You are on page 1of 6

Progress

are almost always based on a statistical

A technicolour approach analysis of small amounts of data from mul-


tiple individuals, rather than on full analyses
of any actual circuit. Indeed, these problems
to the connectome are so severe that, with the exception of
Cajal, few scientists have been able to draw
general conclusions from such material that
Jeff W. Lichtman, Jean Livet and Joshua R. Sanes
have stood the test of time2.
Abstract | A central aim of neuroscience is to map neural circuits, in order to learn
Diffusion or transport of labelling agents
how they account for mental activities and behaviours and how alterations in them
placed at discrete positions. The problem
lead to neurological and psychiatric disorders. However, the methods that are of visualizing long-distance connectivity
currently available for visualizing circuits have severe limitations that make it can be addressed, at least in part, by circuit-
extremely difficult to extract precise wiring diagrams from histological images. tracing techniques, which involve marking
Here we review recent advances in this area, along with some of the opportunities tracts that project from one brain region
that these advances present and the obstacles that remain. to another. Tracts are generally labelled by
mechanically introducing a specific labelling
agent for instance, through a surgical pro-
Understanding how the precise intercon- Single-cell staining by dye impregnation. cedure. The first tract-tracing methods to be
nections of neurons account for brain This was the first and most influential applied, however, took advantage of the fact
functions has been a preoccupation of approach. Single-cell impregnation is rooted that axons degenerate following injury and
neuroscientists for over a century. To in the extraordinary work of Santiago leave behind debris that persists for days to
accomplish this aim, neuroscientists will Ramn y Cajal (18521934), who used weeks before it is cleared. This debris could
need various types of data. First, we Golgis black reaction a silver-staining be stained with silver salts. Thus, following
will need a physical map of the neurons technique that labels neurons with a dark local damage to a neuronal population or
that comprise a circuit and the sites at precipitate. This method stains the entirety tract, the silver stain marked sites to which
which they form synapses with each other. of just a few individual nerve cells and neurons had projected3.
Second, we will need to understand how all their processes (axons and dendrites), By the 1970s, degeneration methods had
electrical signals flow through the circuit thereby making evident shapes that would largely been replaced by a suite of techniques
when a stimulus is perceived, a decision otherwise be indiscernible in the dense in which labels were placed into circum-
is made or an action is taken. Third, if the meshwork of the neuropil1. Using the Golgi scribed regions of the central or peripheral
circuitry undergoes modifications, we will stain, Cajal was able to not only identify nervous systems and then diffused or actively
need information on how circuits and their many different neuronal types in the brain, transported along axons to other sites
signals change over time. Finally, and argu- but also describe their pattern of intercon- (FIG. 1b). A wide range of labels proved useful
ably most demanding, we will need ways nections and discover principles of neuronal for this application: radioactive amino acids
to transform the raw data into useful forms circuit organization (FIG. 1a). or sugars, proteins such as the cholera toxin B
so that we can extract meaning from the Despite their power, the Golgi method subunit, enzymes such as horseradish peroxi-
physical maps. Neuroscientists are hard at and other single-cell labelling techniques dase, and fluorescent organic molecules such
work developing the tools that are needed for example, intracellular injection of dyes as DiI, DiO and Fluorogold4. Most recently,
to accomplish each of these; here we discuss have significant limitations. First, because genetically encoded tracers, including
several technological advances that might the chemicals with which the neurons are fluorescent proteins (see below), have been
provide solutions to the first problem: impregnated must be applied to relatively expressed under the control of subtype- or
obtaining a complete physical map of the small blocks of tissue, they cannot be used region-specific regulatory elements or from
nervous system. to trace long-distance connections. Second, viral vectors59. These methods have several
because of diffraction, neuronal processes advantages over methods that use chemical
Circuit-mapping strategies that come closer to each other than approxi- labels, including the possibility of indelible
Over the past century, neuroscientists mately 0.25 m are not resolvable in the light marking and, for the transgenic approaches,
have used three main sets of anatomical microscope. It is therefore difficult to trace avoidance of the need for surgery. An addi-
approaches to study neural connectivity: slender axons and dendrites without there tional exciting development is the ability to
single-cell impregnation, optically based being any ambiguities. Third, if all or even introduce genetically encoded trans-synaptic
tract-tracing and electron microscopy many of the elements in a circuit are stained, tracers that can cross from a neuron to its
(FIG. 1). In this section, we briefly discuss they become impossible to distinguish from synaptic partners812, thus revealing (with
these methods and their limitations. one another. Th erefore, circuit descriptions some caveats; see reF. 9) connectivity.

NATURe RevIewS | neuroscience vOlUMe 9 | jUNe 2008 | 417

2008 Macmillan Publishers Limited. All rights reserved


Progress

a b c

Figure 1 | circuit-mapping strategies. examples of the three main following the injection of radioactive proline into one eye40. c | serial electron
approaches that have been used to study the connectivity of neurons. microscopy can be used to reconstruct neurons and their processes with the
a | single-cell staining by dye impregnation. The best-known of these tech- Nature Reviews
best attainable resolution. shown here is a reconstruction from | Neuroscience
the adult rat
niques is the golgi staining method, which was used by ramn y Cajal to barrel cortex that was segmented from a three-dimensional image stack
describe the principles of neuronal circuit organization39. b | The introduction obtained by serial block-face imaging16. Part a reproduced, with permission,
of diffusible or transportable labelling agents to discrete areas. In some cases from reF. 39 (1914) Herederos de santiago ramn y Cajal. Part b repro-
the label crosses a synapse to reach a second-order target. A classical exam- duced, with permission, from reF. 40 (1977) royal society of London.
ple is the identification of ocular dominance columns in the visual cortex Part c reproduced, with permission, from reF. 16 (2006) elsevier sciences.

Despite the encouraging progress that brain tissue by looking at backscattered elec- each section. However, the need for sparse
there has been along these lines, difficulties trons with a scanning electron microscope15. labelling when using monochromatic labels
remain. First, tracing from a set of somata After taking the image, the top section of the remained an intractable limitation until
to a terminal field, or vice versa, will in most block is removed with a diamond knife and recently. The obvious solution is to use
cases leave local interneurons unlabelled or the block face is reimaged. This procedure multiple, distinct labels so that nearby pro-
impossible to resolve. Second, because these can now be iterated thousands of times cesses can be distinguished from each other.
methods typically label groups of neurons to give perfectly aligned stacks of digital This approach is exemplified by the use of
rather than individual cells, tract-tracing electron micrographs from which neuronal rainbow cables in electronic devices: the
methods can seldom be used to trace the processes can be traced (FIG. 1c). Other various colours of the wires help people keep
highly complex branching patterns of the approaches use new microtome designs track of them. Several methods designed
thousands of interdigitated axons and involving a rotary lathe and a tape transport along this principle have been applied to
dendrites in each cubic m of brain. system to automate the cutting and collec- the task of neuronal circuit visualization.
tion of serial thin sections. Along with new One, called Diolistics, involves shooting
Electron microscopy. Serial section electron methods in computational segmentation tissues with biolistic metal beads that have
microscopy has been the method of choice that improve tracing and three-dimensional been coated with various combinations
for overcoming the limited resolution reconstruction (see below), these innovations of different coloured lipophilic dyes, such
of light microscopy and the insufficiencies of are likely to restore electron microscopy to as DiI, DiO, and DiD, with the result that
tract-tracing. In pioneering work, levinthal, a position of prominence in circuit analysis. impregnated cells are labelled with different
lopresti and Macagno used this method to Nonetheless, large-scale reconstruction, colours18. However, Diolistic labelling is best
map connections in the optic lobe of the small especially over long distances, remains a dis- done ex vivo on slices, so it is poorly suited
crustacean Daphnia13, and white et al. used tant hope. For example, reconstructing paths for long-range reconstruction.
it to provide a nearly complete map of con- from the retina to the thalamus or from Another approach is based on the green
nectivity in the roundworm, Caenorhabditis the thalamus to the cortex would require fluorescent protein (GFP) revolution19,
elegans14. Serial electron microscopy is so hundreds of thousands or even millions of which has led to a technical renaissance in
laborious, however, that its application has sections to be acquired and analysed, and imaging. Over the past several years, dozens
been infrequent. Fortunately, this situation is even then there would be no obvious way to of spectral and photophysical fluorescent
now changing thanks to recent developments verify the accuracy of the tracing. protein variants (XFPs) have been discov-
in the automation of electron microscopy1517. ered or engineered20, and many of these have
One promising approach is to image the thin The multicolour solution been introduced as intrinsic neuronal labels
surface layer (tens of nanometers) of a block Introducing a marker into the reconstructed in transgenic mice. In some of the mice
of plastic-embedded and heavy-metal-stained neuron allows its identity to be verified in that produce these XFPs, the expression is

418 | jUNe 2008 | vOlUMe 9 www.nature.com/reviews/neuro

2008 Macmillan Publishers Limited. All rights reserved


Progress

Box 1 | Brainbow strategies XFPs are inserted at identical positions in


a pair of homologous chromosomes. These
a c elements remain non-functional until Cre
Yes No Yes recombinase (Box 1) triggers interchromo-
somal recombination to reconstitute active
XFP-encoding genes. Subsequent mitoses
loxP loxP lox2272 lox2272
segregate the alleles such that different cells
inherit different products of recombination
b d and thus express distinct colours.
Construct 1 2 3 Construct Despite their utility, bi- and tricolour
i ii iii
loxN lox2272 loxP mice have far too few labels to disambiguate
loxP loxP loxP loxP one neural process from the thousands
OFP RFP YFP CFP OFP GFP YFP RFP CFP GFP
Promoter Promoter of axons and dendrites that it will closely
Cre recombinase iv v approach as it courses through the nervous
Transient system. Recently, we developed a combi-
Cre recombinase
Outcomes iii activity natorial colour method, called Brainbow26,
Outcomes that addresses this problem by marking
RFP CFP RFP
1 RFP YFP CFP RFP i individual neurons in one of >100 colours
or GFP YFP GFP rather than one of 23 colours. The method
2 YFP CFP
is based on combinatorial and stochastic
YFP CFP RFP CFP
or
expression of multiple XFPs from a single
CFP YFP
transgene. In principle, combinatorial
3 CFP YFP GFP expression of three different XFPs could
colour neurons in one of ten hues (FIG. 2).
Brainbow transgenes drive the combinatorial expression of several fluorescent proteins (XFPs) in
Naturethe
Reviews | Neuroscience However, three XFPs can produce a much
neurons, resulting in the colour-tagging of individual cells. Here we outline methodology that
we used to generate these constructs. larger number of hues if they are expressed
The strategy makes use of the Cre/lox recombination system. Cre recombinase specifically in different amounts in different neurons.
recognizes and catalyses recombination between a pair of 34-nucleotide sequences called loxP. A good analogy is a Tv monitor, which
This reaction leads to the excision of a DNA segment that is flanked by two loxP sites of the combines different intensities of three chan-
same orientation, and to the inversion of a DNA segment that is flanked by loxP sites of opposite nels (red, green and blue) to generate almost
orientation (see figure, part c). the entire colour spectrum that the human
One strategy, Brainbow-1, makes use of mutant lox sites that can recombine among themselves visual system can perceive (FIG. 2b). Our
but which bear mutations that render them incompatible with the canonical loxP site7; see figure, thought was to use such colour combina-
part a). Alternating canonical (wild-type) loxP sites with variant sites creates mutually exclusive tions to distinguish neurons in a circuit by
excision possibilities (see figure, part b). Implementation of this strategy with three lox variants
generating a random mixture of three fluo-
creates four possible outcomes following excision by Cre recombinase: three different products of
recombination plus the unrecombined initial state. In all cases, only the XFP directly following the rescent proteins in each neuron. This sto-
promoter is expressed. A second strategy, Brainbow-2, uses Cre-recombinase-mediated DNA chastic colour expression was accomplished
inversion. The DNA segment can invert repeatedly while Cre recombinase is present but will in two steps. First, we designed genetic
stabilize in a random orientation when Cre recombinase stops acting, offering two possibilities of constructs that could be recombined in
expression. Moreover, when two such invertible segments are arranged in tandem, the number several mutually exclusive ways to give any
of possibilities is increased: additional inversion and excision possibilities create a total of four one of three or four colours (see Box 1 for a
expression possibilities (see figure, part d). detailed description of the method). Second,
Both of these strategies are in essence stochastic: the Cre recombinase enzyme is given a choice we inserted multiple copies of the transgene
and the outcome is unpredictable. This rolling of the molecular dice allows each cell to into the genome. Independent expression
independently make a random choice from several XFPs. In the transgenes, a choice is initially given
from each copy allows a range of colours to
between several recombination possibilities, each leading to a distinct final configuration (that is,
the different sides of the molecular dice) corresponding to the expression of a particular gene. result from combinatorial expression of the
For the generation of the first-generation Brainbow mice26, transgenes were placed under the XFPs (FIG. 2c). As a result, individual neurons
control of Thy1 genomic elements to obtain strong neuronal expression; these animals were express one of many distinguishable hues
mated to other transgenic mice that expressed Cre recombinanse or a ligand-activated variant, (~100), enabling the spectral differentiation
CreER. CFP, cyan fluorescent protein; gFP, green fluorescent protein; oFP, orange fluorescent of individual neurons and their processes
protein; rFP, red fluorescent protein; YFP, yellow fluorescent protein. Figure modified, with (FIG. 3).
permission, from reF. 26 (2007) Macmillan Publishers Ltd.
The role of Brainbow in connectomics
Brainbow transgenes have generated striking
confined to small, quasi-random subsets of for expressing two XFPs in a mosaic man- images and excited considerable interest, but
cells, creating the equivalent of a vital Golgi ner is the ingenious mosaic analysis with how can they actually be expected to con-
stain21. By crossing two such lines of mice double markers (MADM) strategy25. In this tribute to the mapping of neuronal circuits?
expressing spectrally distinct XFPs, one can method, the XFP genes are artificially split Their potential is illustrated by our recent
obtain bicolour or even tricolour animals by a synthetic intron that contains a loxP site experience with perhaps the simplest con-
in which the interactions between two neu- (Box 1). Reciprocally chimeric genes made nectome: the innervation of skeletal muscles
rons can be visualized2124. Another method by pairing the exons that encode the two by motor axons. A few years ago, before

NATURe RevIewS | neuroscience vOlUMe 9 | jUNe 2008 | 419

2008 Macmillan Publishers Limited. All rights reserved


Progress

a b connectome of the muscle. This enterprise


Red Green Blue required several months of work for each
individual muscle, highlighting the scale of
the technical hurdles that would have to be
surmounted to accomplish the same task for
any region of the CNS. By contrast, as we
have begun to reconstruct neuromuscular
connectomes with Brainbow lines, we
have found that the whole process can be
accomplished in an order of magnitude less
time. Indeed, in some cases it is possible to
identify the destination of an axon without
RFP YFP CFP having to trace its path, as its unique colour
remains recognizable along its length.
c1 2 3 Based on these initial encouraging
P RFP YFP CFP P RFP YFP CFP P RFP YFP CFP results, we are hopeful that Brainbow
technology can also be applied to model
nervous systems with limited numbers of
CFP CFP CFP Blue axons in order to further deduce principles
of nervous system connectivity. Brainbow
CFP CFP YFP Light blue transgenes are already being used for mul-
ticolour labelling of the zebrafish sensory
CFP YFP YFP Cyan
nervous system (Y.A. Pan and A. Schier,
YFP YFP YFP Green personal communication), and attempts are
underway to generate Brainbow Drosophila.
YFP YFP RFP Yellow-green A much more ambitious goal is to use
Brainbow methods in the mammalian CNS.
YFP RFP RFP Orange
Here the challenges include the sheer density
RFP RFP RFP Red of the wiring, the very fine calibre of much of
the neuropil, the enormous diversity of
RFP RFP CFP Magenta neuronal types and the interesting fact that
many axons travel very long distances to
RFP CFP CFP Purple
innervate neurons throughout the brain.
RFP CFP YFP Grey These obstacles make it unlikely that com-
plete connectomes of large brain regions will
Resulting colour
be obtainable in the next few years. working
Figure 2 | combinatorial expression of three distinct fluorescent proteins can generate a large towards that end seems a valuable goal, how-
spectrum of colours. a | several spectrally distinct fluorescent proteins (XFPs) are now available,
Nature Reviews | Neuroscience ever, and even partial connectomes for
including ones that emit in red (rFP), green (YFP) and blue (CFP) frequencies. b | The combinatorial
expression of red, green and blue XFPs at various levels is sufficient to encode a colour space analo- example, of the retinal inner plexiform layer
gous to the one that is generated by an rgB video monitor. c | An example showing how ten distinct or of a cortical column would provide
colours can be generated by expressing a trimeric combination of three different XFPs. In Brainbow considerable insight into the design
mice, this outcome would result if three copies of a trichromatic transgene (illustrated at the top of principles of the brain.
the panel; see Box 1 for details) each recombined independently (Box 1). Triangles represent lox sites Moreover, such partial connectomes
(see Box 1 for details). CFP, cyan fluorescent protein; P, promoter; rFP, red fluorescent protein; YFP, might be useful in studying mouse models of
yellow fluorescent protein. psychiatric disorders. There is a growing sus-
picion that defects in the pattern, number or
proportions of connections might underlie
Brainbow lines were available, we began by wrong. In order to get sufficient resolution behavioural disorders with a developmental
using a mouse line in which all motor axons to track all of the axons and at the same time component, such as schizophrenia and
are labelled the same colour21 to reveal the image the whole innervation field, we had autism. The primary causes of such disor-
entire connectional map in a single muscle. to assemble tens of thousands of high mag- ders might include various genetic variants
we worked on a single small muscle that was nification confocal images into hundreds of or environmental insults that might affect
innervated by only 15 or so motor axons stacks and then stitch the stacks together to various molecular cascades or developmen-
(j. lu, personal communication). A com- generate a montage of the whole muscle. Use tal events, but the final common pathway
plete map requires that all axons be labelled, of a motorized computer-automated stage could be a quantitative or qualitative defect
and this is one of the limitations of the now- made it possible to collect the images, which in circuitry. That is, some disorders of this
existing first generation Brainbow mice (for together comprised hundreds of gigabytes sort might be connectopathies. Because
a detailed discussion of these limitations see of data. Then, using computer-assisted trac- Brainbow labelling facilitates the surveying
below). Our thought was that, with only 15 ing, we tracked the entire branching tree of of quantitative and qualitative aspects of
axons innervating ~200 muscle fibres, such each motor axon and its synaptic contacts circuitry in diverse brain regions, it might
a mapping would not be difficult. we were (a motor unit) to reconstruct the entire enable this hypothesis to be tested.

420 | jUNe 2008 | vOlUMe 9 www.nature.com/reviews/neuro

2008 Macmillan Publishers Limited. All rights reserved


Progress

a b c

Figure 3 | Multicolour neuronal labelling in Brainbow transgenic mice. co-integration of several tandem copies of the transgene into the mouse
a | A motor nerve innervating ear muscle. b | An axon tract in the brainstem. genome and the independent recombinationNature of each by Cre recombinase
Reviews | Neuroscience
c | The hippocampal dentate gyrus. In the Brainbow mice from which these (see FIG. 2c). The images were obtained by the superposition of separate red,
images were taken, up to ~160 colours were observed as a result of the green and blue channels. The image in part a is courtesy of ryan Draft.

It will also be valuable to use Brainbow Finally, Brainbow can be used to highlight antibodies to detect the XFPs themselves
transgenes to learn how connectional connections of another sort: the lineage rela- is unfortunately not yet feasible, because
patterns change over the lifespan of an tions among cell populations. If recombina- several of the XFPs (for example, GFP, cyan
animal. For example, the neurobiological tion is induced in neural progenitors with a fluorescent protein and yellow fluorescent
underpinnings of healthy aging remain a ligand-activated Cre recombinase (for exam- protein) differ by only a few amino acids
mystery. Solving this mystery is not only ple, Tamoxifen-dependent CreeR) (Box 1), all and are, in effect, antigenically identical. If
important in its own right, but might also offspring of a particular blast cell should be immunohistochemical detection is used, one
be required if we are to understand the labelled with the same colour. This approach can also localize sites of synaptic contacts on
pathological alterations to which the aging might allow the analysis of the interactions of or between marked cells, using antibodies to
nervous system is especially vulnerable. many clonal sets of cells (each with their own pre- or postsynaptic components. Methods
likewise, circuit modifications that under- colour) in the same piece of tissue. such as array tomography, in which thin
lie the critical period in early postnatal sections of brain material are assayed with
life are incompletely understood, as are Technological challenges an assemblage of antibody probes, provide an
the compensatory changes that make the For more complex circuits, the diffraction- elegant protocol for detecting many antigens
young nervous system so resilient limited resolution of the light microscope (or epitope tags) in single thin sections31.
following injury. is a serious limitation. Fortunately, several A more radical solution to the resolution
In studying these issues, the microscopic solutions to this problem are already emerg- problem might be provided by the new and
analysis that we have used so far will be use- ing. One is to cut extremely thin sections of rapidly growing field of nanoscopy, which
ful. Greater insights might eventually come labelled tissue31,32. By cutting sections that overcomes the resolution limitations of
from time-lapse imaging of circuit altera- are several-fold thinner than the optical light diffraction3438. These new imaging
tions as they occur. XFPs make ideal labels section thickness, the superimposition of modalities provide resolutions of tens of nm
for this purpose, and time-lapse methods multiple neurites in the same focal thickness which, alone or with the addition of spectral
have now been applied to many parts of the is avoided. In addition, the thin samples information, might be sufficient to trace the
peripheral and central nervous systems of scatter light much less, and this improves the finest neuropil.
one- and two-colour XFP mice2730. Further contrast and clarity of the labelled material. In parallel, it will be important to design
improvements in spectral separation, acqui- To make such thin sections, the neural new Brainbow transgenes to increase the
sition rate and detector sensitivity should tissue must be embedded in a hard resin. range of neuronal types and developmental
make it possible to expand the method to This, in turn, requires the XFPs to retain stages to which the method can be applied.
Brainbow mice. their fluorescence following the dehydra- There are several major limitations of
So far, we have only discussed con- tion and embedding steps. To some extent the first-generation Brainbow lines. The
nections among the minority cellular this might be possible; however, Brainbow regulatory elements that are used (from
population of the brain: neurons. Brainbow transgenes could alternatively be redesigned the Thy1 gene) direct high levels of expres-
methods can also be used to map connec- to include epitope tags that would be rec- sion in many projection neurons, but most
tions among the majority population, glia, ognized by antibodies33. This would allow interneurons are poorly marked21. Also,
or between neurons and glia. Indeed, some traditional staining methods to be used after in most lines, transgene expression is low in
Brainbow lines already label some glial sub- the tissue has been cut and would therefore embryos and during the first postnatal week,
sets, including astrocytes, Schwann cells and allow the labelling by the endogenous fluor- so these lines are unsuitable for develop-
Bergman glia; it should be straightforward to escent protein to be augmented or replaced. mental studies. Furthermore, some colours
generate others. The seemingly simple solution of using are dim (especially red shades), primarily

NATURe RevIewS | neuroscience vOlUMe 9 | jUNe 2008 | 421

2008 Macmillan Publishers Limited. All rights reserved


Progress

because the proteins are insufficiently photo- Jeff W. Lichtman and Joshua R. Sanes are at the 19. Tsien, R. Y. The green fluorescent protein. Annu. Rev.
Biochem. 67, 509544 (1998).
stable. Additionally, several bright XFPs Department of Molecular and Cellular Biology and
20. Shaner, N. C., Steinbach, P. A. & Tsien, R. Y. A guide to
Center for Brain Science, Harvard University,
are difficult to distinguish from each other choosing fluorescent proteins. Nature Methods 2,
Cambridge, Massachusetts 02138, USA. 905909 (2005).
(for example, yellow versus green or orange 21. Feng, G. et al. Imaging neuronal subsets in transgenic
Jean Livet is at INSERM, UMR S592, Institut de la
versus red) because their spectra are insuf- mice expressing multiple spectral variants of GFP.
Vision, F-75012, Paris, France and at UPMC University Neuron 28, 4151 (2000).
ficiently distinct. Moreover, although the of Paris 06, UMR S592, F-75005, Paris, France. 22. Walsh, M. K. & Lichtman, J. W. In vivo time-lapse
number of colours is presently large (~100), imaging of synaptic takeover associated with naturally
Correspondence to J.W.L. occurring synapse elimination. Neuron 37, 6773
it is nonetheless insufficient for some pur- e-mail: jeff@mcb.harvard.edu (2003).
poses. There are few conceptual difficulties doi:10.1038/nrn2391
23. Kasthuri, N. & Lichtman, J. W. The role of neuronal
identity in synaptic competition. Nature 424,
in designing second-generation Brainbow Published online 30 April 2008 426430 (2003).
transgenes that circumvent these limitations 24. Lichtman, J. W. & Sanes, J. R. Watching the
1. Sotelo, C. Viewing the brain through the master hand neuromuscular junction. J. Neurocytol. 32, 767775
but, as with the first generation, large num- of Ramon y Cajal. Nature Rev. Neurosci. 4, 7177 (2003).
bers of alternatives might need to be assayed (2003). 25. Zong, H., Espinosa, J. S., Su, H. H., Muzumdar, M. D.
2. Callaway, E. M. & Sanes, J. R. New technologies. Curr. & Luo, L. Mosaic analysis with double markers in mice.
before success is achieved. Opin. Neurobiol. 16, 540542 (2006). Cell 121, 479492 (2005).
It also remains to be seen whether 3. Nauta, W. J. Some early travails of tracing axonal 26. Livet, J. et al. Transgenic strategies for combinatorial
pathways in the brain. J. Neurosci. 13, 13371345 expression of fluorescent proteins in the nervous
multicolour labelling can generate complex (1993). system. Nature 450, 5662 (2007).
connectomes once these technical problems 4. Callahan, C. A., Yoshikawa, S. & Thomas, J. B. Tracing 27. Gan, W. B., Kwon, E., Feng, G., Sanes, J. R. &
axons. Curr. Opin. Neurobiol. 8, 582586 (1998). Lichtman, J. W. Synaptic dynamism measured over
have been solved. If it cannot, or even if it 5. Feinstein, P., Bozza, T., Rodriguez, I., Vassalli, A. & minutes to months: age-dependent decline in an
can, the rapid advances in high-throughput Mombaerts, P. Axon guidance of mouse olfactory autonomic ganglion. Nature Neurosci. 6, 956960
sensory neurons by odorant receptors and the 2 (2003).
electron microscopy might mean this adrenergic receptor. Cell 117, 833846 (2004). 28. Grutzendler, J., Kasthuri, N. & Gan, W. B. Long-term
technique emerges as a viable alternative16. 6. Bareyre, F. M., Kerschensteiner, M., Misgeld, T. & dendritic spine stability in the adult cortex. Nature
Sanes, J. R. Transgenic labeling of the corticospinal 420, 812816 (2002).
Finally, given that all of these methods are tract for monitoring axonal responses to spinal cord 29. Nguyen, Q. T., Sanes, J. R. & Lichtman, J. W.
evolving in parallel, it might be that the injury. Nature Med. 11, 13551360 (2005). Pre-existing pathways promote precise projection
7. Dymecki, S. M. & Kim, J. C. Molecular patterns. Nature Neurosci. 5, 861867 (2002).
optimal solution to connectomics will be a neuroanatomys Three Gs: a primer. Neuron 54, 30. Trachtenberg, J. T. et al. Long-term in vivo imaging
hybrid of techniques that includes not only 1734 (2007). of experience-dependent synaptic plasticity in adult
cortex. Nature 420, 788794 (2002).
8. Song, C. K., Enquist, L. W. & Bartness, T. J. New
Brainbow but also electron microscopy, developments in tracing neural circuits with 31. Micheva, K. D. & Smith, S. J. Array tomography: a
array tomography and advanced pathway- herpesviruses. Virus Res. 111, 235249 (2005). new tool for imaging the molecular architecture and
ultrastructure of neural circuits. Neuron 55, 2536
9. Luo, L., Callaway, E. M. & Svoboda, K. Genetic
tracing methods. dissection of neural circuits. Neuron 57, 634660 (2007).
(2008). 32. Peters, M. F. et al. Differential membrane localization
10. Horowitz, L. F., Montmayeur, J. P., Echelard, Y. & and intermolecular associations of -dystrobrevin
Conclusion Buck, L. B. A genetic approach to trace neural circuits. isoforms in skeletal muscle. J. Cell Biol. 142,
we call wiring diagrams connectomes to Proc. Natl Acad. Sci. USA 96, 31943199 (1999). 12691278 (1998).
33. Fritze, C. E. & Anderson, T. R. Epitope tagging: general
11. Yoshihara, Y. et al. A genetic approach to visualization
highlight the analogy to genomes. Obtaining of multisynaptic neural pathways using plant lectin method for tracking recombinant proteins. Methods
the sequence of the human genome was transgene. Neuron 22, 3341 (1999). Enzymol. 327, 316 (2000).
34. Bates, M., Huang, B., Dempsey, G. T. & Zhuang, X.
12. Wickersham, I. R. et al. Monosynaptic restriction of
difficult and expensive. The quest for con- transsynaptic tracing from single, genetically targeted Multicolor super-resolution imaging with photo-
nectomic information will probably be even neurons. Neuron 53, 639647 (2007). switchable fluorescent probes. Science 317,
17491753 (2007).
13. Macagno, E. R., Levinthal, C. & Sobel, I. Three-
more difficult. like genomics, connectomics dimensional computer reconstruction of neurons and 35. Heintzmann, R. & Ficz, G. Breaking the resolution limit
in light microscopy. Methods Cell Biol. 81, 561580
requires the development of new techniques, neuronal assemblies. Annu. Rev. Biophys. Bioeng. 8,
(2007).
323351 (1979).
the comparison of alternatives and ways 14. White, J. G., Southgate, E., Thomson, J. N. & 36. Hell, S. W. Far-field optical nanoscopy. Science 316,
11531158 (2007).
to make mundane and automatic what Brenner, S. The structure of the nervous system of the
nematode Caenorhabditis elegans. Philos. Trans. R. 37. Huang, B., Wang, W., Bates, M. & Zhuang, X. Three-
is initially difficult and labour-intensive. Soc. Lond. B Biol. Sci. 314, 1340 (1986). dimensional super-resolution imaging by stochastic
optical reconstruction microscopy. Science 319,
Unlike genomics, however, connectomics 15. Denk, W. & Horstmann, H. Serial block-face scanning
electron microscopy to reconstruct three-dimensional 810813 (2008).
might require the parallel application of tissue nanostructure. PLoS Biol. 2, e329 (2004). 38. Shroff, H. et al. Dual-color superresolution imaging of
genetically expressed probes within individual
multiple approaches for labelling, imaging, 16. Briggman, K. L. & Denk, W. Towards neural circuit
reconstruction with volume electron microscopy adhesion complexes. Proc. Natl Acad. Sci. USA 104,
reconstructing and analysing neurons. techniques. Curr. Opin. Neurobiol. 16, 562570 2030820313 (2007).
39. Ramn y Cajal, S. Estudios Sobre la Degeneracin y
Fortunately, the field is now moving at an 17.
(2006).
Hayworth, K., Kasthuri, N., Schalek, R. & Lichtman, Regneracin del Sistema Nervioso (Moya, Madrid,
astonishing pace, and the approaches we J. W. Automating the collection of ultrathin serial 19131914); reprinted and edited with additional
sections for large volume TEM reconstructions. translations by DeFelipe, J. & Jones, E. G. Cajals
have outlined here represent only a subset Microsc. Microanal. 12, 2 (2006). Degeneration and Regeneration of the Nervous
of those that are being developed independ- 18. Gan, W. B., Grutzendler, J., Wong, W. T., Wong, R. O. & System (Oxford Univ. Press, New York, 1991).
Lichtman, J. W. Multicolor DiOlistic labeling of the 40. Hubel, D. H., Wiesel, T. N. & LeVay, S. Plasticity of ocular
ently and energetically to overcome the nervous system using lipophilic dye combinations. dominance columns in monkey striate cortex. Philos.
challenges that lie ahead. Neuron 27, 219225 (2000). Trans. R. Soc. Lond. B Biol. Sci. 278, 377409 (1977).

422 | jUNe 2008 | vOlUMe 9 www.nature.com/reviews/neuro

2008 Macmillan Publishers Limited. All rights reserved

You might also like