Biophysical characterization and simulation of neocortical layer 2/3 pyramidal neurons during postnatal development [Elektronische Ressource] / presented by Thomas Fucke

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Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences presented by Diplom-Physicist Thomas Fucke born in Kiel, Germany thOral examination: 17 October 2007 Biophysical Characterization and Simulation of Neocortical Layer 2/3 Pyramidal Neurons during Postnatal Development Referees: Prof. Dr. Bert Sakmann Prof. Dr. Karl-Heinz Meier Biophysikalische Charakterisierung und Simulation von Schicht 2/3 Pyramidenzellen in der Hirnrinde während der postnatalen Entwicklung Pyramidenzellen der Schicht 2/3 sind der häufigste Zelltyp in der Hirnrinde (Neokortex) von Säugetieren. Trotzdem ist über ihre biophysikalischen Eigenschaften bisher wenig bekannt. In dieser Doktorarbeit wurden grundlegende Eigenschaften von Pyramidenzellen der Schicht 2/3 von 1 bis 6 Wochen alten Ratten untersucht. Hierzu wurden elektrophysiologische Messungen in vitro mit morphologischen Rekonstruktionen und numerischen Rechnersimulationen kombiniert. Insbesondere sollten in dieser Arbeit die Ionenkanäle, die den unterschwelligen integrativen Eigenschaften dieser Zellen zugrundeliegen, und die Entwicklung der Kanalexpression bestimmt werden.

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Dissertation
submitted to the
Combined Faculties for the Natural Sciences and for Mathematics
of the Ruperto-Carola University of Heidelberg, Germany
for the degree of
Doctor of Natural Sciences
















presented by
Diplom-Physicist Thomas Fucke
born in Kiel, Germany
thOral examination: 17 October 2007
Biophysical Characterization and Simulation of Neocortical
Layer 2/3 Pyramidal Neurons during Postnatal Development

























Referees: Prof. Dr. Bert Sakmann
Prof. Dr. Karl-Heinz Meier

Biophysikalische Charakterisierung und Simulation von Schicht 2/3
Pyramidenzellen in der Hirnrinde während der postnatalen Entwicklung
Pyramidenzellen der Schicht 2/3 sind der häufigste Zelltyp in der Hirnrinde (Neokortex) von
Säugetieren. Trotzdem ist über ihre biophysikalischen Eigenschaften bisher wenig bekannt. In
dieser Doktorarbeit wurden grundlegende Eigenschaften von Pyramidenzellen der Schicht 2/3
von 1 bis 6 Wochen alten Ratten untersucht. Hierzu wurden elektrophysiologische Messungen in
vitro mit morphologischen Rekonstruktionen und numerischen Rechnersimulationen kombiniert.
Insbesondere sollten in dieser Arbeit die Ionenkanäle, die den unterschwelligen integrativen
Eigenschaften dieser Zellen zugrundeliegen, und die Entwicklung der Kanalexpression bestimmt
werden. Ein simulierter Erstarrungs-Algorithmus wurde eingesetzt um valide Modelle
unterschiedlichen Komplexitätsgrades zur Reproduktion experimenteller Daten zu erstellen.
Zu allen Altern zeigten Schicht 2/3 Pyramidenzellen deutliche anomale Rektifizierung, die
aufgrund pharmakologischer Experimente und aufgrund Simulationen auf einwärts-rektifizierende
Kaliumkanäle (KIR) zurückzuführen war. Nur ein geringer hyperpolarisations-aktivierter Strom (Ih)
wurde gefunden, sehr im Gegensatz zu anderen Pyramidenzelltypen. Während morphologische
Veränderungen bis zur zweiten postnatalen Woche abgeschlossen waren, änderten sich die
biophysikalischen Eigenschaften weiterhin bis Woche 4-6. Insbesondere der Eingangswiderstand
sank mit steigendem Alter, wodurch die Zellen im reifenden kortikalen Netzwerk weniger erregbar
wurden. In Computersimulationen hatten diese Eigenschaften starken Einfluss auf die Integration
synaptischen Eingangs während spontaner in vivo Aktivität. Daraus kann geschlossen werden,
dass Schicht 2/3 Pyramidenzellen biophysikalische Eigenschaften besitzen, die sich deutlich von
denen anderer Pyramidenzelltypen unterscheiden, und dass die verhältnismäßig lange
postnatale Entwicklung kritisch für die Entwicklung synaptischer Integration und kortikaler
Aktivität in vivo ist.



Biophysical Characterization and Simulation of Neocortical Layer 2/3
Pyramidal Neurons during Postnatal Development
Pyramidal neurons in layer 2/3 of the mammalian neocortex constitute the most abundant
neocortical cell type, yet their biophysical properties are still poorly understood. In this thesis,
fundamental properties of layer 2/3 pyramidal neurons of 1-to-6-weeks old rats were investigated
with an approach combining in vitro electrophysiological characterization, reconstruction of cell
morphologies, and numerical computer simulations. A specific goal was to identify ion channel
mechanisms underlying the sub-threshold integrative properties of these cells and to reveal the
developmental profile of channel expression. A simulated annealing algorithm was employed to
numerically simulate layer 2/3 neurons and to generate valid models of varying complexity and
constrained by experimental data.
At all ages, layer 2/3 pyramidal neurons showed prominent anomalous rectification which
could be attributed to inward-rectifier potassium (KIR) channels based both on pharmacological
experiments and modeling. In contrast to other types of pyramidal neurons little hyperpolarization-
activated current (Ih) was found. While morphological development essentially was complete at
postnatal week 2, biophysical properties continued to change until week 4-6. In particular, input
resistance strongly decreased with age, rendering the cells less excitable as the cortical network
matures. Computer simulations showed that these properties will have a large impact on the
integration of synaptic inputs during ongoing spontaneous activity in vivo. It is concluded, that
layer 2/3 pyramidal neurons possess biophysical properties distinct from other pyramidal cells
and that the prolonged postnatal development is critical for shaping synaptic integration and
neocortical circuit activity in vivo. Contents


1 Introduction
1.1 The mammalian neocortex 1
1.1.1 Laminar organization 2
1.1.2 Concepts of neuronal signaling 5
1.1.3 Neurons under in vivo conditions 7
1.1.4 Development 8
1.2 The L2/3 pyramidal neuron 10
1.2.1 Morphology 10
1.2.2 Electrophysiological properties 12
1.2.3 Input and output 14
1.3 Biophysics of neuronal computation 15
1.3.1 The passive cable equation 15
1.3.2 Voltage-dependent ion channels 17
1.4 Specific goals of this study 22

2 Experiments
2.1 Experimental methods 24
2.1.1 Electrophysiology
2.2.2 Data analysis 29
2.2 Experimental results 32
2.2.1 Morphological changes during development 32
2.2.2 Sub-threshold properties of L2/3 pyramidal cells 37
2.2.3 Supra-threshold properties of L2/3 pyramidal cells 42
2.2.4 Pharmacological Experiments 46
2.3 Discussion 54
2.3.1 Biophysical properties and development of L2/3
pyramidal neurons 54
2.3.2 KIR mediates anomalous rectification 59 2.3.3 Hodgkin-Huxley-fit to I-V curves 61

3 Modeling
3.1 Modeling methods 66
3.1.1 Voltage-dependent ion channels 66
3.1.2 Compartmenal modeling 69
3.1.3 Automated parameter search 71
3.1.4 Simulating UP/DOWN-states 78
3.2 Modeling results 79
3.2.1 Testing the simulated annealing (SA) algorithm 80
3.2.2 Reproduction of experimental data 84
3.2.3 Full morphology models 91
3.2.4 Simulation of in vivo activity 96
3.3 Discussion 100
3.3.1 Automated parameter search by simulated
annealing 100
3.3.2 Age-dependent L2/3 pyramidal cell model 102
3.3.3 UP- and DOWN-states 105
3.3.4 Expanding the model towards supra-threshold
behavior 106

4 Conclusion and Outlook 110

5 References 113

6 Acknowledgments 131

7 List of Abbreviations 132
1 Introduction
During the last century, a growing number of scientists from all disciplines have
become interested in the field of biological neuroscience. Besides more practical
results like the better understanding of neurological and mental diseases on the
cellular and molecular level, the ultimate driving force for the neuroscientific
research field is the expectation that by understanding the biological mechanisms
in the brain, one might one day understand what makes the human being “tick”,
i.e. what the biological basis is of emotions, percepts, attention, qualia and
consciousness. Paradoxically, the object of interest –the human brain – is the
very organ that allows the scientist to perform his research and in the end the
question remains whether the human brain will be able to truly understand itself.
For ethical considerations, of course, experiments on the cellular level
cannot simply be performed in humans (with the few exceptions of patients
undergoing brain surgery). Thus, most knowledge about neuronal mechanisms in
the brain has been inferred from central nervous systems (CNS) of other
organisms. Depending on the question at hand, the complexity of the model
organism may vary, ranging from very simple animals like the fruit fly Drosophila
melanogaster, the sea snail Aplysia californica and the worm Caernorhabditis
elegans over amphibians like Xenopus laevis, fish (zebrafish) and birds (zebra
finch) to mammals up to our next evolutionary relatives, the primate monkey. For
the purpose of this study, the rat (Rattus norvegicus) with its well characterized
CNS has been chosen as the appropriate model system to investigate the
mammalian brain in general and a specific cell type in the neocortex in particular.
In this introductory part of the thesis an overview of the research topic will
be given. During the following chapters, neuroscientific terms will be explained en
passant for those readers who are not familiar with the topic’s terminology. A list
of abbreviations can be found at the end of this thesis.


1.1 The mammalian neocortex
The neocortex is a structure common to all mammals although similar structures
are at least partly present in other vertebrates. It can also be considered the brain
structure defining us as humans since homo sapiens seems to be the animal with
the best developed neocortex in respect to cortical versus total brain volume. The
term neocortex stems from its being relatively young in evolutionary terms.
1 1 Introduction

Fig. 1.1 Historical drawing of the human brain (1543, by Andreas Vesalius). Taken from
Squire et al., 2003.


1.1.1 Laminar organization
In the mammalian brain, the neocortex is a shell-like structure of a few
millimeters thickness engulfing most of the cerebrum. In humans as well as in
other primates it is heavily folded, with its outer appearance reminiscent of a
walnut. The structure of the surface, although appearing random, is conserved
from brain to brain within a species. Anatomical and functional studies of the
neocortex date back to the works of Santiago Ramon y Cajal (Nobel prize in
1906), who described cellular structures and anatomical organization of cortical
tissue in great detail (reprinted in Ramon y Cajal, 1995).
The neocortex contains a variety of cell types. A common feature of
neurons is their general structure: From a cell body (soma) several thin
protrusions stretch out into the surrounding tissue. These thin structures of which
neurons often grow several are termed dendrites. In addition, each neuron
possesses one axon, which establishes the connections to target neurons. While
dendrites stretch out from the soma a few millimeters at most, axons can become
meters in length. Both structures often show pronounced arborizations, which
have characteristic morphological features in different neuronal subtypes and
thus allow distinguishing cell types.


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