About Me:

My name is Charles Frye and I am a graduate student in the Helen Wills Neuroscience Institute at the University of California, Berkeley. These questions are 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This blog is no longer updated.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 list of questions 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?

03: How is the olfactory system organized? How do neural circuits for innate vs. learned olfactory behaviors differ?

04: What principles determine which sensory inputs are over-represented (magnified) within sensory maps in the brain?

05: What are the different roles of the dorsal and ventral processing streams in extrastriate cortex? What are the major brain areas within these streams? Give examples of neural tuning within these areas.

06: Give two examples of multisensory integration, and explain how they are generated in the brain.

07: Describe how spatial locations coded in a retinotopic coordinate system get transformed into representations based on patterns of musclemovements. What are the reference frames for spatial representations in area V1, lateral intraparietal (LIP) area, and M1?

08: How do changes in the amount or statistics of sensory experience alter the topography of sensory maps in primary sensory cortex? Describe one example of this process in development and another example in adulthood.

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

10: What are the differences between the neural substrates of conscious versus unconscious processing of stimuli in the environment?

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.

37: What is the evidence for and against the existence of critical periods in brain development?

38: What is adult neurogenesis? Where does it occur in the brain? Describe evidence that adult neurogenesis is involved in different types of learning

39: What has resting-state fMRI research revealed about the development of large-scale brain networks in humans?

VI. Learning And Memory

40: Define the following types of learning and memory and summarize their neural correlates: working memory, declarative/semantic memory, perceptual learning, procedural learning, episodic memory.

41: What is reinforcement learning? How has it been used to understand neural systems involved in decision-making?

42: What is the major circuit in the hippocampus? What functional role has been posited for each hippocampal subfield within this circuit?

43: What are the major structures and mechanisms that mediate fear conditioning and fear extinction? Is extinction a process of forgetting or learning? What is the evidence?

44: What are place cells and grid cells, and where are they found? How do these cells implement Tolman’s idea of a cognitive map of space?

45: What is a Hopfield network (also known as an ‘attractor neural network’)? Explain the principle by which memories are stored in such networks.

46: How you distinguish whether a difference in behavior between two ages is due to an innate developmental program versus learning?

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?

52: Describe how the receptive field of a visual cortical neuron is measured using reverse correlation or similar approaches. Qualitatively, how well does this description account for the response properties of a typical neuron in V1? V2? MT? IT?

53: A typical cortical neuron receives the vast majority of its synaptic input from other cortical neurons. If each input is roughly Poisson in its firing statistics, then what should the output statistics of the neuron resemble? If this model neuron’s output is not Poisson, then propose some possible explanations for how it is that the output of cortical neurons are highly variable despite the many random inputs they receive.

VIII. Neuromodulation And Brain State

54: Describe how circadian rhythms are generated at the cellular level.

55: How does neuronal activity alter gene expression? Describe one signaling pathway (and its key components) that transduces activity into transcriptional changes.

56: Describe the differences between neural and endocrine signaling. What approaches could one apply to uncover neural circuits involved in hormonal regulation of a behavior versus neural control?

57: What are the major physiological and cognitive/behavioral functions of the following neuromodulators: acetylcholine, dopamine, serotonin, noradrenaline?

58: What are the different types of sleep and their associated neural substrates? Describe current models for the functions of these different types of sleep.

59: Choose your favorite two frequency bands of cortical oscillations (alpha, beta, gamma, delta, theta). What functions have been proposed to arise from them?

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

IX. Attention And Executive Functions

61: What are the similarities and differences between endogenous/top-down and exogenous/bottom-up attention? What is known about their anatomical substrates and physiological mechanisms?

62: Describe the historical debate on early versus late selection theories of attention. What is the physiological evidence supporting each of these theories? (See: Serences & Kastner 2014)

63: What is the role of the amygdala? Describe the standard view and more recent alternative views and provide evidence from non-human animal and human neuroscience studies.

64: What is meant by the ‘value’ of a stimulus in decision-making, and how is this represented in the nervous system?

65: How does the brain process rewards and punishments?

66: Describe the roles believed to be played by (i) orbital frontal cortex and (ii) ventromedial prefrontal cortex in emotional processing, giving evidence from primate (human and/or nonhuman) neuroscience studies.

67: Is there a specialized neural system for processing social information? What is the evidence for and against such a hypothesis? (See: Adolphs 2003)

X. Anatomy And Organization

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

69: Many genes are differentially expressed in only a subset of neurons. What are some functional consequences of this molecular specialization of neurons?

70: What is the neuro-vascular unit? What are the components and regulation of blood-brainbarrier function? How does blood-brain-barrier function affect neural excitability?

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

72: How does the peripheral nervous system regenerate after damage? Why is regeneration much more limited in the central nervous system?

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

74: What is the minimum wiring length principle, and what organizational features of the nervous system are hypothesized to arise from it?

75: Is the frontal cortex organized hierarchically in a similar fashion to the visual cortex? More generally, what evidence is used to demonstrate hierarchy of brain areas?

76: Name two brain areas thought to be involved in language. What roles they seem to play?

XI. Tools And Methods

77: What is channelrhodopsin, what organism was it derived from, and how does it control activity in a neuron?

78: What resources are available at the Allen Brain Atlas?

79: How can you generate a knock-out mouse?

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.

XII. Diseases Of The Nervous System

85: Explain what is meant by templated protein misfolding (seeded protein misfolding). Give some examples of the role of this process in neurological disease.

86: What are the primary neuromodulatory systems affected in depression? What types of drugs are used to treat depression and what are their mechanisms of action?

87: Much of our knowledge of brain function comes from the study of patients with neurological disorders. Give two examples from neuropsychology that have led to important insights into brain organization. Describe limitations or concerns with this method.

88: What is the neurobiological basis for addiction?

89: What neurological or psychiatric diseases are caused by basal ganglia dysfunction, and what specific circuits are affected by these diseases?

90: What are the clinical features of autism spectrum disorders? What is known about the genetic and synaptic/circuit basis of autism?

91: What is the amyloid hypothesis for Alzheimer’s Disease (see: Hardy & Selkoe, Science 2002)