S. D. V. Stephens

notes / Basic Neuroscience and Geometry of Neuroscience / chapter 1: Neurons and Signalling

1 Meet the Nervous System

This first lecture has three learning objectives:

  1. Critically evaluate common neuroscience misconceptions.
  2. Identify the major anatomy of neurons and key brain regions.
  3. Analyze major functional neuroanatomy through disorders.

Fact or fiction?

The lecture opened with a pop quiz: four popular claims about the brain, each to be judged fact or fiction, and why.

“Some people can be considered ‘left-brained’ or ‘right-brained.’” Fiction. The slide shows the poster version of this myth: a brain split down the middle, the left half drawn as a plain outline and labeled analytical thinking, numbers, language, reasoning, logic, and science and math; the right half splashed with paint and labeled emotional intelligence, imagination, expression, art awareness, intuition and creativity.

“The average person does not use 100% of their brain capacity, only about 30% on average.” Fiction. The slide pairs the claim with a functional brain scan (one slice from the side, one from above) in which only a few patches light up red. Patches like these mark where activity changed during a task; the rest of the brain is working too.

The next slide, “These images are bogus, sorry ☹,” takes on a meme that circulates online. It sets a colorful “normal brain” scan beside an “ADHD brain,” a “PTSD brain,” a “bipolar brain” and a “depressed brain,” each captioned with a dismissive remark (“It’s just a made up ailment to give kids an excuse for not paying attention,” “Get over it lots of people have it worse”). The scan comparisons are bogus.

“Learning is facilitated by the creation of new neurons.” Fiction, in the lecturer’s verdict. Learning comes from the brain changing in response to experience, which is the next claim.

“The brain changes (is ‘plastic’) in response to the environment.” Fact.

Definition 1.1. The brain is plastic: it changes in response to the environment and to experience. This capacity for change is called plasticity.

Say hello to your brain

The human brain

  • has about 80 billion neurons;
  • performs, by a popular estimate, about a billion billion () calculations per second;
  • is always changing based on experience.

Neurons

A neuron with its parts labeled: branching dendrites around the soma (cell body), which holds the nucleus; a long axon wrapped in a row of myelin sheaths; and branching axon terminals at the far end. An arrow above shows the message travelling from the dendrites toward the axon terminals.

A neuron has four main parts, and a message always travels through them in the same direction, from left to right in the figure:

  • the dendrites, the branches that take in information;
  • the soma or cell body, which contains the nucleus;
  • the axon, a long fiber leaving the cell body, wrapped along its length in myelin sheaths;
  • the axon terminals, the branched endings at the far end of the axon.

In the lecturer’s words, a neuron takes in information at its dendrites, processes it in the cell body, sends an action potential (its electrical signal) down the axon, and “spits” neurotransmitters (chemical messengers) out of the axon terminals onto the next neuron.

All kinds of neurons

There are a few “flavors” of neuron, told apart by how many processes (branches) leave the cell body and where.

Four kinds of neurons side by side. Unipolar: one myelinated process leaving the cell body and branching at its end. Bipolar: dendrites at one end, the cell body in the middle of a myelinated process, and a sensory receptor at the other end. Pseudounipolar: the cell body off to the side on a short stalk joined to one long process whose lower end branches into sensory receptor endings. Multipolar: many dendrites around the cell body and a single myelinated axon.
  • Unipolar: a single process leaves the cell body. In the figure it is myelinated and branches at its far end.
  • Bipolar: two processes leave the cell body from opposite sides. One end branches into dendrites; the other ends at a sensory receptor.
  • Pseudounipolar: the cell body sits off to one side on a short stalk, joined to one long process that runs in both directions. One end branches into sensory receptor endings.
  • Multipolar: many dendrites leave the cell body, along with a single myelinated axon.

Under the microscope, real neurons look like a dense forest: cell bodies with long, thin processes running between them (on the slide, lit up in fluorescent green).

Two nervous systems

Definition 1.2. The nervous system has two divisions.

  • The central nervous system (CNS) is the brain and the spinal cord.
  • The peripheral nervous system (PNS) is everything else: the neurons that run through the rest of the body.

As the lecturer put it, all you are is a brain and spinal cord piloting a meat suit. The PNS is “just everything else”: you’ve got neurons everywhere.

Tree diagram: the nervous system divides into the peripheral and the central nervous system (brain and spinal cord); the peripheral divides into the autonomic (controls self-regulated action of internal organs and glands) and the somatic (controls voluntary movements of skeletal muscles); the autonomic divides into the sympathetic (arousing) and the parasympathetic (calming).

The peripheral nervous system divides further:

  • the autonomic nervous system controls the self-regulated action of the internal organs and glands;
  • the somatic nervous system controls voluntary movements of the skeletal muscles.

The autonomic nervous system in turn has two branches: the sympathetic (arousing) and the parasympathetic (calming).

On the slide, the diagram is flanked by two body outlines: the peripheral nervous system, with nerves running out to every part of the body, and the central nervous system, only the brain and spinal cord. A further slide (“This is u”) shows the CNS on its own: a classic anatomical drawing of the brain and spinal cord with the spinal nerves branching off, and a photograph of a real human brain and spinal cord dissected out with their nerves attached.

Receptors in the periphery communicate with the CNS

Sensory receptors out in the body pick up information and pass it to the central nervous system. The slide gives two examples.

The skin. A block of skin is drawn with its outer layer, the epidermis, over the deeper dermis, and with these receptors in it:

Receptor What it senses
Free nerve endings pain, heat, cold
Merkel disks touch
Krause end bulbs touch
Root hair plexus touch
Meissner corpuscles touch
Pacinian corpuscles pressure
Ruffini endings pressure

The eye. Light enters through the cornea, pupil and lens and lands on the retina at the back of the eye; the macula is a small patch of the retina, and the optic nerve leaves from the back of the eye. A close-up of the retina shows light passing through layers of retinal neurons to reach the photoreceptors, the rods and cones, which sit against the retinal pigment epithelium at the very back.

Brain regions

Cerebellum and brainstem

The cerebellum and brainstem handle

  • basic biological function, the “life support system”;
  • reflex movement;
  • balance;
  • eye movement control.

The slide’s drawing shows the brain from the side with the cerebellum labeled: the finely ridged structure tucked under the back of the brain, behind the brainstem.

Which division of the nervous system do these regions likely regulate? The peripheral nervous system: broadly all of it, but mainly the autonomic part.

Prefrontal cortex

The prefrontal cortex is the front part of the frontal lobe. Its subregions are named by anatomical direction: dorsal means toward the top and ventral toward the bottom; anterior (or rostral) means toward the front and posterior (or caudal) toward the back; lateral means toward the side and medial toward the middle.

Subregion Functions
Dorsolateral decision-making, working memory
Lateral working memory, reasoning, planning, imagination
Ventrolateral motor control
Ventromedial emotion regulation, self-control
Orbitofrontal emotion regulation, reward, reward/punishment assessment

The slide’s figure shows the brain from the side (front to the left) with regions of the frontal lobe colored and labeled with their Brodmann area (BA) numbers, a standard numbering of cortical regions. At the front tip is the lateral frontopolar cortex (BA 10); behind it are the dorsolateral prefrontal cortex (BA 9/46) above and the ventrolateral prefrontal cortex (BA 47/45/44) below; further back come the anterior premotor cortex (BA 8), the ventral anterior premotor cortex (BA 44/6), the premotor cortex (BA 6) and the primary motor cortex (BA 4).

Why were frontal lobotomies (surgery that cuts into the frontal lobes) once a popular, but highly flawed, method for treating psychosis? The lecturer’s answer: “No think = no think bad thoughts????” Damaging the prefrontal cortex shuts down thinking in general: the disturbing thoughts go, and so do the decision-making, planning, emotion regulation and self-control in the table above.

Amygdala

The amygdala, a small structure deep inside the brain, handles

  • emotional regulation;
  • fear and stress.

Why is stress important? It “makes you not die”: stress responses are what keep you alive in the face of danger.

Amygdala subregions

  • The basolateral and central amygdala receive input from the broader limbic system (see below) and handle the expression of fear and anxiety.
  • The medial amygdala handles behavior, hormonal control, and the expression of social anxiety.
Inputs, nuclei and outputs of the amygdala. Inputs from the associative cortex, thalamus, hippocampus, prefrontal cortex and brainstem (glutamatergic) and from VTA, DRN, LC and BF (neuromodulatory) reach the lateral, basal, central and medial nuclei (LA, BA, CeA, MeA). BA sends glutamatergic outputs to EC, mPFC, hippocampus, NAc and BNST; CeA sends GABAergic outputs to SNL, LC, NTS, VTA, PAG, PBN, BF, hypothalamus and BNST; MeA sends GABAergic outputs to NAc, BNST, hypothalamus and BF. Each output is labeled with the behavior it serves, such as freezing, anxiety, reward, hormones or feeding.

The figure maps the amygdala’s connections. It shows four nuclei: the lateral (LA) and basal (BA) amygdala, which together form the basolateral amygdala; the central amygdala (CeA); and the medial amygdala (MeA). Connections are of three kinds: glutamatergic (excitatory), GABAergic (inhibitory) and neuromodulatory.

  • Inputs. The associative cortex, thalamus, hippocampus, prefrontal cortex and brainstem send glutamatergic inputs to the LA, BA and CeA. Neuromodulatory inputs come from the ventral tegmental area (VTA), dorsal raphe nucleus (DRN), locus coeruleus (LC) and basal forebrain (BF) to the BA, CeA and MeA.
  • Inside the amygdala. The LA projects to the BA, CeA and MeA, and the BA to the CeA and MeA.
  • Outputs of the BA (glutamatergic): entorhinal cortex (EC), for freezing; medial prefrontal cortex (mPFC), for anxiety and freezing; hippocampus, for anxiety; nucleus accumbens (NAc), for anxiety and reward; bed nucleus of the stria terminalis (BNST), for anxiety and fear.
  • Outputs of the CeA (GABAergic): substantia nigra pars lateralis (SNL), for appetitive and aversive learning; locus coeruleus (LC), for anxiety and aversive behavior; nucleus of the solitary tract (NTS), for autonomic regulation; ventral tegmental area (VTA), for reward; periaqueductal gray (PAG), for pain and freezing; parabrachial nucleus (PBN), for feeding; basal forebrain (BF), for motor behavior; hypothalamus, for hormones; and the BNST.
  • Outputs of the MeA (GABAergic): the NAc, BNST, hypothalamus and BF.

The class then did an activity, Personal Space Invaders, which sits among the amygdala slides.

Hippocampus

The hippocampus, shown on the slide as a curved structure deep in the lower part of the brain, handles

  • memory storage and retrieval;
  • spatial memory and encoding.

Damage to the hippocampus causes amnesia, a loss of memory.

The hippocampus also communicates with the amygdala. This matters for survival: you have to remember the thing that hurt you or made you feel bad, so that you can avoid it.

Thalamus

The thalamus is the brain’s sensory and routing center, and it is also involved in sleep and wakefulness. The slide’s figure is a view of the inner face of the brain with the thalamus, hypothalamus, frontal lobe, olfactory bulb, amygdala and hippocampus labeled.

Definition 1.3. Synesthesia is the perception of one sense through another, for example hearing colors.

How might synesthesia work? One possibility: the thalamus sends axons carrying one sense to the wrong sensory cortex, the area of cortex that handles a different sense.

The limbic system

Definition 1.4. The limbic system is the brain’s system for emotion and memory. The slide’s figure shows the thalamus, amygdala and hippocampus deep inside the brain, beneath the cortex.

Hypothalamus

The hypothalamus is the brain’s gateway to the periphery: it runs the neuroendocrine system, through which the nervous system controls the release of hormones. It is involved in

  • stress;
  • sexual behavior;
  • aggression;
  • development;
  • social behaviors.

The slide’s figure shows (a) the brain cut down the middle, with the pineal gland, hypothalamus, pituitary gland and spinal cord labeled, and (b) a close-up of the hypothalamus with the pituitary gland hanging from it on a stalk, the infundibulum; the pituitary has an anterior and a posterior lobe.

Why is communication between the thalamus and the hypothalamus so important? You have to respond hormonally to what you sense in the outside world: the thalamus routes the sensory information, and the hypothalamus turns it into a hormonal response.

Pituitary

The pituitary gland

  • releases hormones into the bloodstream;
  • activates organs and glands in the periphery: the adrenal glands (stress), the gonads (reproduction, development), the heart and lungs, and digestion.

What happens if the adrenal gland receives too much stimulation from the pituitary? It floods the body with stress hormones, chiefly cortisol.

Neuroscience isn’t just the brain! A comic from The Awkward Yeti closes this part: a hooded figure (the hypothalamus, presumably) tells the little pituitary, “You wield great power, Pituitary. Use it wisely! Go now, release the hormone armies and bring balance to the realm!”, and when the pituitary only squeaks, boots it out the door.

Check yourself

The first three questions refer to this neuron.

An unlabeled neuron with three red arrows: A points to the nucleus inside the cell body, B to the axon terminals at the far end of the axon, and C to the tip of a dendrite.

Question 1.5. What is the part of the neuron marked A?

Show solution

The nucleus, inside the cell body (soma).

Question 1.6. What is the part of the neuron marked B?

Show solution

The axon terminals, the branched endings of the axon that pass the message on to the next neuron.

Question 1.7. What is the part of the neuron marked C?

Show solution

The dendrites, the branches that take in information.

Question 1.8. What is a key function of the amygdala?

  • (a) Sensory processing
  • (b) Cognition
  • (c) Memory
  • (d) Stress
Show solution

(d) Stress. The amygdala handles emotional regulation, fear and stress; memory is the hippocampus’s job, and sensory routing is the thalamus’s.

Question 1.9. What is a key function of the hippocampus?

  • (a) Sensory processing
  • (b) Cognition
  • (c) Memory
  • (d) Stress
Show solution

(c) Memory. The hippocampus handles memory storage and retrieval, and spatial memory and encoding.

Question 1.10. A patient has damage to the amygdala. Which symptom will they most likely have?

  • (a) Difficulty discriminating sensory stimuli
  • (b) Confusion and impaired memory
  • (c) Decreased or no fear response
  • (d) Inability to make or execute plans
Show solution

(c) Decreased or no fear response, since the amygdala handles fear. Impaired memory points to the hippocampus instead, and trouble with plans to the prefrontal cortex.

Question 1.11. A patient has damaged connections between the hypothalamus and the pituitary. Which symptom will they likely have?

  • (a) Impaired physical and sexual development
  • (b) Very little interest in social interaction
  • (c) Decreased or no fear response
  • (d) All of the above
  • (e) None of the above
Show solution

(d) All of the above. The pituitary is the hypothalamus’s route to the periphery, so cutting the link disrupts the hormonal side of everything the hypothalamus controls: development and sexual behavior (through the gonads), social behaviors, and the stress response (through the adrenal glands).

Question 1.12 (Exit discussion). You’re a neurologist working at a hospital. A patient is brought in after a biking accident with the following symptoms:

  • poor memory of the event, and confusion;
  • difficulty completing a puzzle;
  • makes inappropriate comments on your clothing;
  • a general sense of apathy.

What region(s) of the brain have likely been damaged? What evidence supports your conclusions?

Show solution

Most likely the hippocampus and the prefrontal cortex. The poor memory points to the hippocampus (memory storage and retrieval); the trouble with the puzzle points to the dorsolateral and lateral prefrontal cortex (working memory, reasoning, planning); and the inappropriate comments and apathy point to the ventromedial and orbitofrontal cortex (self-control, emotion regulation, reward assessment).