About Me:

My name is Charles Frye and as I write this, I am a graduate student in the Helen Wills Neuroscience Institute at the University of California, Berkeley. These questions were one component of my department's oral qualifying exam.

This blog is no longer updated. Check out my personal blog for more blog posts, with a slightly mathier bent.

This page reflects the questions, and my answers, as of May 2016. Fourty-four of the questions (roughly half) are answered on this blog.

The Questions:

I. Sensation

01: What are the signal transduction cascades for sensory detection of light, odors, and tastes in mammals?

02: What were the fundamental findings of Hubel & Wiesel, J. Physiol. 1962?

09: What is the problem of invariance in perception and what are some models for how it is solved in the brain?

11: What is Bayes' Rule? Explain how an aspect of perception can be expressed in terms of Bayes' Rule. (See: Wolpert & Ghahramani)

II. Control Of Movement

12: Describe the key cortical areas and subcortical structures of the motor system. Give an example of how these components contribute to the performance of a simple motor task such as reaching and how they contribute to the performance of a skilled action like playing the piano.

13: How is M1 organized? What features of movement are represented in spiking of M1 neurons?

14: What are the basal ganglia and their major component circuits? What role do the basal ganglia play in movement and choice of movements?

15: What is a central pattern generator? Choose a well-studied CPG and describe how it functions.

16: What is the function of the cerebellum in motor control? Describe the basic microcircuit for integrating sensory cues and motor control signals in the cerebellum.

17: Describe the major components of a generic brain-machine interface for restoring motor function in a paralyzed person.

III. Neuronal Biophysics

18: How do K+ channels pass K+ and Rb+ but exclude Na+ and Cs+?

19: How do ionotropic and metabotropic receptors transduce detection of an extracellular signal into a change in neural activity? Give examples and describe similarities and differences between the receptor classes.

20: What is the structure and mechanism of the voltage sensing apparatus of voltage-gated channels?

21: What is the mechanism of inactivation of voltage-gated channels that results in transient currents in response to sustained membrane depolarization?

22: What is the ionic basis of the resting potential? Draw an equivalent circuit model of the resting membrane.

23: What is the ionic basis of the basic features of an action potential?

24: How do electrical signals propagate or dissipate through a dendritic tree?

25: In computational neuroscience, what is an integrate-and-fire neuron? How does it differ from a real neuron?

IV. Synaptic Transmission And Plasticity

26: What are the steps in synaptic transmission?

27: What are the most common mechanisms responsible for synaptic facilitation and depression?

28: How is neurotransmitter activity terminated, after its release at a synapse?

29: Describe how the NMDA receptor functions, and how it implements the Hebbian model of learning at the synaptic level?

30: What is homeostatic plasticity?

31: What are gap junctions, and how do they impact the function of neural networks?

V. Development

32: What is a morphogen? How do morphogens generate different cell fates in the spinal cord?

33: Which mechanisms cause offspring from the same precursor cell to take on different cell fates?

34: How do axon guidance molecules direct axons to their targets?

35: How is the synapse at the vertebrate neuromuscular junction specified?

36: Give an example of a wiring process mediated by an activity-dependent competitive mechanism.

VII. Neural Networks And Coding

47: Describe the differences between rate coding and temporal coding, and give examples of each in the nervous system.

48: What is the principle of sparse coding? Explain its relation to other coding schemes such as dense codes or grandmother cells, and give examples of each in the nervous system. Why is sparse coding more common higher in sensory hierarchies?

49: What is population coding? Describe the population coding model proposed by Georgopoulos in the 1980s for M1 control of arm direction.

50: Give an example of a specific, well-studied neuronal microcircuit and describe how it performs a specific calculation.

51: Draw a neural circuit representing feedforward inhibition and one representing lateral inhibition. What are the major computational roles of these circuit motifs?

VIII. Neuromodulation And Brain State

60: What is spontaneous activity in the nervous system? Is it random? What does it arise from?

X. Anatomy And Organization

68: What are the basic functions of glia and mechanisms of gliotransmission?

71: Describe the major divisions and functions of the peripheral nervous system.

73: Beginning with Vernon Mountcastle, give three examples of columnar organization in different cortical areas.

XI. Tools And Methods

80: How does an extracellular electrode measure spiking of a neuron? How are spikes different when measured extracellularly verses intracellularly?

81: What is 2-photon microscopy, and how is it used to measure population neural activity?

82: What is information theory? What does entropy measure? Mutual information? How are these quantities relevant to questions of neural coding? (See: Dayan & Abbott, Chapter 4)

83: How does fMRI work? What neurovascular mechanisms generate the BOLD signal?

84: Describe the advantages and disadvantages of each the following experimental methods for cognitive neuroscience studies: PET, EEG, TMS.