Category Archives: Anatomy and Physiology

The Striatum

The striatum is the largest collection of neurons in the basal ganglia. Composed of the caudate nucleus and putamen, the basal ganglia, as the name suggests, sits at the base of the cerebrum. It receives input from regions of the cerebral cortex, the limbic system, and the sensorimotor and motivational systems via the thalamus. In addition to the cerebrum, the striatum receives input from the brainstem including the substantia nigra and the raphe nuclei of the reticular formation. The dopamine and serotonin of these two structures serve a modulatory function. Anatomists organise the striatum on the “basis of differential connectivity and distribution of neurochemical markers” (Redgrave, 2007). Processing strong excitatory input, the striatal neural circuits generate a strong inhibitory output, which controls the output of basal ganglia further along in the motor loop.


The major cytology of the striatum is GABAergic medium spiny neurons (MSN), making up about 95% of the total cellular structure. MSNs are organised into two groups based on the peptide they contain, substance P and enkephalin and the proportion of dopamine receptors (D1 or D2) they contain. MSNs create dense networks of axon collaterals. As projection neurons, the MSNs create this dense network by forming axon collaterals with one another. Tunstall et al, 2002 found that almost 30% form an axon collateral with a neighbouring MSN. Research has shown that the function of these collaterals is in cellular recognition and “classification of cortical patterns” (Blomeley, et al. , 2009).

The striatum is a vital part of the basal ganglia, and all pathways run through it. From the striatum onwards, the pathway either becomes direct or indirect. As shown in the figure below.









Blomeley, C. P., Kehoe, L. A., & Bracci, E. (2009). Substance P mediates excitatory interactions between striatal projection neurons. The Journal of Neuroscience29(15), 4953-4963.

Redgrave, P. (2007). Basal ganglia. Scholarpedia, 2(6): 1825.

Neuroscience: The Nervous System

he nervous system is the body’s speedy, electrochemical communication system. It consists of all the nerve cells of the peripheral and central nervous systems.

The central nervous system consists of the brain and spinal cord. The peripheral nervous system is the sensory and motor neurons that connect the central nervous system to the rest of the body. Nerves are the neural cables of the nervous system containing many axons. They are part of the peripheral nervous system. They are connected to the central nervous system by muscles, glands, and sense organs.

Sensory neurons carry incoming information from the sense receptors to the central nervous system. Interneurons are part of the central nervous system. They internally communicate and intervene between the sensory inputs and motor inputs. They are the most common type of neuron. Motor neurons carry outgoing information from the central nervous system to the muscles and glands.


– The Peripheral Nervous System –

The peripheral nervous system is made up of the somatic nervous system and the autonomic nervous system. The somatic nervous system controls the body’s skeletal muscles. The autonomic nervous controls the glands and muscles of the internal organs. It is broken down into the sympathetic and the parasympathetic nervous system. The sympathetic nervous system arouse the body, mobilising its energy in stressful situations (fight or flight response). The parasympathetic nervous system calms the body, conserving its energy.


– The Central Nervous System –

The spinal cord is the information highway connecting the peripheral nervous system to the brain. Ascending neural tracts send up sensory information. Descending neural tracts send down motor control information. Reflexes are the body’s autonomic response to stimuli controlled by the spinal cord. They are composed of 1 sensory neuron and 1 motor neuron that communicate through one interneuron. Because they only run through your spinal cord, they react automatically without your brain being involved in the process. The spine sends information back to the brain. Bodily pain or pleasure is controlled by the brain.

The brain receives information, interprets it and then decides on a response. It functions like a computer, receiving slightly differing images of an object from the eyes, it computes the differences and infers how far the object must be to project such a difference.

Neural networks are interconnected neural cells which, with experience, can learn, as feedback strengthens or inhibits connections that produce certain results. Stephen Kosslyn and Oliver Koening proposed to think of neural networks as networks of people. Neuron network with nearby neurons with which the can have short, fast connections. Each layer of a neural connects with various cells in the next layer. Learning occurs as feedback strengthens connections that produce certain results. New computer models simulate this process plus the excitatory and inhibitory conniptions to mimic the brain’s capacity for learning.


The Endocrine System


The endocrine system is the body’s slow chemical communication system. It consists of a set of glands that secrete hormones directly into the bloodstream. Hormones are chemical messengers mostly manufactured by the endocrine system. Hormones are produced in one tissue and affect another.

The hypothalamus sits below the thalamus and directs maintenance activities such as appetite, thirst and body temperature. Furthermore, it helps govern the endocrine system via the pituitary gland.

The thyroid gland is located in the front of the neck, below the larynx. The thyroid plays a crucial role in regulating our metabolism and calcium levels. T4 and T3 hormones released by the thyroid stimulate our tissue to produce protein and increase use oxygen to encourage cellular work. The chemical activity that is known as cellular work or activity is known as metabolism. The hormone calcitonin also released by the thyroid works along side the parathyroid hormone to regulate our calcium levels. The thyroid gland is controlled by hormones released by the pituitary gland.

The adrenal glands sit above the kidneys. They secrete epinephrine (adrenaline) and norepinephrine (non-adrenaline). They are vital to the autonomic nervous system.

The pancreas regulates the level of sugar in our blood. The part of the pancreas involved in the endocrine system is made up tiny cell clusters called islets of Langerhansα cells secrete glucagon which increases glucose in the blood, β cells secrete insulin which decreases glucose in blood, delta cells secrete somatostatin which regulates α and β cells. People that suffer from diabetes do not produce enough insulin which causes dangerously high blood sugar levels that must be regulated by an insulin shot or pump.

The ovaries and testes regulate sex hormones, female and male respectively. The ovaries, at the opening of the fallopian tubes, produce estrogen and progesterone, which play a crucial role in female development and reproduction. The testes, inside the male scrotum, produce testosterone, which affects male development and sperm production.

The pineal gland produces several important hormones including melatonin. Melatonin influences sexual development and the sleep-wake cycles.

The thymus gland is not really part of the endocrine system despite being a gland. It’s most important function is the production of T-lymphocytes, a type of white blood cells. This makes the thymus gland a quintessential part of the immune system.


Bailey, Regina. “Pineal Gland.” Biology. N.p., n.d. Web. 10 Sept. 2012. <;.

“Endocrinology Health Guide.” University of Maryland Medical Center. N.p., n.d. Web. 10 Sept. 2012. <;.

Myers, David G. Psychology . 6. Worth Publishers, 2001. Print.Myers, David G. Psychology . 6. Worth Publishers,2001. Print.

“Pancreas: Function.” Pancreas: Function. N.p., n.d. Web. 10 Sept. 2012. <;.

Animal Models in Neuroscience

Invertebrate Models 

The squid giant axon is pretty well renowned for his its applications neuroscience research. J Z Young discovered the giant squid axon and giant squid synapse and was the first to apply it neurophysiological research. The giant squid (loligo pealii) was and is still considered to extrodinarly vital to neuroscience research because of the sheer size of its axon (<1mm). It’s size makes it easy to dissect and support. External and internal perfusion with varying saline levels allowed scientists to determine ion flows in action potential.  Using the giant squid axon, Alan Lloyd Hodgkin and Andrew Huxley won the Nobel Prize in Physiology or Medicine in 1963 for developing Hodgkin–Huxley model mathematical model that describes how action potentials in neurons are initiated and propagated.


In electrophysiology, worms are used as a model for cellular death (apoptosis) and development and are also studied because of their relatively large axon. The C.elegans a nematoda (roundworm) is often studied because its genome, nervous system and genetic regulation of behaviour has been fully mapped. Specifically, these roundworms are an ideal model for apoptosis.

Fruit flies or drosophilia melangosaster have probably come up a fair few times if you have ever taken biology. Fruit flies are used in neuroscience for the identification of genes regulation nervous system development. In particular, the role of pax-6 in the development and evolution of the eye.

Vertebrate Models 


Italian physician Luigi Galvani in his frog studies showed that muscles can be caused to twitch when electrically stimulated.

German physician and physicist Hermann von Helmholtz isolated the nerve conduction velocity to be between a range of 24.6 – 38.4 meters per second.


Ross G. Harrison was the first person to make observations of axonal growth whilst studying tadpoles in vitro.

Katz and Miledi whilst studying frogs observed the role of calcium ions in the release of neurotransmitters.

The neuropsychologist Roger W. Sperry, known for his split-brain research that lead his Nobel Prize in 1981, observed rats and frogs discovering how nerves pathfind.


The domestic chicken (gallus domesticus) have been used again and again the study of brain development because of how easy they are to study. Chickens are so easy to study because of how ‘simple’ it is for scientists to manipulate the embryo. Being able to manipulate the embryo means the scientists have been able to transplant genes, tissue and nerve growth factors to study the effects.

Konrad Lorenz an Austrian zoologist,ethologist, and ornithologist studied imprinting in chicks, which is when an animal comes to believe the first person, thing or animal they see is there mother.


English biologist Steven Rose also used chicks to study passive avoidance learning, which is when a person or animals learns to stop doing a certain behaviour when it results in punishment.

Nichole Le Douarin transplanted regions of nervous system between quails and the domestic chicken to create a chimera, which has led to critical insights into the development of the nervous system and the immune system. Other notable researchers that have worked with the domestic chicken are Viktor Hamburger and Rita Levi-Montalcini.

Mammals and Non-Human Primates

Hitzig and Fritsch both German physicians used dogs to map out the motor cortex of dogs.

Using cats, dogs and apes English neurophysiologist, histologist, bacteriologist, and a pathologist Sir Charles S. Sherrington made huge progress to our current knowledge of reflexes, motor control and localisation in addition to coining the term synapse.

German pharmacologist Otto Loewi who discovered of acetylcholine, used dogs to study chemical neural transmissions. This discovery came from the stimulation of the vagus nerve releasing vagustoff, which caused a reduction  in the heart rate. This vagustoff was later confirmed to be acetylcholine. English neuroscientist Henry Hallett Dale later expanded on this discovery to study the release of ACh from the motor nerves in cats, dogs and frogs. He came up with Dale’s principle that individual nerves release a single neurotransmitter, which of course, was later proved false.

British physiologist John Langley named the autonomic nervous system and studied cats, dogs and rabbits to formulate the receptor theory.

American psychologist Karl Lashley searched for the engram (physical embodiment of memory) using ablations in rats to see how it would affect their memory performance in maze tasks.


To famous psychological experiments involving mammals are those of American psychologist B.F. Skinner and Russian psychologist Ivan Pavlov. Pavlov conducted studies on dogs and coined the term what is now known as classical or passive conditioning via the pairing of stimuli. B.F. Skinner using a ‘Skinner Box’ and rats coined the term active or operant conditioning via reinforcement.

Kuffler (Hungarian-American neurophysiologist), Hubel (Canadian neurophysiologist) and Weisel (Swedish neurophysiologist) worked together on cats and monkey brains to map out receptive fields related visual processing.

Mice transgenics have also widely been used to study molecular dissection of behaviour and diseases in particular in relation to reward systems and development abnormalities.

Non-human primates are of particular interest to neuroscientists because they are of few animals with brains similar to ours, in particular they have a frontal lobe.

Anotomical References

Anatomical references are not only important in surgery, but knowing them facilitates speech and orientation in various fields.

Main Definitions 

Anterior or rostral (Latin for ‘beak’): direction pointing towards head

Posterior or caudal (Latin for ‘tail’): direction pointing towards feet

  • The spinal cord runs anterior to posterior with a ventral and dorsal side.

Dorsal (Latin for ‘back): direction pointing upwards; think dorsal fin

Ventral (Latin for ‘belly’): direction pointing downwards


Bilateral symmetry: the right side of the brain and spinal cord is the mirror image of the left side

Midline: invisible line running down the middle of the nervous system

  • Medial: structures closer to the midline
  • Lateral: structures further from the midline

Ipsilateral: two structures that are on the same side of the midline

Contralateral: two structures that are on opposites sides of the midline

Making Sections of Tissue 

The standard approach when making sections or slices of tissue is to cut parallel to one of the three anatomical planes.

  • Midsagittal plane: plane of the section resulting from splitting in the brain into left and right halves
  • Coronal plane: splits in the brain into dorsal and ventral halves
  • Horizontal plane: splits the brain into anterior and posterior halves



Bear, Mark F., Barry W. Connors, and Michael A. Paradiso. Neuroscience: Exploring the Brain. Philadelphia, PA: Lippincott Williams & Wilkins, 2007. Print.

The Cranial Nerves

cranial nerves


The majority of the cranial nerves emerge from the brain stem on the ventral surface of the brain. Cranial nerves I and II emerge from the forebrain and cranial nerve XI from the brain stem as well as the spinal cord. As they are nerves they are classified as part of the peripheral nervous system; however, two of the cranial nerves are also considered part of the central nervous system, I and II. Each nerve often has fibers performing many different functions. Also they have associated cranial nerve nuclei in the midbrain, pons and medulla of the brainstem.

I. Olfactory: a special sensory cranial nerve responsible for our sensation of smell.

II. Optic: a special sensory cranial nerve responsible for our sensation of vision.

III. Oculomotor: a somatic and visceral motor cranial nerve responsible for the movement of the eye and eyelid as well as the parasympathetic control of pupil size.

IV. Trochlear: a somatic motor cranial nerve responsible for the movements of the eye.

V. Trigeminal: a somatic sensory and motor cranial nerve responsible for the sensation of touch on the face and the muscles of mastication.

VI. Abducens: a somatic motor cranial neuron responsible for the movements of eye.

VII. Facial: a somatic and special sensory cranial neuron responsible for the movement of muscles of facial expressions as well as the sensation of taste in the anterior 2/3 of the tongue.

VIII. Auditory-vestibular: a special sensory motor neuron responsible for the sensation of hearing and balance.

IX. Glossopharyngeal: a somatic and visceral motor cranial neuron as well as a visceral and special sensory cranial neuron responsible for the movement of muscles in the throat and the parasympathetic control of salivary glands in addition to the detection of blood pressure changes in aorta and the sensation of taste in posterior one third of tongue.

X. Vagus: a visceral motor and sensory cranial neuron as well as a somatic motor neuron responsible for the parasympathetic control of heart, lungs and abdominal organs as well as the sensation of pain associated with the viscera and movement of muscles in the throat.

XI. Spinal accessory: somatic motor neuron responsible for the movement of muscles in the throat and neck.

XII. Hypoglossal: a somatic motor cranial neuron responsible for the movement of the tongue.

cranial nerves2


Bear, Mark F., Barry W. Connors, and Michael A. Paradiso. Neuroscience: Exploring the Brain. Philadelphia, PA: Lippincott Williams & Wilkins, 2007. Print.