Kay
(Stanford) for providing the pRC-DJ plasmid used to produce AAVDJ, the
Stanford Viral and Vector Core for packaging AAVDJ, and D. Kim for
supplying pGP-CMV-GCaMP6f (Addgene plasmid #40755), which was re-
cloned in our lab by C. Ramakrishnan. We thank the UNC vector core for sup-
plying the AAV5 and AAV8 vectors used in these studies and the Salk Vector
Core for supplying rabies (amplified in-house by the L.L. lab). T.N.L. was sup-
ported by a Stanford Dean’s Postdoctoral Fellowship and by an NRSA
Postdoctoral Fellowship (1F32MH105053-01). K.A.Z. was supported by an
NRSA Predoctoral Fellowship (1F31MH105151-01). This work was also
supported by the Hughes Collaborative Innovation Award (HCIA) and the
NIMH Silvio Conte Center at Stanford (P50 MH086403 to R.C.M.). K.D. is sup-
ported by the DARPA Neuro-FAST program, NIMH, NIDA, NSF, the Simons
Foundation, the Gatsby Foundation, the Wiegers Family Fund, the Nancy
and James Grosfeld Foundation, the H.L. Snyder Medical Foundation, the
Samuel and Betsy Reeves Fund, the Vincent VC Woo Fund, and the
Albert Yu and Mary Bechman Foundations. All optogenetics (http://www.
optogenetics.org), CLARITY (http://clarityresourcecenter.org), and COLM
(http://clarityresourcecenter.com/COLM.html) reagents and protocols are
distributed and supported freely.
Received: May 11, 2015
Revised: June 26, 2015
Accepted: July 8, 2015
Published: July 30, 2015
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Supplemental Figures
DMSDLS
M1/2 S1
Cortex (
Other) NAc
Dorsal S
triatu
m
FS (IPAC)
GPeSI/V
PBNST
CeA
Hypothala
mus
Thalamus
LHb SC ICSNc
SNrVTA
PAG
Dorsal R
aphe
MRNPPN PB
0
10
20
30
40
% c
ontra
late
ral i
nput
s DLS-projecting***DMS-projecting
ΔRG-GFP only
THRVdG-GFP
No CAV-creA B
THRVdG-GFP RVdG-GFP
DM
S-p
roje
ctin
gD
LS-p
roje
ctin
g
GP
GP
E
F
G
RVdG-GFP D1-tmt merge DMS-projecting 92/97 ≈ 95% DLS-projecting 210/214 ≈ 98%
D1-tmt mergeRVdG-GFP
D
C
DM
S-p
roje
ctin
gD
LS-p
roje
ctin
g M1
M1
LHb
LHb
HY
HY
PAG
PAG
MRNVTASNr
SNc
VTASNr
SNc
MRN
Figure S1. Proper EnvA-Pseudotyping of RVdG-GFP and Cre Dependency of Long-Range Tracing of Inputs, Divisions of the DMS and DLS
Subregions of Dorsal Striatum, Contralateral Inputs to DMS- and DLS-Projecting SNc Dopamine Neurons, and Dopamine D1 Receptor-
Expressing Identity of Striatonigral Inputs Identified by TRIO, Related to Figure 1
(A) Coronal slice showing the SNc of a mouse injected with only the RVdG-GFP virus. TH staining for dopamine neurons is shown in blue. The lack of GFP+ cells
indicates that the RVdG-GFP virus was not able to infect cells in the absence of TC expression.
(B) Coronal slices showing the SNc and striatum of a mouse injected with all the TRIO viruses except for CAV-cre. Left, some GFP+ cells are observed locally in
the SNc, indicating leak of the TC virus. This local background precludes conclusions about local connectivity in TRIO, but does not prohibit conclusions about
long-range connectivity. TH staining for dopamine neurons is shown in blue. Right, no GFP+ neurons are observed in the striatum (or any other structures that
provide long-range inputs to SNc dopamine neurons), indicating that long-range TRIO tracing of inputs here was indeed dependent on CAV-cre injections in the
DMS or DLS.
(C) Example coronal atlas images showing the divisions between DMS (yellow) and DLS (magenta).
(D) Example images showing coronal sections of the dorsal striatum at three distinct locations along the anterior-posterior axis (locations similar to the atlas
images shown in A).
(E) Example images of RVdG-GFP labeling of contralateral inputs to DMS- and DLS-projecting SNc dopamine neurons from various brain regions. M1, motor
cortex. HY, hypothalamus. LHb, lateral habenula. VTA, ventral tegmental area. SNc, substantia nigra pars compacta. SNr, substantia nigra pars reticulata. PAG,
periaqueductal gray. MRN, midbrain reticular nucleus.
(F) Whole-brain quantification of contralaterally labeled inputs to DMS- and DLS-projecting SNc dopamine neurons, expressed as a percentage of all contra-
lateral inputs. Other abbreviations: motor cortex (M1/2), somatosensory cortex (S1), fundus of the striatum/ interstitial nucleus of the posterior limb of the anterior
(legend continued on next page)
Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc. S1
commissure (FS/IPAC), globus pallidus external segment (GPe), substantia innominata/ventral pallidum (SI/VP), bed nucleus of the stria terminalis (BNST), central
amygdala (CeA), superior colliculus (SC), inferior colliculus (IC), pedunculopontine nucleus (PPN), parabrachial nucleus (PB).
(G) Images showing strong overlap of RVdG-GFP labeling in the dorsal striatumwith expression of the D1 dopamine receptor (labeled in a D1-tmt BAC transgenic
mouse). Scale bars are 50 mm.
S2 Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc.
CAV-cre DMS CAV-cre DLS
str
V
D
ctxctx
str
M LV
D
A
BDMS-projecting DLS-projecting
anterior
posterior
M LV
DM L
V
D
C
D
NAc core
NAc med
shell
NAc lat
shell
DMSDLS
0.0000
0.0005
0.0010
0.0015
0.2
0.4
0.6
0.8
1.0
Pro
ject
ion
Frac
tion
DMS-projectingDLS-projecting
DMS-projecting DLS-projecting
PFC
amyg
dala
Figure S2. CAV-cre Injections Contained within Distinct Dorsal Striatal Subregions and Anterior-Posterior Extent and Specificity of Stria-
tonigral Projections to DMS and DLS, Related to Figure 2
(A) CAV-cre was injected into striatum of Ai9 td-Tomato cre reporter mice. Left, CAV-cre injected into DMS. Right, CAV-cre injected into DLS. Dotted white line
highlights the corpus callosum. Ctx, Cortex. Str, Striatum.
(B) Example images of patterns of mGFP expression in the striatal projections of DMS- or DLS-projecting dopamine neurons, showing the full range of slices from
most anterior to most posterior. Green images show the original mGFP expression pattern. Black and white images to the right of each of the green images show
the analyzed image after background subtraction and thresholding.
(C) Projection fraction of DMS- and DLS-projecting SNc dopamine neurons in NAc core, NAc medial shell, NAc lateral shell, DMS and DLS. Error bars are SEM.
Data for the DMS and DLS are the same as shown in Figure 2G. This graph simply displays the full results, which included quantifications of the projection
fractions in NAc subregions.
(D) Histology sections showing a lack of mGFP-labeled axons from DMS- or DLS-projecting dopamine neurons in the PFC and amygdala. No mGFP expression
was observed despite GFP immunostaining to enhance the signal. DAPI counterstaining (light blue) shows the location of the tissue. Scale bars are 0.5 mm.
Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc. S3
GFP+ TH+GFP+ TH-
lateral SNc
95.4%
medial SNc
91.8%
lateral VTA
91.6%
midline VTA
37.3%
B lateral SNc
A
C
VTA
SN
c
TH Ab
TH Ab
TH-GFP
TH-GFP
medial SNc lateral VTA midline VTA
TH A
bTH
-GFP
mer
ge
Figure S3. Specificity of the TH-GFP Mouse Line for TH Immunopositive Neurons in the SNc and Lateral VTA, but Not the Midline VTA,
Related to Figure 3
(A) Low magnification (10x) images showing GFP expression (TH-GFP, green) and TH immunostaining (TH Ab, blue) in the midbrain (SNc and VTA) of TH-GFP
mice. Scale bars are 0.5 mm.
(B) High magnification (40x) images showing TH-GFP expression (TH-GFP, green) and TH immunostaining (TH Ab, blue) in four regions of the midbrain – lateral
SNc, medial SNc, lateral VTA, and midline VTA – which were quantified separately in C. Scale bars are 50 mm.
(C) Quantification of the percentage of GFP+ neurons that were also TH+ in the midbrains of TH-GFP mice (n = 3 mice). Pooled VTA data give a specificity of
71.8%, comparable to the specificity of 69% reported by Lammel et al. (2015).
S4 Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc.
-1 0 1 2 3 4 520
25
30
35
40
45
Peak During Reward
Rew
ards
Ear
ned
R2 = 0.08p = 0.53
-4 -3 -2 -10
5
10
15
20
Peak During Shock
% T
ime
Free
zing
R2 = 0.005p = 0.93
-4 -3 -2 -10.0
0.5
1.0
1.5
2.0
2.5
Peak During Shock
Post
-Sho
ck A
ctiv
ity B
urst
(s)
R2 = 0.18p = 0.57
0 1 2 3 420
25
30
35
40
45
Peak During Reward
Rew
ards
Ear
ned R2 = 0.22
p = 0.21
-1 0 1 2 3 40
5
10
15
20
25
Peak During Shock
% T
ime
Free
zing
R2 = 0.42p = 0.17
-1 0 1 2 3 40.0
0.5
1.0
1.5
2.0
Peak During Shock
Post
-Sho
ck A
ctiv
ity B
urst
(s)
R2 = 0.47p = 0.13
DLS
-pro
ject
ing
DM
S-p
roje
ctin
g
E
F
G
H J
THGCaMP6f
THGCaMP6f
THGCaMP6f
GCaMP6f
GCaMP6f
Striatum SNc SNc
M LV
D
ML
L
V
D
ctx
str
ctx
str
I K
Baseline47
5nm
400n
mA B
D
Stimulation C
filter filter
fit
subtract
400
300
200
100
0
Fluo
resc
ence
Inte
nsity
(A.U
.)
151050Time (s)
50 Hz e-stim
475nm 400nm
490nm Signal405nm Control
20 s2% Δ
F/F
L THGCaMP6f
Figure S4. Fiber Photometry Artifact Correction Using an Isosbestic Excitation Wavelength Control Signal, Expression of GCaMP6f in DMS-and DLS-Projecting Dopamine Neurons, and the Relationship of Recorded Fiber Photometry Signals with Behavior, Related to Figure 5
(A) Cultured neuron expressing GCaMP6f showing increased fluorescence upon 50Hz electrical field stimulation when illuminated with 475 nm but not 400 nm
light.
(legend continued on next page)
Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc. S5
(B) Quantification of the fluorescence time course represented in A.
(C) Schematic of the bleaching and artifact correction workflow. Both the calcium-dependent and –independent signals are filtered. The calcium-independent
(control) signal is then fitted to the calcium-dependent signal and subtracted from it to remove artifacts. A DF/F is further calculated by dividing by the control
signal.
(D) Sample trace from a GCaMP6f-expressing mouse under 405 nm or 490 nm illumination. Red dotted lines indicate reward retrieval times. Note the non-
responsiveness of the 405 nm signal to rewarding outcomes.
(E) Left, Histology showing the expression of GCaMP6f in terminals in the either the DMS or the DLS. Dotted line highlights the corpus callosumdividing the cortex
(ctx) and striatum (striatum). Middle, Histology showing the expression of GCaMP6f in SNc cell bodies in relation to TH staining (blue) and fiber optic placement
(dotted rectangle). Right, higher magnification images of GCaMP6f-expressing cell bodies in the SNc, showing healthy expression and overlap with TH staining
(blue).
(F) The number of rewards earned by individual mice expressing GCaMP6f in DMS-projecting SNc dopamine neurons did not correlate with the photometry
signals observed during reward collection.
(G) The number of rewards earned by individual mice expressing GCaMP6f in DLS-projecting SNc dopamine neurons did not correlate with the photometry
signals observed during reward collection.
(H) The time spent freezing during the shock session by individual mice expressing GCaMP6f in DMS-projecting SNc dopamine neurons did not correlate with the
photometry signals observed during shock delivery.
(I) The time spent freezing during the shock session by individual mice expressing GCaMP6f in DLS-projecting SNc dopamine neurons did not correlate with the
photometry signals observed during shock delivery.
(J) The time of post-shockmotor activity (running or jumping) by individual mice expressingGCaMP6f in DMS-projecting SNc dopamine neurons did not correlate
with the photometry signals observed during shock delivery.
(K) The time of post-shock motor activity (running or jumping) by individual mice expressing GCaMP6f in DLS-projecting SNc dopamine neurons did not correlate
with the photometry signals observed during shock delivery.
S6 Cell 162, 635–647, July 30, 2015 ª2015 Elsevier Inc.
Cell
Supplemental Information
Intact-Brain Analyses Reveal Distinct Information
Carried by SNc Dopamine Subcircuits
Talia N. Lerner, Carrie Shilyansky, Thomas J. Davidson, Kathryn E. Evans, Kevin T.
Beier, Kelly A. Zalocusky, Ailey K. Crow, Robert C. Malenka, Liqun Luo, Raju Tomer,
and Karl Deisseroth
Supplemental Experimental Procedures Animals. All animal experiments were approved by the Stanford University IACUC
committee, protocol #10747. All mice used in this study were on a C57BL/6J background.
In addition to wildtype mice (Jackson, strain 664), Ai9 tdTomato cre reporter mice
(Jackson, strain 7909), TH-‐GFP transgenic mice (MMRRC, stock #000292-‐UNC) and D1-‐
tdTomato transgenic mice (Jackson, strain 16204) were used where indicated. Only
heterozygote transgenic mice, obtained by backcrossing to C57BL/6J wildtypes, were used
for experiments. All mice were 2-‐4 months old. Males were used for TRIO and output
tracing. Electrophysiology experiments and behavior were performed in both males and
females (counterbalanced across conditions) with no significant effects of sex observed.
Injection and Implant Surgeries. Mice were anesthetized in an isoflurane induction chamber
at 3-‐4% isoflurane, and then injected with buprenorphine (0.05 mg/kg, s.q.) and carprofen
(5 mg/kg, s.q.) prior to the start of surgery. Anesthesia was maintained using 1-‐2%
isoflurane. Hair was trimmed from the scalp and the skin was cleaned with a povidone-‐
iodine solution (Betadine) prior to incision. The scalp was opened using a sterile scalpel
and holes were drilled in the skull at the appropriate stereotaxic coordinates (relative to
bregma: +0.75 AP, 1.5 ML, -‐2.8 DV for DMS, +0.25 AP, 2.5 ML, -‐3.4 DV for DLS, -‐3.1, 0.8 ML, -‐
4.7 DV for DMS-‐projecting SNc, and -‐3.1, 1.3 ML, -‐4.2 DV for DLS-‐projecting SNc.) Viruses
were infused at 100-‐200 nl/min through a 33-‐gauge injection needle using a syringe pump
(World Precision Instruments). Red Retrobeads IX (Lumafluor, diluted 1:2 in sterile saline,
80 nl) were infused using the same syringe pump system run at 80 nl/min. The needle was
left in place for 5 min following the end of the injection, then slowly retracted to avoid
leakage up the injection tract. For fiber photometry experiments, a fiber optic cannula was
then implanted over the SNc through the same hole as made for the virus injection. To
reduce autofluorescence artifacts and maximize light collection, cannulae (special ordered
from Doric Lenses) were fabricated using 0.48 NA 400μM BFH48-‐400 fiber, non-‐
fluorescent epoxy and metal 2.5mm ferrules. Cannulae were fixed to the skull using a thin
later of opaque Metabond dental cement (Parkell, S396 Radiopaque L-‐powder), followed
by Flow-‐it ALC light curing dental cement (Pentron Clinical, N11VH). After surgery, mice
were allowed to recover until ambulatory on a heated pad, then returned to their
homecage.
Viruses. Viruses were injected where indicated in the main text at the following volumes at
titers: CAV-‐cre, 2.5 x 1012 vg/ml, 250 nl; AAVDJ-‐hSyn1-‐mGFP-‐T2A-‐mRuby, 2.9 x 1013 vg/ml,
250 nl; AAV5-‐CAG-‐FLeX-‐TC, 2.6 x 1012 vg/ml, 325-‐500 nl; AAV8-‐CAG-‐FLeX-‐G, 1.3 x 1012
vg/ml, 325-‐500 nl; RVdG-‐GFP, 5 x 108 pfu/ml, 500 nl; AAV5-‐CaMKIIα-‐ChR2(H134R)-‐EYFP,
4 x 1012 vg/ml 250-‐500 nl; AAV5-‐EF1α-‐DIO-‐GCaMP6f, 1.9 x 1013 vg/ml, 1000 nl.
Transcardial Perfusions. Mice received lethal i.p. injections of Beuthanasia (Merck), a
combination of sodium pentobarbital and sodium phenytoin, to induce a smooth and rapid
onset of unconsciousness and death. Once unresponsive to a firm toe pinch, an incision was
made up the middle of the body cavity. An injection needle was inserted into the left
ventricle of the heart, the right atrium was punctured and solution (NMDG cutting solution
for electrophysiology, or PBS followed by 4% PFA for traditional histology, or PBS followed
by CLARITY monomer solution for CLARITY) was infused as the mouse was exsanguinated.
The mouse was then decapitated and its brain was quickly removed for further
experimentation.
CLARITY. Mice were perfused with CLARITY monomer solution containing 1% acrylamide,
0.0125% bis-‐acrylamide, 4% PFA, and 0.25% VA-‐044 diluted in PBS and left for two
overnights at 4°C to allow the monomer to fully penetrate the tissue. Then, the samples
were degassed and moved to a 37°C water bath for 6-‐7 hours to polymerize. After
polymerization, excess hydrogel was poured off and the brains were rinsed with PBS, then
transferred to clearing solution containing 4% SDS and 200mM boric acid in water,
adjusted to pH 8.5 with NaOH. Whole brains were incubated in clearing solution, shaking,
at 37°C for 4-‐5 weeks (until brains were clear). Clearing solution was changed once per
week. After clearing, brains were stored in PBS + 0.02% sodium azide at room temperature
until ready for COLM imaging. For imaging, brains were equilibrated in Focusclear
(CelExplorer Labs).
Tissue Sectioning
After perfusion, brains were fixed overnight at 4°C in 4% PFA, then transferred to solution
of 30% sucrose in PBS, where they were stored for at least two overnights at 4°C before
sectioning. For TRIO, tissue was embedded in OCT (Tissue-‐Tek) and sectioned on a cryostat
at 60 μm and mounted on slides for counterstaining. All other tissue was sectioned on a
freezing microtome at 40 μm, stored in cryoprotectant (25% glycerol and 30% ethylene
glycol in PBS, pH 6.7) at 4°C, then stained as free-‐floating sections before mounting.
Histology and Immunostaining.
TRIO sections were counterstained with Neurotrace 435/455 Blue Fluorescent Nissl Stain
and DAPI (Life Technologies, Cat. No. N-‐21479, D1306) on slides. Slides were rinsed with
PBS for 5 minutes, permeabilized with 0.3% Triton X in PBS (PBS-‐T) for 20 minutes,
stained with Neurotrace (1:500 in PBS) for 2 hours at room temperature, stained with
DAPI (300nM) for 20 minutes, then rinsed with PBS for 5 minutes and coverslipped with
Fluoromount G mounting medium (Southern Biotech). Tyrosine hydroxlase (TH) staining
was performed where indicated in the text. Staining was performed on free floating
sections, which were blocked with 3% normal donkey serum in PBS-‐T for 1 hour at room
temperature, then stained with 1:500 primary antibody (Aves Labs, Cat No. TYH) in
blocking solution at 4°C overnight. Secondary staining was performed using 1:500 goat
anti-‐chicken Alexa Fluor 647 secondary antibody (Life Technologies, Cat. No. A-‐21449).
Anti-‐GFP staining was performed to amplify signals from all sections containing mGFP and
GCaMP6f by blocking in 3% normal donkey serum in PBS-‐T for 1 hour at room
temperature, then using 1:500 primary antibody conjugated directly to either Alexa Fluor
488 or Alexa Fluor 647 (Life Technologies, Cat. No. A-‐21311, A-‐31852) in blocking solution
at 4°C overnight.
Traditional Imaging.
Axon collateralization mapping sections and TRIO sections were imaged on a
epifluorescent slide scanner system (Leica, DM6000 B with Ariol SL200 slide loader) with a
5x air objective using Neurotrace or DAPI counterstaining to focus the images. All other
images were taken using a confocal microscope (Leica, TCS SP5) with 5x or 10x air
immersion objectives, or 40x or 63x oil immersion objectives. In sections where
fluorescence intensity was quantitatively compared, all acquisition settings were held
constant.
Axon Collateralization Analysis.
Images of mGFP expression were acquired from a systematic image series from each
mouse corresponding to the full anterior-‐posterior span of the striatum (5-‐6 sections per
brain). All images were acquired using identical settings and were analyzed using ImageJ.
Regions of interest were defined using the DAPI reference channel. Images were then
background subtracted (rolling ball radius of 50 pixels), thresholded and binarized (pixel
values >30 = black). The projection fraction was calculated as (black area in region of
interest) / (total black area in all regions).
COLM Imaging and 3D volume rendering. Whole brain imaging was performed using COLM
(Tomer et al., 2014) or second generation COLM (Tomer et al., in preparation), as described
in detail (Tomer et al., 2014). The images were acquired along the dorsal-‐ventral axis.
Whole brain volume rendering movies were prepared using 4x4 fold downsampled data in
the x-‐y dimensions or using full resolution data in the case of Movie S5. Data stitching was
performed using an adapted Terastitcher based pipeline (Bria and Iannello, 2012) and
volume rendering using Amira (FEI) and ImageJ software.
Cell Counting. Cell counting was performed in a semi-‐automated fashion using Imaris
software (Bitplane). For each brain region counted, Imaris spot detection parameters were
defined that most accurately counted GFP-‐labeled cell bodies as determined by manual
verification. Brain regions were defined with reference to the Allen Mouse Brain Reference
Atlas (http://mouse.brain-‐map.org/static/atlas), using the Paxinos and Franklin atlas
(Paxinos and Franklin, 2004) as a secondary resource (e.g. for NAc core vs. shell). For
subdivision of the dorsal striatum into dorsomedial and dorsolateral portions, an in-‐house
atlas was created (Fig. S1C-‐D). Regional boundaries were defined a priori without biasing
by reference to labeling in our experiments.
Slice Electrophysiology. Three weeks after injections, mice were transcardially perfused
with a room-‐temperature NMDG slicing solution (containing in mM: 92 N-‐methyl-‐D-‐
glucamine, 2.5 KCl, 30 NaHCO3, 1.2 NaH2PO4-‐H2O, 20 HEPES, 25 glucose, 5 sodium
ascorbate, 2 thiourea, 3 sodium pyruvate, adjusted to pH 7.4 with HCl) and the brain tissue
was sliced in the same NMDG solution using a vibratome (VT1200S, Leica). Slices
containing the striatum were fixed in 4% PFA and saved for verification of the ChR2 and
retrobead injection sites. 300µm coronal slices containing the substantia nigra were
allowed to recover for 10 minutes at 33°C in NMDG solution, then another 20 minutes at
33°C in a modified HEPES artifical cerebrospinal fluid (containing in mM: 92 NaCl, 2.5 KCl,
30 NaHCO3, 1.2 NaH2PO4-‐H2O, 20 HEPES, 25 glucose, 5 sodium ascorbate, 2 thiourea, 3
sodium pyruvate), then another 15 minutes at room temperature in the modified HEPES
solution. Finally, slices were transferred to standard artificial cerebrospinal fluid (aCSF;
containing in mM: 125 NaCl, 2.5 KCl, 2 CaCl2, 1 MgCl2, 26 NaHCO3, 1.25 NaH2PO4-‐H2O, 11
glucose) bubbled with 95%O2/5%CO2 and stored at room temperature until recording.
Whole-‐cell patch clamp recordings were performed in the same aCSF solution at 30-‐32°C.
Signals were amplified with a Multiclamp 700B amplifier, acquired using a Digidata 1440A
digitizer, sampled at 10 kHz, and filtered at 2 kHz. All data acquisition and analysis were
performed using pCLAMP software (Molecular Devices). Neurons were visually identified
for patching using an upright microscope (Olympus BX51WI) equipped with IR-‐DIC optics,
filter sets for visualizing YFP and RFP, and a CCD camera (RoleraXR, Q-‐Imaging). Resistance
of the patch pipettes was 2.5–4MΩ when filled with intracellular solution. To record action
potentials and Ih currents, we used intracellular solution containing the following (in mM):
150 K-‐gluconate, 5 NaCl, 0.2 EGTA, 10 HEPES, 1MgCl2, 2 Mg-‐ATP, 0.3 Na-‐GTP, adjusted to
pH 7.3 with KOH. To measure Ileak and Ih, we held neurons at -‐40mV and stepped for 500ms
to -‐120mV. The average of three sweeps was taken, then Ileak was calculated as the change
in current between the baseline before the voltage step was applied and the current at ~40
ms after the voltage step was applied. Ih was calculated from the change in current between
~40 and 498 ms after the voltage step was applied. To record EPSCs and IPSCs, neurons
were voltage-‐clamped at -‐70mV. To record EPSCs, we added picrotoxin (50µM) to the
extracellular solution and used intracellular solution containing the following (in mM): 120
CsMeSO3, 15 CsCl, 8 NaCl, 0.2 EGTA, 10 HEPES, 2 Mg-‐ATP, 0.3 Na-‐GTP, 10 TEA
(tetraethylammonium), 5 QX-‐314 (lidocaine N-‐ethyl bromide), adjusted to pH 7.25 with
CsOH. To record IPSCs, we added NBQX (5µM) and APV (50µM) to the extracellular
solution and used intracellular solution containing the following (in mM): 130 CsCl, 1
EGTA, 10 HEPES, 2 Mg-‐ATP, 0.3 Na-‐GTP, 10 TEA (tetraethylammonium), 5 QX-‐314
(lidocaine N-‐ethyl bromide), adjusted to pH 7.25 with CsOH. Miniature EPSCs and IPSCs
were recorded in the presence of TTX (1µm). To isolate monosynaptic IPSCs from the DMS
and DLS, we added TTX (1µm) and 4-‐AP (100µM) to the extracellular solution. To stimulate
ChR2 expressed in axon terminals from the striatum, 5ms blue light pulses (475nm,
~10mW/mm2) were generated using a Spectra X LED light engine (Lumencor) and
delivered to the slice via a 40x/0.8 water immersion objective focused onto the recorded
neuron. Pulses were delivered once every 30 seconds. Response sizes were calculated by
baseline-‐subtracting and averaging 10-‐15 traces together, then calculating the peak
amplitude in a 50ms window after the light pulse. Neurons that did not show a peak
amplitude in this window that exceeded 5 SD of the baseline noise were counted as non-‐
responders. To measure qIPSC amplitude, we replaced extracellular calcium with 2mM
strontium to induce asynchronous release. We then calculated the average amplitude of
events occurring between 50ms and 250ms after the blue light pulse. The amplitude of
each event was measured from a local baseline just before the event (from 5-‐20ms prior to
the start of the event to the start) to avoid artifacts arising from the decaying transient of
the initial synchronous release.
Reward Behavior. Mice were water-‐restricted to ~1mL/day (maintained at >85% ad
libitum weight) and trained to press a lever for 25µl of 20% sucrose water on a 1:1
continuous reinforcement schedule. Med Associates operant boxes (ENV-‐307A-‐CT) were
arranged with an extra-‐tall sucrose port on one wall (to allow for head entry with the
implant attached) and active levers both to the right and to the left of the port. Mice were
required to retrieve each reward before the onset of the next trial. Mice were trained on
this schedule to criterion performance of >60% available rewards earned in one hour,
which required 4-‐8 days. Mice were then advanced to testing on a random ratio (RR10)
schedule in which each lever press had a 10% chance being rewarded. This schedule was
chosen to allow for increased total number of trials per session and for within-‐session
comparisons of rewarded and non-‐rewarded trials. One mouse was not advanced to testing
due to complications of surgery becoming evident during training. All sessions from start of
task habituation and training were performed with the mouse plugged in to a 400 µm
BFH48-‐400 patch cord using a metal ferrule sleeve, regardless of whether signals were
being recorded in order to habituate the mouse to tethering.
Shock Exposure Behavior. Mice were placed in an operant chamber (Med Associates,
different from the reward training chamber, but of the same dimensions) with a shock
floor, with their fiber optic implant plugged in to a 400 µm BFH48-‐400 patch cord using a
metal ferrule sleeve. Fifteen mild shocks (0.4 mA, 0.5 s) were delivered at random, about
once per minute (RI60 schedule). Photometry signal was recorded throughout session and
behavior was recorded by overhead camera. Freezing, defined as the complete absence of
movement except as required for respiration, was manually scored. Activity burst, defined
as abrupt increase in velocity of movement, was manually timed until return to baseline
movements in cage. Behavioral scoring was completed for a subset of animals by a single
experimenter blind to mouse group and photometry results.
Fiber Photometry. As in Gunaydin et al. (2014), we measured bulk fluorescence from deep
brain regions using a single optical fiber for both delivery of excitation light and collection
of emitted fluorescence. The fluorescence output of the calcium sensor is modulated by
varying the intensity of the excitation light, generating an amplitude-‐modulated
fluorescence signal that is demodulated to recover the original calcium sensor response.
This ‘upconversion’ of the calcium signal avoids contamination of the signal by changes in
ambient light levels with behavior , as well as avoiding low-‐frequency ‘flicker noise’ in our
photodetector. We have extended this method to the case of multiple excitation
wavelengths delivered over the same fiber, each modulated at a distinct carrier frequency,
to allow for simultaneous multicolor measurements. Two excitation LEDs (490nm ‘blue’
and 405nm ‘violet’, Thor Labs M490F1 and M405F1) were controlled via an RP2.1 real-‐
time processor (Tucker Davis Technologies) running custom software. Blue excitation was
sinusoidally modulated at 211Hz and passed through a GFP excitation filter (Thor Labs,
MF469-‐35); violet excitation was modulated at 531Hz and passed through a 405nm
bandpass filter (Thor Labs, FB405-‐10). These carrier frequencies were chosen to avoid
contamination from overhead lights (120Hz and harmonics) and cross-‐talk between
channels (the bandwidth of GCaMP6f was observed to be <15Hz), while remaining within
the 30-‐750Hz bandwidth of the photoreceiver. Excitation light from each LED was coupled
into a 0.39NA, 200um-‐core fiber (chosen to avoid overfilling the patchcord to the animal),
collimated, then combined by a 425nm long-‐pass dichroic mirror (ThorLabs, DMLP425).
The excitation light was coupled into a high-‐NA (0.48), low-‐autofluorescence 400µm patch
cord (manufactured by Doric Lenses,, using BFH48-‐400 fiber from ThorLabs) using a fixed-‐
focused high NA (0.51) coupler/collimator (Thor Labs, F240FC-‐A). Each LED was set to
30µW at the far end of the patch cord, which was terminated with a 2.5 mm ferrule. The far
end of the patch cord and the 2.5mm metal optical implant ferrule were cleaned with
isopropanol before each recording, then securely attached via a metal or zirconia sleeve.
The GCaMP6f emission signal was collected through the patch cord and collimator, passed
through a GFP emission filter (Thor Labs, MF525-‐39) and focused onto a femtowatt
photoreceiver (Newport, Model 2151) using a lens (Edmund Optics, Cat. No. 62-‐561). The
photoreceiver signal was sampled at 6.1 kHz, and each of the two modulated signals
generated by the two LEDs was independently recovered using standard synchronous
demodulation techniques implemented on the RP2.1 real-‐time processor: the detector
output was routed to two product detectors, one using the selected channel’s modulation
signal as a reference, and the other using a 90-‐degree phase-‐shifted copy of the same
reference. These outputs were low-‐pass filtered (corner frequency of 15Hz), and added in
quadrature. This dual-‐phase detection approach makes the output insensitive to any phase
delay between the reference and signal. The resulting fluorescence magnitude signals were
then decimated to 382 Hz for recording to disk and further filtered using an ~2Hz low-‐pass
filter before analysis. Behavioral variables, such as lever presses, reward port entry times
and shock times, were fed into the real-‐time processor as TTL signals from the operant
chambers. Files were then exported for analysis to MATLAB (MathWorks) using a custom
script. A least-‐squares linear fit was applied to the 405nm control signal to align it to the
490nm signal. The ΔF/F time series was then calculated for each behavioral session as
((490nm signal -‐ fitted 405nm signal) / fitted 405nm signal). Peristimulus time histograms
(PSTHs) were created using the TTL timestamps that had been fed in from the operant
chambers. Peak reward ΔF/F was calculated as the maximum ΔF/F value in the rewarded
port entry PSTH in a one second period around the reward retrieval (time 0). No reward
ΔF/F was calculated as the ΔF/F at time 0 in the non-‐rewarded port entry PSTH. Peak ΔF/F
during shock was calculated as the most extreme ΔF/F value (positive or negative)
observed during the shock period (time 0-‐0.5 seconds). Mean ΔF/F at 1-‐5 seconds post
shock was calculated as the mean ΔF/F value at time 1-‐5 seconds, where the shock
occurred at time 0-‐0.5 seconds.
Statistics. Unpaired t-‐tests were used for comparisons between two groups (DMS-‐ and DLS-‐
projecting SNc dopamine neurons). Two-‐way ANOVAs were used to assess how the
properties or responses of DMS-‐ and DLS-‐projecting SNc dopamine neurons were affected
by other factors (e.g. input area). When a statistically significant effect was observed using
a two-‐way ANOVA, post-‐hoc testing with correction for multiple comparisons was
performed using Sidak’s or Tukey’s multiple comparisons test. Statistics were performed
using Prism 6 (GraphPad) software.
Supplementary Tables Table S1. Percent Ipsilateral and Contralateral Inputs to DMS-‐ and DLS-‐projecting SNc Dopamine Neurons, Related to Figures 1 and S1 N= 4 brains per condition. Shown are means ± SEM. % Ipsilateral Inputs % Contralateral Inputs Input Area DMS-‐
projecting DLS-‐
projecting DMS-‐
projecting DLS-‐
projecting M1/2 1.66 ± 0.17 1.90 ± 0.20 3.04 ± 0.97 2.33 ± 0.58 S1 0.99 ± 0.07 1.21 ± 0.08 0.91 ± 0.36 0.52 ± 0.22 Cortex (Other) 0.67 ± 0.08 0.78 ± 0.16 2.27 ± 0.70 1.42 ± 0.13 NAc core 7.88 ± 2.03 3.49 ± 1.01 1.90 ± 1.39 1.15 ± 0.73 NAc med shell 4.23 ± 0.74 1.87 ± 0.62 NAc lat shell 2.83 ± 0.33 3.12 ± 0.16 DMS 18.09 ± 3.67 11.72 ± 1.33 0.84 ± 0.39 0.63 ± 0.29 DLS 27.90 ± 2.12 34.78 ± 3.81 FS (IPAC) 0.93 ± 0.45 2.10 ± 0.38 0.42 ± 0.15 0.07 ± 0.07 GPe 4.47 ± 0.28 6.01 ± 1.20 0.17 ± 0.1 0.66 ± 0.66 SI/VP 2.04 ± 0.12 2.45 ± 0.20 5.33 ± 1.79 2.91 ± 1.70 BNST 1.87 ± 0.43 2.21 ± 0.39 0.34 ± 0.13 0.40 ± 0.31 CeA 1.44 ± 0.35 1.83 ± 0.38 0.24 ± 0.13 0.10 ± 0.07 Hypothalamus 12.11 ± 1.55 11.37 ± 1.50 29.61 ± 0.92 23.49 ± 6.74 Thalamus 2.13 ± 0.17 1.63 ± 0.32 4.89 ± 1.37 3.23 ± 0.72 LHb 0.10 ± 0.03 0.31 ± 0.16 2.79 ± 0.69 1.52 ± 0.18 SC 1.83 ± 0.24 1.50 ± 0.30 4.48 ± 0.56 2.81 ± 0.59 IC 0.28 ± 0.10 0.10 ± 0.10 1.25 ± 0.81 0.63 ± 0.30 SNc 1.80 ± 0.49 1.65 ± 0.57 1.30 ± 0.53 1.96 ± 1.14 SNr 1.61 ± 0.28 1.83 ± 0.41 1.40 ± 0.76 2.86 ± 0.66 VTA 2.93 ± 0.52 2.27 ± 0.56 3.60 ± 2.08 5.82 ± 2.41 PAG 2.64 ± 0.58 2.45 ± 0.64 11.52 ± 2.98 11.74 ± 2.20 Dorsal Raphe 0.41 ± 0.22 0.62 ± 0.15 0.73 ± 0.43 7.53 ± 1.26 MRN 4.41 ± 1.10 3.38 ± 0.87 11.09 ± 3.12 22.83 ± 5.13 PPN 1.44 ± 0.32 0.66 ± 0.22 0.81 ± 0.51 1.70 ± 0.90 PB 0.72 ± 0.10 0.76 ± 0.33 9.86 ± 4.15 2.75 ± 1.45
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Paxinos, G., and Franklin, K.B.J. (2004). The Mouse Brain in Stereotaxic Coordinates (San Diego: Academic Press).