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UTD / Science / ACN 6338001 / How is the cns built?

How is the cns built?

How is the cns built?


School: University of Texas at Dallas
Department: Science
Course: Functional Neuroanatomy
Term: Spring 2017
Tags: neuroscience, appliedcognitionandneuroscience, neuroanatomy, Functional Neuroanatomy, #neuroanatomy, and humanbrain
Cost: 50
Name: Neuroanatomy Exam 1 (Chapters 1-8)
Description: Chapter 1: Introduction the Nervous system, the material covers directional planes, parts of the CNS and the PNS, and the cells that make up the nervous system, along with different types of Neuroimagi
Uploaded: 02/10/2017
16 Pages 63 Views 1 Unlocks

Thursday, February 9, 2017

How the cns is built?

Functional Neuroanatomy

Feb 9 Flex day (Catch-up, Brain Atlas Study, and/or brief Test review)  - Reading: Blunt Dissection of the Human brain

- EXAM 1 (Chapters 1-8) - BRING SCANTRON, 50 QUESTIONS


- Directions: Anterior, Posterior, Dorsal, Ventral, Superior ⬆ , Inferior ⬇ - Imaging Planes: Sagittal, Coronal, and Axial views

- CNS vs. PNS

* Intra-hemispheric fissure = Divides cerebral hemispheres (space  between)

* Pons = Means bridge

- CELLS (Neurons and Glia)

Schwann cells only type of glia in PNS 

* Needed for insulation, faster information travel, and metabolic support * Also help to regrow axons if peripheral nerve injury occurs


* Maintain ionic balance of cells, transfer metabolites in/out of neurons,  respond to neuronal injury forming scar tissue

Ependymal cells 

* Create the lining of ventricles and choroid plexus


* The immune cells of the brain

* Become macrophages to eat cellular debris

We also discuss several other topics like What are the major types of organic molecules?



Thursday, February 9, 2017


• X-ray (2D only) no brain differentiation

• CT/CAT scans – several 2D slices, differentiates bone, CSF, gray and white matter

• MRI (3D) – can differentiate brain regions

• CT scan

• Compilation of multiple w-rays

• Bone = white, air = black, CSF = dark, white matter = darker than gray matter

• Used for acute injury

• Cheap fast, can image patients with metal

• Drawbacks: exposure to radiation, low resolution


• T2 – measure time to lose coherence

• T1 – recover from being tipped

• Very clear images of soft tissues (3D) – voxels

• Not radioactive Don't forget about the age old question of What is spliceosome?

• Drawbacks: cost and time (30min), no metal

• Diffuse Tensor Imaging (DTI)

• Look at the flow of water molecules in brain on structural MRI scans

• Isotropic

• In open medium the molecules will bounce around (diffuse) at random

• No principle direction of movement Don't forget about the age old question of How should one approach topics in behavioral economics?

• Anisotropic

• White matter is fatty, so water cannot pass it

• Water molecules run parallel to fiber tracts

• Storm gutter

• Can be used

• Map connections between regions

• Measure of white matter integrity

• Imaging of brain function = imaging of changes in blood flow

• SPECT (single photon emission computed tomography) 10mm resolution

• PET (positron emission tomography) 5mm resolution

• 2x the resolution of SPECT

• subtraction technique like fMRI where you have subject go into PET scanner, do baseline condition similar to actual  condition wanted to study, and subtract out which part of brain gets blood flow from active condition. What you have left  should be regional changes in blood flow that only have to do with cognitive task at study. We also discuss several other topics like What is the definition of market segment?

• Both SPECT and PET are radioactive techniques

• fMRI (functional magnetic resonance imaging) 2.5mm resolution

• fMRI

• Blood Oxygenation Level-Dependent signal (BOLD)

• Local blood flow differences that are completely dependent on what oxygenation level is in those voxels • Capitalizes on the difference between oxygenated and deoxygenated blood in local brain regions (hemoglobin iron  levels) Don't forget about the age old question of What is the study of matter?

• Brain areas that are active receive more blood flow than they need, so blood leaving these areas has a higher  concentration of oxygen than those regions that are inactive

• MRI signal reflects the ratio of hemoglobin : deoxyhemoglobin and serves as a measure of changes in blood flow  and we use this as an indirect measure of neural activity If you want to learn more check out Define classical conditioning.

• Gives you changes in intensity of a given voxel based upon the statistical model you specify • Uses

• Great spatial resolution

• Can be used to explore cognitive studies

• Map sensory experience

• Functional connectivity

• Event-related vs. blocked designs

• Limitations

• Not as sluggish as PET, but still very bad

• Indirect measure of neuronal firing

• Changes are often small (1%), misrepresentation by media

• EPI (echo-planar image)

• Resolution is bad because collecting so quickly


Thursday, February 9, 2017



1. How the CNS is built

1. Process of primary neurulation and secondary neurulation

1. 3 primary vesicles and 2 flexures

2. 5 secondary vesicles and 3 flexures

2. Rotation, gyrification, ventricles and CP, white matter

2. Development gone wrong

1. Birth defects by gestational timeline

3. How a CNS is built

1. Neural plate —> folds inward to make neural groove —> neural folds fuse  together = neural tube —> zips up except for posterior pore

2. Primary neurulation = neural tube becomes CNS, the cavity becomes  ventricles

3. 2 days later (Day 26) posterior end closes at spinal cord end = Secondary  neurulation

4. Spinal cord formation

1. Neural tube closes, dorsal part becomes sensory neurons, ventral part becomes  motor neurons. In adult spinal cord, this is reflected in posterior horns and  anterior horns of axons.

5. Three primary vesicles and two flexures

1. The vesicles are the bulges from the neural tube

2. The flexures are the bends in the neural tube

3. Three vesicles:

1. Prosencephalon = forebrain (becomes cerebrum)

2. Mesencephalon = midbrain (becomes midbrain of brainstem) 3. Rhombencephalon = hindbrain (becomes brainstem and cerebellum) 6. Two flexures:

1. Cervical and cephalic flexure

7. Five secondary vesicles and three flexures (Weeks 5-6)

1. Procencephalon divides into: telencephalon (becomes cerebral hemispheres)  and diencephalon (becomes thalamus and hypothalamus)

2. Mesencephalon stays the same

3. Rhombencephalon divides into: metencephalon (becomes pons and  cerebellum) and myelencephalon (becomes medulla)

4. Pontine flexure —> becomes 4th ventricle

8. Telencephalon grows dramatically to form cerebral hemispheres 1. Lamina terminalis —> anterior commissure and corpus callosum 9. Rotation of cerebral hemispheres (Month 2-4)

1. As neocortex of the frontal and temporal lobes grow quickly, brain takes on C  shape


Thursday, February 9, 2017

2. Hippocampus goes form dorsal surface down into temporal lobe. Insula gets  pushed in and covered over, the cerebellum “lips” come together and fuse to  make the CB, the olfactory bulb protrudes and then elongates along the ventral  surface

10. Gyrification

1. MRI at 23 weeks. See anterior and posterior horns of lateral ventricles, 3rd  ventricle, and depression where insula will be. No gyri/sulci yet.

2. Infant brain at 26 weeks. See some gyri but sulci are still shallow and few, lateral  fissure apparent, insula still exposed, no opercula covering yet.

3. Gyrification increases drastically from 31 weeks to term. Early on only see major  sulci.

11. Making ventricles

1. The cavity of the neural tube becomes the ventricular system:

1. Lateral ventricles fold with the telencephalon to make the C shape 2. Depression in telencephalon deepens to form intraventricular foramen  (Monro)

3. Thalamus and hypothalamus develop as diencephalon and forms the walls of  the 3rd ventricle

4. Cephalic flexure bends more inward and borders the Sylvian aqueduct 5. The pontine flexure folds inward and is adjacent to the 4th ventricle 12. Ventricles need choroid plexus

1. At 6 weeks no choroid yet. But at 7 weeks can see first sprouts of CP starting to  grow.

2. During early development, lateral and 3rd ventricles flow freely into one another 3. At 15 weeks lateral ventricles are constricted from the 3rd ventricle by the  interventricular foramen. CP are now a large convoluted structure in the lateral  ventricles and can be seen lining the roof of 3rd and 4th ventricle.

4. During 3rd – 5th months of development, neurons and glia migrate to *** 13. White matter connections

1. Axons are all in place early in development, but myelination takes place after  birth.

14. Development gone wrong

1. Lots of processes must go precisely right during gestation to build a brain 2. A flaw in any of these processes can lead to congenital malformations 3. The nature of the malformation can generally be localized in time to the  developmental window of the fetus

4. As development is better understood, birth defects are also better understood 5. Table 2.2 is a nice summary of what develops when during gestation and what  malformations are most likely during those stages


Thursday, February 9, 2017



Gross Anatomy and General Organization of the CNS

* Humans vs. Other Animals 

Human brains relatively large compared to body size

On average 3 lbs

Regions bigger for special purposes

* Ex: olfaction in lions, executive function in humans

Size not huge correlate of intelligence across species, however gyrification and number  of synapses is a better correlate

* Gyri and Sulci 

Gyrification is a product of evolution; we had to fold up our evolving cortex to fit in the  same size skull over time

Stretched out we have 2 ½ ft2 of cerebral cortex

* 2/3 of which is hidden in sulci

Very large are called “fissures”

Pattern of gyri and sulci are surprisingly different in different people * Makes neuroimaging difficult

Lateral sulcus divides temporal lobe from frontal and parietal lobes

* Hemispheres and Midline 

Corpus callosum

* 3 parts: rostrum, genu, splenium

* Genu hooks together PFC on both sides

* Splenium hooks together occipital and parietal

* Lobes defined by major sulci 

Frontal, parietal, temporal, occipital, (limbic lobes) and the insula

* Central sulcus (Rolandic fissure): parietal-occipital sulcus

* Lateral sulcus (sylvian fissure)

* Pre-occipital

* Cingulate sulcus

Insula is under the lid (operculum) of the frontal, parietal and temporal junction and  borders the circular sulcus

* Frontal lobes 

Superior, middle

Inferior: orbital, triangular, operculum parts

Gyrus rectus – orbitofrontal cortex

Olfactory bulb

Anterior paracentral lobule


Thursday, February 9, 2017

* Parietal lobes 

Post central gyrus – somatosensory strip

Superior parietal lobule – somatosensory in nature

Inferior parietal lobule – hetero-modal association cognitive part of brain * Supramarginal, angular gyrus

Pre-cuneus – hertero-modal associative, integrative part of brain

* Temporal lobes 

Superior, middle, inferior, temporal gyrus

Occipito-temporal (fusiform) gyrus – from occipital to temporal

Lingual gyrus – back of parahippocampal gyrus to occipital

* Occipital lobes 

Lateral occipital gyrus (complex of LOC)


Lingual gyrus

Calcarine sulcus – where all visual cortex us (V1, V2, V3…)

Fusiform gyrus

* Subcortical in 3D


Thursday, February 9, 2017

* Limbic “lobe” 

Cingulate gyrus

Parahippocampal gyrus


Rhinal sulcus



* C-shaped structures 


Hippocampus and fornix


Cingulate/parahippocampal gyrus

* Basal ganglia and limbic structures 

Caudate, putamen, globus pallidus = basal ganglia (separated by the internal capsule) Fornix, mammillary bodies, amygdala, hippocampus, cingulate, parahippocampal gyrus  = limbic system

Putamen, globus pallidus = lenticular nucleus

* Diencephalon – thalamus and hypothalamus

* Brainstem

* Cerebellum

* Cranial nevers

* In 2D coronal slices: through frontal lobes

Septum pellucidum – separates lateral ventricles


Thursday, February 9, 2017


- Three Layers of Meninges

1. Dura mater (“tough/hard mother”)

1. tough, thick sheet of collagen

2. Periosteum- side attached to skull

3. Continually attached except for spaces

1. Epidural- between dura and skull

2. Subdural- Between dura and arachnoid

4. Dural septum

1. Where the dura folds into brain fissures

1. Falx cerebri, tentorium cerebelli

2. Make two compartments – supratentorium (cerebrum) and  

infratentorium (cerebellum and brainstem) aka posterior fossa

5. Dural Sinuses

1. At the edge of the dural septa are the sinuses

1. Where the blood vessels drain blood back down to the heart from  the brain

2. Major Sinuses

1. Superior sagittal sinus – attached to the falx

2. Transverse sinus – runs along cerebellum

3. Sigmoidal sinuses (L/R) – continues part of transverse going along  cerebellum

4. Drain into a confluence and then dump into the jugular vein

6. Dura has its own blood vessels

7. No pain receptors in brain


1. Trigeminal nerve – eye, temple, forehead headaches

2. Vagus nerve – behind ear and neck headaches

2. Arachnoid (“spiderweblike”)

• Very thin, attached to bottom of dura

• Wispy, spiderlike layer

• Filled with CSF (the only CSF filled space outside the brain)

• Arachnoid trabeculae

• Cisterns

- Where the arachnoid space becomes wide

- Two common ones we hear about

- Cisterna magna

- Ambient cistern (superior cistern)


Thursday, February 9, 2017

* CSF Reabsorption

The arachnoid villi, the large ones are called arachnoid granulations One way valves that let CSF out of the arachnoid

* Arachnoid as a Barrier

Brain is privileged environment where many things are blocked from  entry

Arachnoid serves as part of this barrier

* BBB is the other

3. Pia mater (“tender mother”)

• Very thin, lines every bit of brain tissue

• Pia is where blood vessels penetrate into the brain

• Space around blood vessels and brain is called perivascular space of  Volchow-Robin spaces

• They enlarge with age and can be seen on MRI

Arachnoid + Pia = Leptomeninges

• Meninges on Spinal Cord

• Dura – instead of 2 layers, spinal cord has one layer suspended in CSF on  both sides (the outside of the spinal cord is dura)

• Subarachnoid space same

• Arachnoid attached to pia by connective tissue called denticulate ligaments • Lumbar cistern – biggest arachnoid cistern

• Where lumbar punctures happen


Thursday, February 9, 2017

- Pathology of the Meninges

- Meninges protect the brain, butpathology exists

- Mostly in tears and bleeds, but also in tumors

- Spaces are vulnerable (EPIDURAL and SUBDURAL, and in the arachnoid  space)

- Blood polls in meninges and expands the space which compresses the brain - cysts

Leptomeningeal cyst (arachnoid)


Herniation due to a cyst

- infections

- Meningitis= Inflammation of the leptomeninges - Bacterial (less common, more severe)  - Viral (more common, less severe)

• Epidural Hematoma 

• Between skull and dura 

Severe headaches Stiff neck

Dislike of bright lights Fever/ Vomiting

Drowsy & less  

responsive/ vacant Rash (develops  

anywhere on the body)

• Meningeal arteries can get torn and cause a bleed (hematoma) • Compresses brain tissue and shifts it out of place 

• Subdural Hematoma 

• Veins that enter the sinuses can also get torn causing a subdural  hematoma 

• This one is acute 

• Acute – happened in the moment 

• Chronic – bleed over time 


Thursday, February 9, 2017



• Intraventricular foramen (Monroe) connects lateral ventricles to third ventricle • Sylvian aqueduct from third to fourth ventricle

• Lateral ventricles run through all 4 lobes

• Has 5 parts —> atrium is commonly called the trigone

• Surrounding parts

• Caudate laterally

• CC superiorly

• HC inferiorly (horn)

• Thalamus posteriorly

• Septum pellucidum medially

• Third ventricle

• Runs through diencephalon on midline

• Massa intermedia (interthalamic adhesion) in the middle

• Anterior is lamina terminalis (where rostrum of CC ends)

• Narrows into the Sylvian aqueduct and goes through midbrain

• Fourth ventricle

• Between pons, medulla and the cerebellum

• Superior medullary velum is roof (white matter)

• Inferior medullary velum is bottom (pia + ependymal = choroid plexus) • Where ventricles interact with subarachnoid space

• Most of CSF is in subarachnoid space compared to ventricles

• Choroid Plexus

• Strands of cells and vascular capillaries

• CP found in all four ventricles

• Where ventricles meet pia

• CP biggest in atrium (trigone) and is called glomus (“ball of thread”)

• CSF Circulation Summary 

• Lateral ventricle —>  

• through foramen of monroe —>  

• third ventricle (in diencephalon; massa intermedia; aka interthalamic adhesion  is in the 3rd ventricle)—>  

• through Sylvian aqueduct in the midbrain—>  

• to the fourth ventricle—>  

• connects through the central canal down the spinal cord


Thursday, February 9, 2017

• CSF• Produced/secreted by CP (mostly)

• Transports nutrients, vitamins and other chemicals

• Produce half a liter per day, completely replaced 2-3 times per day • Removed/reabsorbed through sinuses and out the veins

• Allows brain to move and expand when needed to offset injury

• Controls/balances ion concentration

• Might also help transport hormonal transmitters

• Hydrocephalus

• Disruption of CSF flow causes hydrocephalus

• If path blocked CSF continues to pump and expands ventricles

• Communicating hydrocephalus – only one lateral ventricle is blocked so  ventricle and subarachnoid can still communicate

• Non-communicating hydrocephalus – obstructive

• CSF easily seen in different types of imaging techniques so detected/Dx by  imaging


Thursday, February 9, 2017



1. Blood supply is critical

1. Brain needs a lot of continuous blood supply because it can't store oxygen or  glucose

2. Brain is only 2% of body, but it uses ~20% of blood in the body and ~25% of  its oxygen

1. 10s without blood/oxygen (called ischemia) = loss of consciousness 2. 20s without blood/oxygen = electrical activity in brain stops

3. Few minutes without blood/oxygen = irreversible brain damage and  eventual death

2. Blood vessels are densely packed

1. Denser in gray matter than in white matter

2. Metabolic need is much greater in cell bodies

3. So tightly packed that no neuron is more than 100 micrometers from a  capillary (also why fMRI works)

3. Arterial supply overview

1. Common carotid arteries – 80% of brain (anterior)

1. 2 on each side of neck in front

2. Vertebral arteries – 20% of brain (posterior)

1. 2 on each side of neck in back

4. Major arteries

1. Anterior, middle, posterior

5. Arterial territories: inferior surface

1. Anterior cerebral – medial wall of frontal and parietal

2. Middle cerebral – lateral surface of frontal and parietal

3. Posterior cerebral – medial and lateral temporal and occipital 1. Table 6.1 very helpful learning which arteries perfuse which part of the  brain

2. Ch 5-7, 9

6. Arterial territories: medial wall

1. Deep arterial supply

2. Perforated substance – brain region where arteries plunge into deep areas to  perfuse BG, thalamus and choroid plexus

3. Cerebellar arteries

1. AICA – anterior inferior cerebellar artery

2. PICA – posterior inferior cerebellar artery

3. SICA - superior inferior cerebellar artery


Thursday, February 9, 2017

7. Circle of Willis

1. Anastomoses – connections among blood vessels

1. Can enlarge to compensate for blockage elsewhere

8. Angiography

1. 3D MRA

9. Cerebral blood flow: Autoregulation

1. Overall blood flow rate to the brain is fixed at a constant rate

1. Brain hates irregular blood flow or pressure

2. Auto-regulated by cerebral blood vessels that can dilate to reduce blood  pressure, keeping constant flow

3. Different brain regions can increase/decrease rate inside brain which  correlates with fMRI activity

10. Blood vessels gone wrong

1. Most common cause

1. Cerebrovascular disease (CVD) and cerebrovascular accidents (CVA) 2. Ischemic stroke from blockage

1. Primary core damage, secondary progressive damage (penumbra) from  excitatory firing and inflammatory response

2. TIAs more mild

3. Lacunes are small lesions in basal ganglia from stroke

4. Infarct is the necrotic tissue from stroke

3. Hemorrhagic stroke from rupture of arteries (often lenticulostriatal) 1. Seen with uncontrolled hypertention

4. Aneurysm

1. A balloon-like swelling of artery wall, can compress nearby brain tissue 2. If burst then hemorrhage occurs

5. AVM

1. A congenital condition where arteries and veins connect together (no  capillaries0 and can cause neurological problems if grow and make one  part insufficient or if burst

11. Arterial territories = function

1. Damage (e.g. stroke) to a specific artery gives rise to specific neurological  deficits

1. Anterior cerebral artery (ACA)

1. Because some precentral and post central gyri are in this territory,  restricted contralateral somatosensory and motor deficits (usually leg) 2. Middle cerebral artery (MCA)

1. Major contralateral somatosensory/motor deficits

2. Most pre/pot central gyrus is irrigated by MCA

3. Posterior cerebral artery (PCA)


Thursday, February 9, 2017

1. Because visual cortex is in this territory, stroke here leads to visual  problems

12. Border zones or watershed areas

1. Border zones between the territories of two major arteries

2. Watershed area is where this border zone has decreased blood flow 3. Watershed areas (2 types: cortical and internal) are more vulnerable to blood  clots and strokes

13. “Blood Brain Barrier”

1. System of barriers that helps control extracellular fluid from body from  mingling too freely with extracellular fluid in the brain

2. Barrier at ends of capillary (astrocyte end feet) tightly spaced and keep  certain objects out

3. Good for toxins, bad for medicines

4. Leaky BBB implicated in diseases lately (MS) and age related


Thursday, February 9, 2017


Circuits and Wiring Principles: Connections and Crossings

* Information flow

Afferent – “coming towards” 

* Sensory neurons * A = Approach Efferent – “going away” 

* Motor neurons

* E = Exit


* Only participate in local circuit

* Motor Circuits 

 2 types

 * Primary afferent – convey information to the brain from the body

 * Lower motor neurons – send signal to muscle fibers to signal contraction

 All IPSILATERAL and none are contralateral

Where pathways cross is important for knowing which side of the body/hemisphere is involved * Why paralysis can be only one side

* Somatosensory Circuits 

Afferent information comes into the CNS (primary), connects to a secondary neuron in the spinal  cord and

* Sends sensory information to the cerebellum

* To the thalamus which relays sensory information

* To the somatosensory cortex

* Also involved in reflexes

Types of somatosensory 

* Pain, temperature, touch, proprioception, etc.

* Somatosensory Crossing 

Individual axons don’t cross the midline of the spinal cord

The somatosensory pathways on their way to the brain do cross the midline

All sensory information goes through the cerebellum ipsilaterally and is then used to coordinate  movements based on feedback

* Homunculus 

* Motor Tract (ascending) 

Voluntary movements are controlled by the corticospinal tract (CST)

As CST descends it does not go through the thalamus

* Motor System Fine Tuned by Cerebellum 

Afferents from spinal cord go (ascending) through the cerebellum (ipsilaterally)

Decussate in pons

Feedback loop

* Motor System Planned by Basal Ganglia 

Involved in planning motor movements

Basal ganglia project ipsilaterally to the cortex thalamus to cortex to putamen down to globus  pallidus and back to thalamus


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