Introduction to Neuroscience

Week2, Lecture1:
Methods in Neuroscience,
Anatomy

Mohammad Darainy
Recap: Neuron
Recap: The building blocks
Neuron

Circuit

System
 Neurons, circuits, systems
◼ Diverse subsets of neurons
constitute ensembles called
neural circuits which are the
primary components of
neural systems that process
specific types of information
 Neural systems serve broad
purposes
◼ Sensory systems : acquire & process
information from the internal & external
environment

◼ Motor systems: respond to information

(e.g. sensory) by generating movements

◼ Association systems: lie between input &

output systems
 Anatomical organization of the
human nervous system
◼ Central nervous system (CNS)
◼ Brain
◼ Spinal cord

◼ Peripheral nervous system (PNS)

◼ Sensory neurons
◼ Somatic motor division
◼ innervates skeletal muscles
◼ Visceral/autonomic motor division
◼ Innervates smooth muscles,
cardiac muscles, glands
 Basic principles of neural
systems
Neural systems are characterized by

◼ Unity of function
◼ A system is defined by all the neurons and connections
dedicated to a function
e.g. visual system defined by all neurons and connections dedicated
to vision

◼ Components of a system are often distributed throughout the

body and brain
◼ Sensory systems include peripheral sensory specializations e.g.
eye, ear, skin, nose
◼ Motor systems include peripheral motor nerves and target
muscles
Basic principles of neural systems
Neural systems are characterized by

◼ Orderly representation of specific information

at various levels

◼ Division of the function of the system into

subsystems that are relayed and processed in
parallel
◼ Information from sub-modalities is processed separately but in parallel
e.g. frequency and volume of an auditory signal, color & motion of a
visual stimulus
 Basic principles of neural systems
◼ Systems that distinguish differences
between neighboring points (e.g.
vision, in visual field or touch, on
the body’s surface) represent
information topographically

◼ Topographic maps reflect a point-to-

point correspondence between the
sensory periphery and neurons
within the CNS
 Basic principles of neural systems
◼ Other systems (e.g. smell, taste) use
computational maps to compare, assess, &
integrate multiple stimulus attributes to
extract essential information about stimuli

◼ Higher order systems (e.g. language,

emotion) are less well understood and may
not follow the neat organization of sensory
& motor systems
 Terminology in the nervous
system: collections of neurons
◼ gray matter: cell bodies in the brain, appear grey in freshly
dissected brain

◼ cortex: thin sheet of neurons, usually at the brain’s surface

◼ nucleus: clearly distinguishable mass of neurons, usually deep in

the brain (nucleus is Lain for “nut”)

◼ substantia: related neurons, but with less distinct boundaries

than a nucleus

◼ locus (pl: loci): small, well-defined group of cells

◼ ganglion (pl: ganglia): collection of neurons in the PNS (ganglion

is Greek for “knot”). Only the basal ganglia in the CNS
Terminology in the nervous system:
collections of axons
◼ nerve: a bundle of axons in the PNS. Only nerve in the CNS is the optic
nerve

◼ white matter: generic term for collection of axons; appear white from
myelination

◼ tract: collection of CNS axons having common origin and destination

◼ bundle: collection of axons that run together but do not necessarily have a
common origin/destination

◼ capsule: axon collection that connects cerebrum with brainstem

◼ commissure: axon collection that connects one side of the brain to the
other

◼ lemniscus: a tract that meanders through the brain like a ribbon

 Methods to study neural
systems
◼ Genetic Analysis of neural System
◼ Genetic variation shapes structure &
function of the nervous system

◼ In humans this has been studied by:

◼ genetic analysis in families affected by
inherited diseases
◼ Look for genetic variation between affected
& unaffected individuals
 Genetic analysis of neural systems

◼ genome wide association

studies (GWAS)

◼ Large scale population

studies that assesses
statistical correlation
between genetic variation
and frequency of
clinically diagnoses
conditions to identify ‘risk
locus’ for a particular Alzheimer’s GWAS from Lambert et al. 2013
condition
Genetic analysis of neural systems
 Genetic analysis of neural systems

◼ Once candidate genes

have been identified in
humans, these can be
studied in cell models
or animal models to
understand the
biological function of
these genes
Genetic engineering
 Structural analysis of neural
systems
◼ Lesion studies
◼ Inferences of functional location made
by correlating post-mortem
observation of gross brain damage
with functional deficits observed in life

◼ e.g. Henry Molaison (HM) lost the

ability to form new lasting
autobiographical memory.
◼ Inherent limitations include
◼ Biased recall of functional changes
◼ Uncontrolled damage

◼ Animal studies experimentally induce

lesions but still limited
 Structural analysis of neural systems

◼ Tract tracing
permits detailed
assessment of
connections
between brain
regions
◼ Retrograde
◼ Anterograde
 Functional analysis of neural systems

◼ Historically, the
most widely used
methods were
electrophysiological
recording and
functional brain
imaging
 Functional analysis of neural
systems: non-invasive techniques
◼ EEG

◼ Transcranial magnetic stimulation

◼ CT

◼ fMRI
Anatomy
Basic concepts
 Anatomical references
◼ We need directions
for the 3D structure
of the brain

◼ In animals that walk

on all fours, the
directions for body &
brain are the same
 Anatomical references
• Since humans walk
upright, our head is at an
angle to the our body
• Anterior, posterior,
superior and inferior
refer to the long axis of
the body so have the
same direction for
forebrain and brain stem
 Anatomical references
• Dorsal, ventral, rostral &
caudal refer to the long axis
of the CNS
• Brain stem & spinal cord
• Dorsal is to the back
• Rostral is towards the top of
the head
• Forebrain
• Dorsal is toward the top of
the head
• Rostral is towards the face
 Anatomical references
• 3 different planes
• Sagittal
• Horizontal (axial)
• Coronal (frontal)

• When we cut the brain

along the midline, we
observe the brain has
bilateral symmetry
 Contralateral, Ipsilateral
• Contralateral: on opposite sides
of the midline

• Ipsilateral: on the same side of

the midline

• E.g. The left visual cortex

receives both ipsilateral
projections from the left eye and
contralateral projections from
the right eye
 Subdivisions of the central
nervous system (CNS)

• The CNS has 7 basic parts • ‘Brainstem’: medulla,

• Spinal cord pons, and midbrain
• Medulla
• Pons • ‘Forebrain’:
• Midbrain diencephalon and
• Cerebellum cerebral hemispheres
• Diencephalon (cerebrum)
• Cerebrum
 Subdivisions of the central
nervous system (CNS)

• Cerebrum
• generally receives and sends information to the contralateral
side of the body

• Cerebellum
• ‘tiny brain’
• contains as many neurons as cerebrum
• Movement control

• Brain stem
• Relay between cerebrum/cerebellum and spinal cord
• Basic vital functions e.g. breathing
 Surface anatomy of the cerebral
hemisphere

• Gyrus (plural: Gyri)

• Sulcus (Plural: Sulci)
Surface anatomy of the cerebral
hemisphere
 Spinal Cord- External Anatomy
◼ The peripheral nerves that innervate
much of the body arise from the
spinal nerves

◼ Sensory information carried by

afferent axons of the spinal nerves
enters the cord via the dorsal roots

◼ Motor commands carried by the

efferent axons leave the spinal cord
via the ventral roots

◼ Once the dorsal and ventral roots join,

sensory and motor axons usually
travel together in the spinal nerves
 Spinal Cord- Internal Anatomy
◼ Interior of the cord is formed
by gray matter, surrounded
by white matter

◼ Cervical and lumbosacral

enlargements accommodate
the greater number of nerve
cells and connections
required to process
information from upper and
lower limbs
 Spinal Cord- Internal Anatomy
◼ The white matter of the
spinal cord is divided into
dorsal, lateral and ventral
columns

◼ Dorsal columns carry

ascending sensory
information from somatic
mechanoreceptors
 Spinal Cord- Internal Anatomy
◼ Lateral columns include axons
that travel from the cerebral
cortex to interneurons and
motor neurons in the ventral
horns (‘lateral corticospinal
tract’)

◼ Ventral columns carry both

ascending information about
pain & temperature, and
descending motor information
from the brainstem & motor
cortex
 Spinal Cord- Internal Anatomy
◼ In transverse sections we can
identify the dorsal and ventral
horns in the gray matter

◼ Neurons of the dorsal horns

receive sensory information that
enters via the dorsal roots of
spinal nerves

◼ The ventral horns contain the

cell bodies of motor neurons
that send axons via the ventral
roots of spinal nerves to striated
muscles
 Brainstem & Cranial Nerves
◼ Midbrain, pons,
medulla

◼ Located between
the diencephalon
and spinal cord
 Brainstem & Cranial Nerves
3 fundamental functions
◼ Target & source for cranial nerves that deal with
sensory and motor function of head & neck

◼ A ‘throughway’ for
◼ ascending sensory tracts from spinal cord
◼ sensory tracts for head & neck
◼ Descending motor tracts from forebrain
◼ Local pathways linking eye movement centers

◼ Regulating levels of consciousness through

extensive forebrain projections
 Brainstem & Cranial Nerves

◼ Brainstem structures are tightly packed

◼ Cranial nerve nuclei in brainstem are the target

of cranial sensory nerves and the source of
cranial motor nerves

◼ As in the spinal cord, there is a separation of

sensory & motor nuclei in the brainstem
◼ Sensory nuclei are found laterally
◼ Motor nuclei are found more medially
Lateral surface of the Brain
Parietal Lobe
Frontal Lobe
Occipital
Temporal Lobe Lobe

• Lateral fissure separates temporal lobe from frontal &

parietal lobes

• Central sulcus separates frontal and parietal lobes

• Parieto-occipital sulcus separate parietal and occipital lobes

Lateral surface of the Brain

• Precentral gyrus locates motor cortex

• Postcentral gyrus locates somatic sensory cortex

• Insula cortex is hidden beneath frontal and temporal lobes

 Dorsal and Ventral Surfaces of
the Brain
◼ Bilateral symmetry of Longitudin
al
cerebral hemispheres fissure

Dorsal
◼ Corpus callosum bridges view
the two hemispheres,
carrying axons Olfactory

originating from neurons

bulb

in cerebral cortex of each Dorsal view with

hemisphere to contact
Optic
chiasma cerebral cortex
target neurons in the removed
opposite cortical region
 Midsagittal surface of the Brain
• Calcarine sulcus locates
primary visual cortex

• Cingulate gyrus is part of

limbic system

• Corpus callosum
 Midsagittal surface of the Brain
• Components of
diencephalon:

• Thalamus- relay of
sensory and motor
signal to relevant
primary cortical cortex
and also distributer of
high order signals from
one part of cortical
area to another.

• Hypothalamus-
homeostatic and
reproductive functions
 Thalamus: A Cortical Relay
◼ The sensory
pathways from the
eye, ear, and skin
all relay in the
thalamus before
terminating in the
cerebral cortex

◼ ~50 nuclear
subdivisions
maintain distinct
inputs & outputs
 Thalamus: A Cortical Relay

• Receives input from throughout

brain and spinal cord

• Sends axons to different cortical

areas

◼ Sends information back to brain

stem via internal capsule and basal
ganglia
 Internal Anatomy of Forebrain
◼ Amygdala located in front
of hippocampus

◼ Basal ganglia: caudate,

putamen & globus pallidus

◼ Anterior commissure-
axon tract connecting the
two hemispheres

◼ Internal capsule- major

pathway linking cerebral
cortex to brain & spinal
cord
 Blood Supply
◼ Damage to major blood vessels by trauma or stroke
results in combinations of functional deficits caused by
◼ Local cell death
◼ Disruption of axons passing through area of vascular
damage

◼ Neurons are highly sensitive to oxygen (& glucose)

deprivation because they have a high metabolic rate
 Blood Supply

◼ Even brief loss of blood supply (ischemia) can cause

cellular changes that may end in cell death

◼ Prolonged loss of blood supply leads to cell death &

degeneration

◼ A ‘stroke’ refers to the death or dysfunction of brain

tissue that follows compromised blood supply
 The Blood-Brain Barrier (BBB)
◼ BBB protects the brain from toxins
& fluctuations in ionic milieu

◼ Interface between walls of

capillaries and surrounding tissue
are observed throughout the body

◼ In the brain, tight junctions form

between capillary endothelial cells
that are not seen elsewhere in the
body
 The Blood-Brain Barrier (BBB)

◼ To enter the brain,

molecules must move
through endothelial
membranes:
◼ Lipid soluble
◼ Actively transported e.g.
glucose
 The Meninges
Meninges (Greek for “covering”)

◼ Membranes protecting the brain

and spinal cord preventing direct
contact with skull or bone

◼ Dura mater: outermost, Latin for

“hard mother”
 The Meninges
◼ Arachnoid membrane: middle
layer with a web-like
consistency, from the
Greek for “spider”
• Blood vessels pass between the
Dura and Arachnoid membranes-
ruptures to these cause subdural
hematomas
• Fluid build-up here is dangerous
because is puts pressure on the CNS
 The Meninges
• Pia mater: inner layer,
adheres closely to the brain
and includes many blood
vessels, Latin for “gentle
mother”
• The Pia is separated from the
Arachnoid by the subarachnoid
space which contains
cerebrospinal fluid (CSF)
 The ventricular
system
◼ Ventricles are canals through the brain filled
with cerebrospinal fluid (CSF)

◼ Provide useful anatomical landmarks in the brain

◼ CSF is produced by the choroid plexus, special tissue

lining the ventricles of the brain
◼ Produces 500ml CSF/day
◼ Normal volume in ventricular system is 150ml
◼ CSF turnover multiple times daily

◼ CSF flows through the ventricles and exits the CNS into
the subarachnoid space by small openings along the
dorsal midline of the forebrain, where it is absorbed by
subarachnoid villi into the blood
 Glymphatic system of the brain

• The brains waste clearance system

• CSF passes from arterial perivascular

space through the substance of the
brain

• The CSF rinses metabolic waste and

discarded proteins

• The waste-carrying CSF passes out of

the brain via the perivascular space
surrounding veins

• CSF flow increases during sleep when

extracellular spaces expand
 Additional resources for exploring
brain anatomy
BrainFacts.org