Chemoarchitectonic Atlas of the Rat Brain

By George Paxinos, Mustafa S. Kassem, Matthew Kirkcaldie and Pascal Carrive

The complement to The Rat Brain in Stereotaxic Coordinates, Chemoarchitectonic Atlas of the Rat Brain, Third Edition, features a single brain series of high-quality plates stained with eight different markers, extensively annotated and labelled throughout. Plates from the previous edition of Chemoarchitectonic Atlas of the Rat Brain have been re-scanned at high resolution and are shown in color. Labeled structures have been revised, corrected, and updated, providing users with a streamlined, up-to-date, and highly accurate compendium of chemical markers. Researchers with a need to understand the detailed organization of the rat brain as well as structure/function relationships will need this atlas and its array of stains.

• Provides an archive of chemical markers in the rat brain used in many areas of research
• Discusses primary data to help researchers identify structures in their own preparations from neuroanatomical, physiological, neuropharmacological, and gene expression studies
• Accompanies the gold standard reference on the neuroanatomy of the nervous system of the most important model animal in neuroscience and experimental psychology
• Covers both the rat forebrain and the rat brainstem
• Thoroughly revised identification of structures following the new data from The Rat Brain in Stereotaxic Coordinates 7th edition and the Chick Brain in Stereotaxic Coordinates 2nd edition
• Includes the Expert Consult eBook version, compatible with PC, Mac, and most mobile devices and eReaders, which allows readers to browse, search, and interact with content

• Language: English
• Publisher: Academic Press
• Release date: Nov 18, 2021
• ISBN: 9780128189634

George Paxinos

Professor Paxinos is the author of almost 50 books on the structure of the brain of humans and experimental animals, including The Rat Brain in Stereotaxic Coordinates, now in its 7th Edition, which is ranked by Thomson ISI as one of the 50 most cited items in the Web of Science. Dr. Paxinos paved the way for future neuroscience research by being the first to produce a three-dimensional (stereotaxic) framework for placement of electrodes and injections in the brain of experimental animals, which is now used as an international standard. He was a member of the first International Consortium for Brain Mapping, a UCLA based consortium that received the top ranking and was funded by the NIMH led Human Brain Project. Dr. Paxinos has been honored with more than nine distinguished awards throughout his years of research, including: The Warner Brown Memorial Prize (University of California at Berkeley, 1968), The Walter Burfitt Prize (1992), The Award for Excellence in Publishing in Medical Science (Assoc Amer Publishers, 1999), The Ramaciotti Medal for Excellence in Biomedical Research (2001), The Alexander von Humbolt Foundation Prize (Germany 2004), and more

Book preview

9780128189634_FC

Chemoarchitectonic Atlas of The Rat Brain

Third Edition

George Paxinos

Neuroscience Research Australia and The University of New South Wales

Mustafa S. Kassem

Neuroscience Research Australia and The University of New South Wales

Matthew Kirkcaldie

The University of Tasmania

Pascal Carrive

The University of New South Wales

Academic Press

Table of Contents

Cover image

Title page

Copyright

Dedication

Preface

Acknowledgements

Introduction

Methods

Surgery

Histology

Cresyl Violet Staining

lmmunohistochemical Processing (Pv, Cb, Cr, SM132, TH)

NADPH-d Histochemistry

AChE Histochemistry

Mounting

Stereotaxic levels and scales

Variations in section presentation among the atlas photographs

Imaging

Nomenclature and Abbreviations

Special Features Revealed by Chemoarchitectonic Markers

Olfactory System

Taenia Tecta

Navicular Nucleus

Basal Ganglia

Septum

Diagonal Band Nuclei

Circumventricular Organs

Hypothalamus

Diencephalon

Prethalamus - prosomere 3

Thalamus - prosomere 2

Pretectal Nuclei - prosomere 1

Amygdala and Bed Nucleus of the Stria Terminalis

Hippocampus

Cerebral Cortex

Auditory System nuclei of the midbrain and hindbrain

Visual System and Eye Motor Nuclei of the Midbrain and Hindbrain

Oculomotor, Trochlear, Abducens Nuclei

Somatosensory Nuclei of the Midbrain and Hindbrain

Vestibular Nuclei

Orofacial Motor Nuclei

Periaqueductal Gray

Tegmental Nuclei of the Hindbrain

Raphe Nuclei

Parabrachial Nuclei

Benthic nucleus

Lateral Terminal Nucleus

Substantia Nigra

Reticular Nuclei of the Hindbrain

Nucleus of the Solitary Tract

Red Nucleus and Precerebellar Nuclei

Cerebellum

References

List of Structures

A

B

C

D

E

F

G

H

I

J

K

L

M

N

O

P

R

S

T

U

V

X

Z

Index of Abbreviations

Figures

Copyright

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ISBN: 978-0-12-818959-7

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Unlabelled Image

Dedication

To

Alexander

Jemima

Callie and Edie

Jean-Pierre and Anne

Preface

While the rat brain has not evolved in the 13 years since the publication of the second edition of this atlas (Paxinos et al., 2009b), our understanding has. A new edition gives us the opportunity to include the acetylcholinesterase series (AChE), previously omitted, and to bring the book in harmony with our rodent and human atlases in delineations and nomenclature.

The distribution of a chemical marker in the brain gives clues to regional organization. In this book, we map the distribution of eight marker substances and, on the basis of these maps, we attempt to define better the position of brain structures. We would be delighted to hear from users about suggested corrections/improvements to the benefit of future editions and those who use them; please email them to: [e-mail].

This book features:

•Fully labeled photographs of sections stained for parvalbumin (Pv), calbindin (Cb), calretinin (Cr), Nissl substance, dephosphorylated neurofilament protein subunits (SMI32 antibody), tyrosine hydroxylase (TH), nicotinamide adenine dinucleotide phosphate diaphorase (NADPH-d) and acetylcholinesterase series (AChE).

•All 559 coronal sections taken from a single brain, displayed in labeled photographs.

•Thoroughly revised identification of structures.

Acknowledgements

Our greatest thanks to Kristie Smith for help with delineations, index construction and page layout. We are indebted to Hongqin Wang for excellent histological preparations and Ping-Yu Wang, Laura Kus, Ken Ashwell and Charles Watson for their intellectual contribution to the first and second editions. We thank Jared Wyles for his amazing work on the index. We thank Yvette Paxinos (http://www.paxifilm.com/) for the cover design and Ani Lack for proofing the introduction. David Kopf provided us with their accurate stereotaxic instrument to do our work. We acknowledge the help of the talented staff at Academic Press Elsevier, Natalie Farra, Kathy Padilla and Andrew Riley. This research was supported by NHMRC grants (APP1188744, APP1140295, APP1086083).

Introduction

This book uses the distribution of eight marker substances to delineate all the structures in the rat brain. The calcium-binding proteins (Pv, Cb, Cr) were chosen because of their historical use across mammal and vertebrate species as markers of subpopulations of interneurons in the forebrain (Ascoli et al., 2008). Non-phosphorylated medium and heavy neurofilament subunits (recognised by the antibody SMI32, BioLegend Ltd.), were chosen as an outstanding marker of cortical areas (e.g., Kirkcaldie et al. (2002) & Paulussen et al. (2011)). Tyrosine hydroxylase (TH) was chosen to demonstrate catecholaminer- gic nuclei supplying adrenaline, noradrenaline and dopamine. Nicotinamide adenine dinucleotide phosphate diaphorase (NADPH-d), was chosen for its Golgi-like staining and to demonstrate synthesis of the intercellular messenger nitric oxide. Acetylcholinesterase (AChE), was chosen for direct comparison with The Rat Brain in Stereotaxic Coordinates, 7th edition (Paxinos and Watson, 2014). We used most of the same markers to delineate the marmoset brain (Paxinos et al., 2012).

Methods

Surgery

Three rat brains were sectioned and stained in this study, but the data presented in this atlas are exclusively derived from one of them, an adult male Wistar rat weighing 274 g. The rat was deeply anesthetized (120 mg/kg of Nembutal, intraperitoneally) and placed in a Kopf small animal stereotaxic instrument with an incisor bar adjusted until the lambda and bregma heights were equal. This flat-skull position was achieved when the incisor bar was lowered 3.3 mm below horizontal zero. A fiducial mark was made by passing a needle horizontally from the back of the cerebellum to the olfactory bulb. This needle mark, visible on the left side of some the plates, is located 5 mm above the interaural line and 2 mm lateral to the midline.

Histology

For perfusion, the rat was deeply anaesthetized with pentobarbitone and the thoracic cage cut open. A blunt needle was inserted into the left ventricle and advanced a few mm into the ascending aorta. After the left atrium was cut open, perfusion was commenced at a constant flow using a peristaltic pump. The perfusate consisted of 250 ml of saline delivered over a period of 3 min, followed by 600 ml of a 4% paraformaldehyde solution in 0.1 M phosphate buffer (PB, pH 7.4) over a period of 25 min. The first 200 ml of the fixative was delivered at the same speed as the saline. The speed was then gradually reduced to pass the remaining 400 ml. The head was gently rolled to the right and left to allow an even perfusion on both sides of the brain. The brain was then carefully removed and immersed in a sucrose solution (30% in PB) for 2 nights at 4°C.

The brain was blocked in gelatine placed dorsal surface down in a small aluminium foil boat containing 1.5% gelatine dissolved in 0.9% saline (Franklin and Paxinos, 1997). The dorsal surface is almost exactly parallel to the flat-skull horizontal plane. Once the brain was correctly positioned, the boat was placed in a refrigerator for 20 min to allow the gelatine to set. The gelatine block was then frozen in dry ice and its caudal end attached to the moving stage of a cryostat. The angle of the stage was adjusted by eye until the longitudinal axis of the brain was perpendicular to the plane of the blade. Small adjustments were made during cutting, where necessary, to maintain symmetry. These adjustment points resulted in partial loss of some sections (e.g. Figs. 257-261).

The brain was cut at -12°C with a newly sharpened C-profile stainless steel blade. The section thickness was set at 31 μm and each section was collected for subsequent staining for Pv, Cb, Cr, Nissl, SMI32, TH, NADPH-d, and AChE. Sections were collected individually with a paintbrush and placed in sequence in a series of eight jars filled with cold PB, sitting on a tray of crushed ice to keep the solutions cold. Sections placed in the fourth jar were transferred to PB and immediately mounted on gelatine-coated slides; they were allowed to dry overnight and then stained for Nissl substance with Cresyl Violet.

Cresyl Violet Staining

See Paxinos and Watson (2014) or see the online protocol at: https://www.neura.edu.au/nissl-ache-staining-protocols-beginners/.

lmmunohistochemical Processing (Pv, Cb, Cr, SM132, TH)

All washes were carried out on an orbital shaker at room temperature. To minimize damage to the sections, tea strainers were used to lift and transfer the sections between washes. Jars, tea strainers and paint brushes were cleaned in 50% alcohol and distilled water. The processing consisted of the following steps:

1.Wash in PB for 10 min.

2.Wash in 50% alcohol for 30 min.

3.Wash in 50% alcohol and 1% hydrogen peroxide for 30 min.

4.Wash in 5% normal horse serum in PB for 30 min.

5.Incubate with primary antibody in PBH [PB solution with normal horse serum (2%) and Triton X-100 (0.2%)]. The incubations were done in scintillation glass vials on the orbital shaker at 4°C for 32 hours in a 3.0 ml volume. The antibodies and dilutions were as follows:

-anti-parvalbumin (mouse monoclonal IgG1; SWant Cat. No. 235), 1:128,000;

-anti-calbindin D28k (mouse monoclonal IgG1; SWant Cat. No. 300), 1:20,000;

-anti-calretinin (rabbit polyclonal; SWant Cat. No. 7696), 1:64,000;

-SMI32 (mouse monoclonal IgG1; Sternberger Monoclonal, Inc.), 1:32,000;

-anti-tyrosine hydroxylase (mouse monoclonal IgG1; Incstar Cat. No. 22941), 1:64,000

6.Wash four times in PB, 10 min each wash.

7.Incubate with biotinylated secondary antibody in PBH, in scintillation glass vials on an orbital shaker at room temperature for 1 hour in a 4.0 ml volume. The two antibodies and dilutions used were:

-anti-mouse IgG (goat biotin-SP-conjugated Affini Pure; Jackson ImmunoResearch Laboratories), 1:200;

-anti-rabbit IgG (goat biotin-SP-conjugated Affini Pure, Jackson ImmunoResearch Laboratories), 1:200.

8.Wash four times in PB,