Neuroscience
Cyber Technology
Laboratory Manual
Terence Bazzett
SUNY Geneseo
2013
© Terence Bazzett
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© Terence Bazzett
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Table of Contents
© Terence Bazzett
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Chapter 1: Organelle Staining
Introduction:
A wide range of cell staining techniques are used in Neuroscience. Simple staining techniques
can be used to visualize neuronal cell bodies, neuronal projections, or glial cells. More
sophisticated techniques can also be used to visualize functional elements of cells. In particular,
most organelles within the cell can be individually stained allowing researchers to visualize, and
in some cases quantify, the integrity of intracellular structures. Characterizing changes within
neurons during the progression of neurodegenerative diseases can be invaluable for verification
of a diagnosis. Furthermore, if those changes are found to be contributing factors to the
degenerative process, they may become a starting point for testing treatments to slow or halt
progression of an illness. As such, research designed to elucidate organelle changes in
degenerative disorders is a potentially valuable form of applied research in Neuroscience. Read
the following article, paying particular attention to the Introduction and Discussion sections,
which provide the rationale for the methods used. Within the Experimental Procedures section
focus on the Immunocytochemistry section which gives a brief summary of the methodology
required for staining of the Golgi apparatus and the mitochondria within the neuron.
Background reading:
Nakagomi, Barsoum, Bossy-Wetzel, Sütterlin, Vivek Malhotra, and Liptona (2008). A Golgi
fragmentation pathway in neurodegeneration. Neurobiology of Disease, 29, 221-231.
© Terence Bazzett
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ERIN resource:
Authors: Invitrogen
Topic / Subtopic: B. Neural Excitability, Synapses, and Glia: Cellular Mechanisms; I.
Neuroanatomy / I.05. Anatomical Techniques Neuroanatomy
Resource Type: Image - Photograph, Simulation
Educational Level: 1 Introductory undergraduate, 2 Intermediate undergraduate, 3 Advanced
undergraduate
Listing Date: October 23, 2012
http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Cell-StainingTool.html?CID=fl-cellstaintool
Although the images are not from a neuron, this clever and realistic simulation allows students to
stain specific cellular structures using fluorescent antibodies. Up to four structures can be stained
simultaneously. Stains can be deleted so that other structures can be stained instead, a flexibility
that encourages exploration. Cellular structures include the membrane, cytoskeletal components,
mitochondria, the nucleus, Golgi, ER, and others. Using real images rather than diagrams makes
the simulation especially persuasive.
Lab exercise:
Consider the immunocytochemistry methods described by Nakagomi et al. Use the resource link
above to select appropriate stains for this laboratory preparation. Note: you do not need to use
the same stains cited in the Nakogomi et al. article, but you must select stains that would be
appropriate for your sample.
Student quiz questions:
1. When is Golgi fragmentation anticipated and possibly even functional within the cell?
Mitosis
2. Nakagomi and colleagues cite Gonatas et al., 2006 when noting that Golgi fragmentation is
believed to be associated with neuronal degeneration in what two disorders?
a. Alzheimer
b. ALS
3.
Using the immunocytochemistry methods of Nakagomi et al., approximately how much time
would you anticipate needing to complete the staining procedure used in their paper?
a. 5 minutes
b. 15 minutes
c. 1 hour
d. 14-16 hours
e. 16-19 hours
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4. In Nakagomi et al. fragmentation was quantified after Golgi staining. What was the effect of
NMDA on the fragmentation process?
a. Increased fragmentation
b. Decreased fragmentation
c. Had no effect on fragmentation
5. In your own words, describe how the image of the Golgi apparatus from the control group
differs from that of the image of the Golgi apparatus from the NMDA group.
The staining is more diffuse (fragmented) in the NMDA image.
6. What is general effect of NMDA on cell activity?
a. Increases activity
b. Decreases activity
c. Has no effect on activity
7. In the experiment by Nakagomi et al., NMDA exposure was used to mimic which of the
following? (circle all that apply)
a. Effects of a neurodegenerative disorder
b. Excitotoxicity
c. Neuroprotection
d. Neuronal sprouting
e. Mitosis
8. Which green Golgi stain(s) available from Invitrogen would be appropriate to use for this
experiment?
Golgin-97 is the only stain for fixed tissue as describe in the article.
9. Which orange-red mitochondrial stain(s) available from Invitrogen would be appropriate to
use for this experiment?
The two Oxphos stains are the only stains for fixed tissue as described in the article.
10. What doe Nakagomi and colleagues suggest can be accomplished by inhibiting Golgi
fragmentation such as that seen in response to NMDA stimulation?
They believe it can dlay apoptiotic-like cell death
11. Generate a useful, concise question from the background reading for this Chapter.
12. Generate a useful, concise question from the cyber laboratory exercise for this Chapter.
© Terence Bazzett
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Chapter 2: Epigenetics
Introduction:
There has been long standing debate about the relative importance of genetics versus the
importance of environment on phenotype expression. Since the origins of this “nature vs.
nurture” debate, many researchers have argued vehemently that the one or the other of these
factors reigns as most influential. In particular, the famous behavioral psychologist John B.
Watson is oft cited for his 1930 statement promoting the importance of environmental
influences:
"Give me a dozen healthy infants, well-formed, and my own specified world to bring
them up in and I'll guarantee to take any one at random and train him to become any
type of specialist I might select–doctor, lawyer, artist–regardless of his talents,
penchants, tendencies, abilities, vocations and race of his ancestors"
More recently, there seems to be a growing consensus among researchers that, for most
behaviors, it may be difficult to determine a comparable difference in contributions of genetics
and environmental influences. Perhaps more importantly, researchers are now finding that an
equally influential factor might, in some cases, be the effect of a an interaction between these
two elements. Epigentics is the study of modifications to the genome that do not involve a
change in the nucleotide sequence. Such modifications are brought about by variables in the
environment in which the genome resides. Such variables may, in turn, be directly influenced by
the environment in which an organism resides, behaviors of the organism, experiences of the
organism, and so on.
© Terence Bazzett
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Background reading:
Roth and Sweatt (2011). Annual Research Review: Epigenetic mechanisms and environmental
shaping of the brain during sensitive periods of development. J Child Psychology and Psychiatry
52, 398–408.
ERIN resource:
Authors: Genetic Science Learning Center, University of Utah
Topic / Subtopic: A. Development / A.02. Neurogenesis and Gliogenesis, A.03. Postnatal
Neurogenesis, A.06. Synaptogenesis and Activity-Dependent Development; C.Disorders of the
Nervous System / C.16. Cognitive, Emotional, and Behavioral State Disorders; E. Homeostatic
and Neuroendocrine Systems / E.01. Neuroendocrine Processes, E.03. Behavioral
Neuroendocrinology, E.04. Autonomic Regulation, E.05. Stress and the Brain; F. Cognition and
Behavior / F.02. Language; G. Novel Methods and Technology Development / G.07.
Computation, Modeling, and Simulation
Resource Type: Animation, Simulation
Educational Level: 1 Introductory undergraduate, 2 Intermediate undergraduate
Listing Date: March 22, 2012
http://learn.genetics.utah.edu/content/epigenetics/
A series of web links to readings and interactive videos describing epigenetics. Links provide
information directly related to the assigned reading. Emphasis is on developmental periods in
animals, but information about lifespan changes and human research is also included.
Lab exercise:
After completing the background reading, begin by watching the video “The Epigenome at a
Glance” followed by the interactive lab “Gene Control”. These two exercises will give you some
basic information on epigenomics. Next, view the video “Insights from Identical Twins” and
finish the lab by completing the interactive lab entitled “Lick Your Rats”. In this exercise, take
the time to lick several rat pups with a range of vigor. Begin with what you feel would be a
“normal” level of licking. Then try another pup with very vigorous licking. Finally, try a pup
with only a few licks. See what differences occur in the epigenome, and listen to the explanation
given for your licking activity in each case.
Student quiz questions:
1. From the Roth and Sweatt (2011) article, a rat model of an “abusive” caretaker, is described.
In this model, what behaviors exhibited by mother rats toward their pups that are considered,
and quantified as, abusive.
Frequent stepping on, dropping, dragging, actively rejecting, rough handling.
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2. From the Roth and Sweatt (2011) article, rats raised by mothers who displayed high levels of
pup licking/grooming had significantly less methylation of glucocorticoid receptor DNA in
their ____ than did rats raised by mothers who displayed low levels of pup licking/grooming.
a. Amygdala
b. Hypothalamus
c. Hippocampus
d. Thyroid gland
e. Entire brain
3. have been found to show decreases in which of the following?
a. Glucocorticoid receptor mRNA
b. Dopamine receptor mRNA
c. Cell number
d. Tissue volume
e. All of the above
4. From the movie, The Epigenome at a Glance, you learned that epigenome does which of the
following?
a. Changes the DNA code
b. Alters the sequence of genes within the DNA
c. Stimulates DNA self-replication
d. Shapes the physical structure of the DNA
e. All of the above
5. While the epigenome in identical twins may initially be nearly identical, factors throughout
life can create significant differences between the epigenome of twins as they age. As a
result, while identical twins may continue to share physical features established during early
development, behavioral characteristics tend to be less similar over time. From the
laboratory video, list the four categories of environmental factors that were cited as
potentially contributing to such epigenomic changes.
1.
2.
3.
4.
Diet
Physical Activity
Toxins
Stress
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6. From the interactive lab Gene Control, you learned that growth of cancerous tumors is
mediated in part by out of control cell growth that has two primary effects on gene coding.
Describe those two effects in very basic terms.
Out of control growth leads to cancer by both turning off genes coding for proteins that
slow cell growth, and turning on genes coding for proteins that speed up cell growth.
7. From the interactive lab Gene Control, list the effects on the following factors when you
increase and decrease the external signal using the control knob.
Stimulation
Increase
Decrease
GFP Gene
Structure
coils/tightens
uncoils/loosens
GFP mRNA
Increases
Decreases
GFP
Increases
Decreases
Cell image
Brightens
Dims
8. List from highest percentage (1) to lowest percentage (5), the traits listed below that may be
shared by identical twins.
2 Autism
4 Bipolar disorder
1 Height
3 Hypertension
5 Stroke
9. In adulthood, rats that were vigorously licked as pups tend to have more GR protein in the
hippocampus. This is particularly important because GR protein binds circulating
_______________ released during stressful periods, and helps to reduce the brain’s stress
response resulting in a calmer, generally more adaptive, animal.
a. Dopamine
b. Glutamate
c. Cortisol
d. Adrenaline
e. Oxytocin
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10. After completing the Lick Your Rat interactive lab, briefly describe the difference in
appearance of the epigenome in a pup that was licked vigorously versus a put that received
very little licking. Also describe the primary behavioral difference that will be seen between
these two rats as a result of this licking, when they become adults.
Vigorous Licking
Epigenome appearance
Loosely coiled
Adult Behavior
Easily relaxes
Little Licking
Tightly coiled
Does not relax easily
11. Generate a useful, concise question from the background reading for this Chapter.
12. Generate a useful, concise question from the cyber laboratory exercise for this Chapter.
© Terence Bazzett
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Chapter 3: Pedigree Mapping
Introduction:
Understanding inheritance patterns of disorders is one of the first, and most basic, steps in
establishing genetic influences that may cause, or contribute to a disorder. Generating a family
pedigree chart allows researchers to summarize information about inheritance patterns over
several generations. The pedigree chart is also an easily interpreted visual aid that offers a
concise summary of basic and essential information. In simple terms, a pedigree chart is a great
example of the old adage “a picture is worth a thousand words”. In reviewing a simple pedigree
chart, researchers can identify, at a glance, family members as living or deceased, male or
female, affected or unaffected, and so on. Pedigree charts are generally considered a staple for
studying qualitative traits, such as single gene disorders. However, they also provide useful
information for studying quantitative traits, including diseases that are influence by multiple
genes. With the advent of the Human Genome Project, and the subsequent increase in the
prevalence and utility of pedigree charts, the National Council of Genetic Counselors assembled
a Pedigree Standardization Task Force (PSTF) in the early 1990s and charged its members with
creating a universal coding system of symbols to be used in pedigree charts. The standardization
of pedigree symbol usage helped legitimize the use of these charts for medical and research
purposes. Today, regardless of the area of neuroscience, the pedigree chart is a useful if not
essential tool for understanding inheritance patterns, co-morbidity, genetic contributions and
more.
Background readings:
Ahearn, Steffens, Cassidy, Van Meter, Provenzale, Seldin, Weisler, & Krishnan (1998). Familial
leukoencephalopathy in bipolar disorder. American Journal of Psychiatry, 155, 1605-7.
© Terence Bazzett
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Bennett, Steinhaus, Uhrich, O'Sullivan, Resta, Lochner-Doyle, Markel, Vincent, & Hamanish
(1995). Recommendations for standardized human pedigree nomenclature. American journal of
human genetics, 56, 745-52.
ERIN resource:
Authors: Genetic Science Learning Center, University of Utah
Topic / Subtopic: B. Neural Excitability, Synapses, and Glia: Cellular Mechanisms / B.01.
Neurotransmitters and Signaling Molecules, B.02. Ligand Gated Ion Channels, B.03. G-Protein
Linked Receptors, B.06. Neurotransmitter Release, B.07. Synaptic Transmission; C.Disorders of
the Nervous System / C.17. Drugs of Abuse and Addiction, C.18. Behavioral Pharmacology; H.
Teaching, History and Societal Impacts of Neuroscience / H.03. Public Awareness of
Neuroscience
Resource Type: Animation
Educational Level: 1 Introductory undergraduate, 2 Intermediate undergraduate, 3 Advanced
undergraduate
Listing Date: March 22, 2012
http://learn.genetics.utah.edu/content/addiction/genetics/
This web site is expansive, with many related web links. You are encouraged to browse about
some of the other links when your assignment is complete. There are audio links, some video
links of related lectures, several animated exercises (including the Pedigree Investigator lab
assigned for this chapter), and links to other related sites.
Lab exercise:
Read the Ahearn et al., article as background information and to help you understand how
familial studies are conducted and how pedigree charts can be used to represent results. You do
not need to read the Bennett et al. article, but instead you should use it to help develop a greater
understanding of the depth and utility of pedigree charts. Understanding the possible complexity
of such charts is important for this lab assignment, since Ahearn et al., and the cyber lab both use
highly simplistic representations that may give an overly simplistic impression of this area of
research. After reading the Adhearn et al. article and reviewing Bennett et al., visit the web link
listed above and from there the Pedigree Investigator link. Read all of the information associated
with the Pedigree Investigator lab exercise and view all interview videos. After completing the
Pedigree Investigator lab exercise, return to the original web link page, and listen to both audio
recordings by Dr. Glen Hanson.
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Student quiz questions:
1. Adhearn et al. (1998) note the use of SCID in their research. What does SCID stand for?
Structured Clinical Interview for DSM III-R
2. From the Ahearn et al. (1998) article, it was noted that Dupont, Jernigan and Butters were the
first to report white matter hyperintensities in a large number of young patients diagnosed
with bipolar disorder. In what year was that early report published?
a. 1980
b. 1985
c. 1990
d. 1995
e. The year of that publication is not known
3. In reviewing the pedigree chart from Adhearn et al. (1998), indicate the following:
Number of males showing Unipolar Disorder symptoms __3___
Number of deceased females showing Bipolar symptoms __1__
Number of living females showing Unipolar Disorder symptoms __4__
Number of sets of twins evaluated__0__
4. What was the earliest age of Bipolar Disorder symptom onset for a participant in this study?
At what age was that participant interviewed for this pedigree. Is that participant male or
female?
Age of onset __8 years old__
Age at time of interview __20 years old__
Sex of participant __Female__
5. When gathering information from a client about severe combined immune deficiency
syndrome (SCIDS) you are told that she had elected to have an earlier pregnancy terminated
when it was discovered through a genome analysis that the fetus she was carrying tested
positive for SCIDS. With consideration to Bennett et al. (1995), what would be the
appropriate symbol to use in your pedigree chart to note this pregnancy termination if the
fetus was female? What would be the symbol used if the fetus was male? (note, symbols can
be created using the Insert Shapes function of your Word program).
Female
Male
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6. In some cases, dizygotic twins may closely resemble each other in physical appearance,
making it difficult to determine if they are dizygotic or monozygotic. Actresses Mary Kate
and Ashley Olsen, for example, are often believed to be monozygotic twins, but are
reportedly dizygotic. Without genetic testing to positively establish twin status, pedigree
charts may necessarily include some level of uncertainty. With consideration to Bennett et
al. (1995) what would be the appropriate way to represent twin sisters if zygote status is
unknown? Also indicated that one of the sisters is affected and the other unaffected for the
condition of interest.
?
7. From the cyber technology laboratory entitled Pedigree Investigator, which of the following
most closely represents the explanation for why researchers typically examine multiple
affected families when studying genetic influences on a complex trait such as addiction?
a. It is possible that multiple genes contribute and these genes may vary between families
b. Families may withhold information, particularly about sensitive traits such as addiction.
c. When multiple families are used, they may benefit from forming social support groups.
d. Multiple families increase the number of participants and therefore the statistical power
e. All of the above are noted in the lab exercise
8. From the cyber technology laboratory entitled Pedigree Investigator, are Todd and Alex
monozygotic or dizygotic twins? What was their age at the time of the interview? Which of
the twins shows signs of the addiction trait? Do either of the twins report treatment for
ADHD?
Monozygotic or Dizygotic
Age __31__
Addiction trait ___Both show this trait__
ADHD treatment __Both were treated for ADHD__
9. From the cyber technology laboratory entitled Pedigree Investigator, what is the approximate
number of cigarettes Tess reports smoking in a day? What is her age at the time of the
interview? Which of her parent’s reported being a tobacco user?
Number of cigarettes ___A pack a day__
Age __16__
Parent who uses tobacco __Father__
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10. In the audio clips associated with this laboratory exercise, Dr. Glen Hanson notes that
genetics may contribute to the addiction process. He then continues that thought, suggesting
a particular brain region that might be associated with the decision making process that leads
to drug usage, and continuation of drug use. What is the brain regions cited by Dr. Hanson
as possibly contributing to drug use and addiction in this way?
Frontal Cortex
11. Generate a useful, concise question from the background reading for this Chapter.
12. Generate a useful, concise question from the cyber laboratory exercise for this Chapter.
© Terence Bazzett
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Chapter 4: Basic Neurophysiology
Introduction:
A clear understanding of basic neurophysiological mechanisms is essential when trying to learn,
or teach, elements of more complex neural functioning. Included in this basic information is a
simplistic description of neural membrane structure, an explanation of how voltage and ligand
sensitive protein channels contribute to neural signaling, and a description of agonist and
antagonist effects. Beyond these elements, a well prepared student should also be familiar with
the concept of functional plasticity in the nervous system. This concept was eloquently
represented in the seminal work of Eric Kandel who demonstrated the physiological basis of
rudimentary learning (i.e. habituation, sensitization) in the aplysia.
One feature common to all areas of study in neurophysiology is the dynamic nature of
the phenomenon that are described. Written descriptions may clearly present the elements of the
activity, but it is in fact the activity itself that is focus of physiological function. As an analogy,
imagine writing a paper, or giving a lecture, trying to describe to students the elements of
classical ballroom dancing, traditional tap dancing, or modern jazz dancing. Such descriptions,
whether written or presented orally, would be profoundly improved if the students were actively
engaged in the dance forms, or at the very least could view examples of the each form of dance.
The present exercise has no require background reading, but you are strongly encouraged
to use one of your own textbooks that describes basic neurophysiological functions as a guide.
Read a basic description of the activities presented in the animations for this lab. Imagine the
activities that are described in the written work. Then view the video animations. Evaluate that
animations to see how they compare to your imagined explanation. Try to identify strengths and
weaknesses in the animation series. Think actively about how you could integrate these
animations into a lecture designed to teach basic neurophysiological functioning to your peers.
© Terence Bazzett
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Background reading:
For background or supplemental reading, students should use a basic Neuroscience,
Biopsychology, or Neurophysiology textbook.
ERIN resource:
Authors: Sumanas, Inc.
Topic / Subtopic: Neural Excitability, Synapses, and Glia: Cellular Mechanisms / B.00. Action
Potentials, B.01. Neurotransmitters and Signaling Molecules, B.02. Ligand Gated Ion Channels,
B.04. Ion Channels, B.07. Synaptic Transmission, B.08. Synaptic Plasticity, B.10. Intrinsic
Membrane Properties
Resource Type: Animation
Educational Level: 1 Introductory undergraduate, 2 Intermediate undergraduate, 3 Advanced
undergraduate, 4 Graduate
Listing Date: March 20, 2012
http://www.sumanasinc.com/webcontent/animations/neurobiology.html
A set of animations that accompany Purves et al. (2008) "Neuroscience" (4th edition). This site
provides a very nice series of animations, several of which describe basic elements of
neurophysiology. You are encouraged to view the other animations to determine if they have
any value as supplemental materials for other courses you may be taking.
Lab exercise:
For the present exercise, view the following video animations. It may be helpful, though not
essential, to view the videos in the following order: 1) The Resting Membrane Potential 2) The
Action Potential 3) Synaptic Transmission 4) AMPA and NMDA Receptors 5) Sensitization in
the Aplysia. Ideally, you should view each animation in full, and then answer the quiz questions
associated with that video. After completing the quiz questions, review the video to check your
answers. In doing this, you will be able to identify areas where you may require additional
information for a complete understanding. For any questions that remain unclear after reviewing
the video animations, refer to your background textbook for a written explanation that may be
more complete than the information provided in the animation.
Student quiz questions:
1. By definition, when is equilibrium achieved? Are ions in neuronal intracellular fluid at
equilibrium with ions in the extracellular fluid? If not, describe the imbalance.
Equilibrium is reached when ion concentration is equally distributed. The intracellular
and extracellular fluids are not at equilibrium for ions. The intracellular fluid has a net
negative charge compared to the extracellular fluid
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2. Neuronal membrane protein channels designated as “potassium” channels also allow which
of the following ions to pass through the membrane?
a. Sodium
b. Chloride
c. Calcium
d. All of the above since these channels are relatively nonselective
e. None of the above since these channels are highly selective
3. In a resting neuron, potassium channels may be in an open state. Considering that potassium
is in much higher concentration inside of the cell relative to outside of the cell, why does
diffusion fail to bring intracellular and extracellular potassium to equilibrium?
Intracellular electrical gradient keeps intracellular potassium in higher concentration.
Sodium potassium pump may also contribute.
4. Depolarizing a cell membrane to its threshold level triggers events that evoke an action
potential. What is the response of the cell when the membrane is depolarized beyond
threshold (suprathreshold) level?
a. An action potential of greater amplitude is seen
b. An action potential of longer duration is seen
c. An action potential comparable to that produced by a threshold depolarization is seen
d. The membrane enters a tonic state, and no action potential is seen
e. The membrane enters a state of reverse polarization and hyperpolarizes
5. List the six stages of the action potential.
1. Resting phase
2. Rising phase
3. Overshoot
4. Falling
5. Undershoot
6. Recovery
6. Not all vesicles in the synapse are free floating and ready for immediate use. Some vesicles
are actually held in reserve. Where are these reserve vesicles docked, or tethered?
a. On the myelin
b. Within the soma
c. On the cytoskeleton
d. On membrane transporter proteins
e. On the mitochondria
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7. Synaptic vesicles are drawn together at the terminal membrane by protein complexes known
as “SNAREs”. SNARE is an acronym for what?
SNARE is an acronym derived from "SNAP (Soluble NSF Attachment Protein)
REceptor"
8. CAM kinase has two primary effects on AMPA receptors. One of these effects is to
phosphorylate the receptors which ultimately has what effect on ion conductance?
a. Increase conductance to sodium ions
b. Decrease conductance to sodium ions
c. Increase conductance to potassium ions
d. Decrease conductance to potassium ions
e. Increase conductance to all ions
f. Decrease conductance to all ions
9. The sensory neuron that transmits neural signals from the aplysia siphon utilizes which of the
following neurotransmitters?
a. Dopamine
b. Serotonin
c. Acetylcholine
d. Glycine
e. None of the above
10. Interneurons that modulate the sensitization response in the aplysia utilize which of the
following neurotransmitters?
a. Dopamine
b. Serotonin
c. Acetylcholine
d. Glycine
e. None of the above
11. Generate a useful, concise question from the cyber laboratory exercise for this Chapter.
12. Generate a second, concise question from the cyber laboratory exercise for this Chapter.
© Terence Bazzett
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Chapter 5: Rat Brain Anatomy – Modeling Parkinson
Disease
Introduction:
Animal models have long been a research staple for increasing understanding of brain damage
and neurological dysfunction. Among the most prevalent and enduring models are rodents with
induced damage to the nigrostriatal pathway, designed to mimic Parkinson disease (PD).
Because PD has a relatively well defined region of degeneration (the substantia nigra), early
researchers found that nonselective cell damage to this structure, typically produced by
electrolytic lesions, resulted in motor deficits that could be roughly equated to PD. More
recently, neurotoxic lesion, using intracranially injected 6-hydroxy dopamine (6-OHDA) or
systemically injected 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), have been used to
produce more selective damage, destroying dopamine producing cells in the substantia nigra
while leaving other cells and fibers of passage relatively intact. For several decades now, these
neurotoxins have been used for modeling PD and testing potentially therapeutic drugs. In the
case of intracranial injections, researchers have also developed a method by which behavioral
effects of neurotoxic damage can be readily quantified. To do this, animals are subjected to
unilateral lesions, which produce asymmetrical posturing and turning behavior when the animal
walks. Turning behavior is easily quantified as the number of rotations an animal exhibits in a
given time period. This paradigm can then be expanded upon by challenging the animal with
drugs or environmental influences (e.g. amphetamine or stress) that exacerbate rotating behavior.
Likewise, therapeutic compounds can be tested for effectiveness in reducing rotations. The
simplicity of this behavioral model, combined with its intuitively applied results, explain why
unilateral nigrostriatal lesions have endured for so long in neuroscience research.
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Background readings:
Creese, Burt, & Snyder (1997). Dopamine receptor binding enhancement accompanies lesioninduced behavioral supersensitivity. Science, 197, 596-8.
Ungerstedt, & Arbuthnott (1970). Quantitative recording of rotational behavior in rats after 6hydroxy-dopamine lesions of the nigrostriatal dopamine system. Brain Res, 24, 485-493.
ERIN resource:
Authors: Rose Feor, Davidson College; Nicole Mah , Davidson College; Donna Molinek,
Davidson College; Mur Muchane, Davidson College; Todor Penev, Davidson College; Julio J.
Ramirez, Davidson College
Topic / Subtopic: C.Disorders of the Nervous System / C.03. Parkinson's Disease
Resource Type: Animation, Laboratory Exercise
Educational Level: 2 Intermediate undergraduate, 3 Advanced undergraduate
Listing Date: March 20, 2012
http://www.davidson.edu/neuroscience/neuronconnection/default.aspx
Lab exercise:
You are going to perform a virtual experiment using the unilateral 6-OHDA model. Your rats
will be given neurotoxic 6-OHDA injections to the substantia nigra of the right hemisphere. The
toxin will selectively destroy dopaminergic neurons beginning within 24 hours, leading to
Parkinson-like symptoms. You will select the amount of denervation you would like to induce,
choose a drug with which to challenge your animals, and view graphs of the rats' rotational
behavior both pre- and post- lesion.
Student quiz questions:
1. Creese and colleagues (1977) pointed out that like rats with 6-OHDA lesions, rats subjected
to long-term treatment with neuroleptics seemed to develop apomorphine supersenstivitity.
They noted that this rat model may be useful for studying which of the following?
a. Hallucinations reported by patients receiving chronic treatment for Parkinsonism
b. Hallucinations reported by patients receiving chronic treatment for schizophrenia
c. Tardive dyskinesia reported by patients receiving chronic treatment for Parkinsonism
d. Tardive dyskinesia reported by patients receiving chronic treatment for schizophrenia
e. Tremor reported by patients receiving chronic treatment for Parkinsonism
f. Tremor reported by patients receiving chronic treatment for schizophrenia
2. From the Cresse et al. (1977) reading, what did the authors identify as the major finding of
their study?
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“Haloperidol binding sites increase in rats with lesions of the nigrostriatal dopamine
pathway”
3. What was the rate of delivery and concentration of 6-OHDA used by Ungerstedt and
Arbuthnott (1970)?
a. 4 microliters per minute @ 8 micrograms per microliter
b. 16 microliters per minute @ 16 micrograms per microliter
c. 8 microliters per minute @ 8 micrograms per microliter
d. 4 microliters per minute @ 4 micrograms per microliter
e. 1 microliter per minute @ 2 micrograms per microliter
4. It seems reasonable to assume that even without disruption of the nigrostriatal dopamine
system, an animal stimulated by amphetamine might be inclined to exhibit rotational
behavior if it is put into a spherical chamber. Was this concerned addressed by Ungerstedt
and Arbuthnott (1970)?
Yes. They noted that though animals were highly active, there were very few rotation
counts recorded in sham lesioned animals.
5. From the information provided in the cyber technology laboratory exercise, approximately
what percentage of striatal dopamine depletion is required before behavioral symptoms
become apparent?
a. 20%
b. 40%
c. 60%
d. 80%
e. 100%
6. When viewing coronal sections of the rat brain, what is anterior/posterior reading that is
given at the point where you are able to visualize the most anterior portion of the superior
colliculus? At this same point, what structure can be visualized in an adjacent ventral/medial
location relative to the superior colliculus?
-5.6 mm, PAG
7. From a horizontal perspective, what structure appears in a lateral location relative to you
lesion at all levels from bregma?
Hippocampal region
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8.
In a group of 9 animals with 60% damage, what is the prominent direction of the rotation
and the mean number of post surgery rotations per minute in that direction, after treatment
with amphetamine?
Ipsilateral (mean number varies)
9.
What is the percentage of damage that must be apparent in the substantia nigra for the
simulation to show mean apomorphine induced rotations in excess of 70 per trial session?
90%
10. The authors of this laboratory exercise suggest that when testing rats for apomorphine and
amphetamine induced rotational behavior, it may be desirable to randomly administer these
drugs, so that rats do not rotate in the same direction on several consecutive trials. What is
the reason for avoiding successive trials using the same drug to induce the same rotational
direction?
It reduces the likelihood of “learned rotation” in rats being tested
11. Generate a useful, concise question from the background reading for this Chapter.
12. Generate a useful, concise question from the cyber laboratory exercise for this Chapter.
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Chapter 6: Cognitive Neuroscience
Introduction:
Neuroscientists have long been interested in the processes of mental imagery and in particular
how the brain functions when interpreting complex images. Research in this realm is filled with
challenges. First, most questions on this topic are specific to humans, limiting the use of animal
models. Related to the lack of animal models, is a significant restriction in the use of
experiments that allow direct observation of neural functioning, such as intracranial recording.
These limitations in research methods have required researchers to use techniques that rely
largely on observation of human responding to perception of external stimuli. For example, if
asked “How many windows are on your family home?”, most people report creating a mental
image of their home, from which they then count windows using a systematic movement around
that mental image. Related to this, if asked to compare two similar objects presented from
different visual orientations, observers are believed to create mental images of the objects and to
then systematically move, or rotate, those images into equivalent orientations as a strategy for
making accurate comparison. The original theories suggesting humans use such manipulation of
visual imagery have been researched extensively. Among the most convincing evidence
supporting the “mental rotation” hypothesis has been the finding that the amount of time required
to compare objects is highly correlated to the degree of difference in orientation between the
images of objects being compared. For example, an object needing to be rotated 20o to be
brought into congruence with a second object can be evaluated more quickly than an object
needing to be rotated 40 o which can be evaluated more quickly than an object needing to be
rotated 80 o and so on. Classic experiments used to evaluate mental rotation demonstrate the
utility of basic procedures being used to provide evidence for highly complex questions.
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Background readings:
Shepard & Metzler (1971). Mental rotation of three-dimensional objects. Science, 171, 701-3.
ERIN resource:
Authors: John H. Krantz, Hanover College
Topic / Subtopic: D. Sensory and Motor Systems / D.02. Auditory
Resource Type: Animation
Educational Level: 1 Introductory undergraduate
Listing Date: March 8, 2012
http://psych.hanover.edu/Krantz/sen_tut.html
Lab exercise:
From the Krantz home page, that is loaded with interesting exercises and labs, click on the
“Cognition Laboratory Experiments” link. From the new page, select the “mental rotation” link
listed under the “mental imagery” subtitle. Carefully review the instructions page for the mental
rotation experiment. Once you are comfortable with your understanding of these instructions,
click on the link to start the experiment (a little more than halfway down the page). Activate the
Java plug in to begin the experiment. The Java page will show you the parameters for the study.
You need change only the first setting (to original 3D) for the stimulus type, the rest of the
default settings work well for this exercise. Your parameters page should be set up as follows:
Stimulus type: change to “original 3D”
All other settings can be left at the following default settings:
Number of Rotations = 7
Stimulus should “Rotate”
Stimulus size = 100
Number of trials per level = 10
Show “No Lines”
Distance from fixation = 0.150
Delay before stimulus = 1000 msec
Stimulus on Till Response = yes
Click on the “done” button at the bottom of the screen to begin the experiment. The first screen
of the experiment requires a prompt (space bar) to initiate the sequence of stimuli used for this
study.
Complete the experiment and record your own personal results. Then, if you are male, recruit a
female to complete this experiment. If you are female, recruit a male to complete this
experiment. Record their results.
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Student quiz questions:
1. Metzler and Shepard (1971) concluded that when a mental image is rotated within the plane
of a picture, _________ time is needed compared to when a mental image is rotated in depth.
a. significantly more
b. significantly less
c. about the same amount of
2. What was the explanation given by Metzler and Shepard (1971) for using mirror images of
objects for the “different” pair category, rather than just using objects that had random
differences in shape?
This prevented participants from identifying distinctive features of to establish
noncongruence without requiring them to carry out the process of mental rotation.
3. The results presented by Metzler and Shepard (1917) indicate that there was ___________
variability in reaction time scores for objects that required a greater degree of mental rotation
when compared to those that required a lesser degree of mental rotation.
a. less
b. greater
c. about the same amount of
4. How many scientific articles are referenced in the Metzler and Shepard (1971) paper?
None
5. According to the Metzler and Shepard (1971) article, approximately how long, on average,
would it take a participant to mentally rotate an object 150o?
a. 1.0 second
b. 1.5 seconds
c. 2.0 seconds
d. 2.5 seconds
e. 3.0 seconds
6. According to the Metzler and Shepard (1971) article, approximately how long does it take a
participant, in their paradigm, to identify two objects as the same when no mental rotation is
required?
1 second
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7. From the mental rotation exercise, when viewing the results, what number would represent a
“perfect score” for accuracy?
a. 1.0
b. 10
c. 100
d. 1000
e. A perfect score cannot be achieved on this test
8. From the mental rotation exercise, which of the following is not an option in the
experimental set-up for a “stimulus type”?
a. Original 2D
b. Original 3D
c. Random 2D
d. Number
e. Letter
9. From the mental rotation exercise,
Did you find a sex related difference in either speed or accuracy of completing this task?
Yes No (circle one)
Which subject did you recruit
Male Female (circle one)
When your score was compared to the participant you recruited, it was
Faster Slower (circle one)
When your score was compared to the participant you recruited, it was
More accurate Less accurate (circle one)
10. List an article reference (in APA format) that might be useful for evaluating the results you
circled for responses to the previous inquiries (responses to #9).
11. Generate a useful, concise question from the background reading for this Chapter.
12. Generate a useful, concise question from the cyber laboratory exercise for this Chapter.
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Chapter 7: Transduction of Sensory Input - Auditory
Introduction:
From the neuroscience perspective transduction is, in general, the conversion of environmental
energy into neural energy. The processes of auditory transduction are particularly interesting for
a number of reasons. Among these is the role of hair cells that act as mechanoreceptors within
the inner ear. Mechanoreceptors are rapidly responding cells that require no chemical processes
to initiate depolarization or hyperpolarization. In addition, basic hair cell functioning in the
auditory system is nearly identical to that of the vestibular system. Thus, to understand
transduction processes of the auditory system, is to likewise understand the basic processes used
in transducing energy used for balance and kinesthetic function. Beyond basic transduction, the
auditory system is designed with an intricate systematic arrangement of receptor cells within the
inner ear. The tonotopic representation of cells within the cochlea is a unique example of how a
basic process, such as transduction, can be integrated into a highly complex process, such as
pitch perception. In this case, the complex process of pitch perception utilizes relative location
and distribution of receptors, physical properties of the inner ear, and timing of neural signals. In
general to understand the working of the auditory system is to understand a relatively simple yet
elegant neural process that has evolved so that organisms may interact more readily with the
environment around them.
Background reading:
Hudspeth A.J (2005). How the ear's works work: mechanoelectrical transduction and
amplification by hair cells. C R Biologies, 328,155-62.
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Background video viewing:
http://www.youtube.com/watch?v=PeTriGTENoc
ERIN resource:
Authors: John H. Krantz, Hanover College
Topic / Subtopic: D. Sensory and Motor Systems / D.02. Auditory
Resource Type: Animation
Educational Level: 1 Introductory undergraduate
Publication Date: 0001
Listing Date: March 8, 2012
http://psych.hanover.edu/javaTest/NeuroAnim/audition.physiology.html
This website gives an overview of behavioral, anatomical, and computational aspects of working
memory. A major feature is an interactive computer model. The example here is tuned
persistent delay activity in the prefrontal cortex of non-human primates observed during
oculomotor delayed-response tasks. Some parameters in the simulation of the network model can
be changed interactively to study how the strength of inhibition and excitation in the microcircuit
affect the capacity of the model to store information in working memory.
A series of Java applets that animate aspects of audition. Components include: 1) Illustration of
the sound stimulus including the effects of intensity and frequency on perception of sound and
various features of a sound wave, e.g, compression, rarefaction and phase. 2) Reception and
transduction concepts illustrated for middle ear including the working of the ossicles and how
their motions depend upon the frequency of sound. Cochlea illustrations show functions of the
inner including how sound stimuli affect hair cells to cause transduction.
Lab exercise:
From the Hanover College audition animation home page, visit each of the web links. The sound
basics link allows you to visualize compressions and rarefactions of air molecules produced by
sounds of different frequencies. Frequency of sound can be adjusted using the slide bar on the
left of the screen. Sound corresponding to the different frequencies is also produced by this link.
There are four links listed under reception and transduction, but if the link for “the ear” is
opened, the other three links can be accessed from this one web page and movement from the
entire ear to the individual components allows better visualization of the workings of the entire
ear. From “the ear” page, sound frequency and amplitude can be adjusted to see how these
changes affect reception and transduction processes within the ear. The youtube video gives a
nice continuous animation of the processes shown on the Hanover College web page, as well as a
nice descriptive explanation of these processes.
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Student quiz questions:
1. Hudspeth (2005) notes that the auditory system utilizes a general principle whereby objects
may be “tuned” to certain frequencies, causing them to vibrate when that frequency is
emitted. What is the analogy he uses to describe this example?
a. A person playing a piano
b. A plane causing a window pane to rattle
c. A dog whistle that is not perceived by humans
d. A person playing a pipe organ
e. None of the above, Hudspeth describes this process as unique to the auditory system.
2. What are the two properties of the basilar membrane that contribute to its ability to vibrate
sympathetically in specific regions to specific frequencies?
a. Length and girth
b. Mass and tension
c. Fluid content and fiber density
d. Ionic concentration and protein content
e. Ionic concentration and lipid content
3. Which of the following sound detecting organs/structures is not found in humans?
a. Lateral line organ
b. Cochlea
c. Vestibular labyrinth
d. All of the above are found in humans
e. None of the above are found in humans
4. When the hair bundle is moved toward the short edge (the shorter hair cells), the result is a
________________ in _______________ causing a net _______________________.
a. Decrease, cation influx, depolarization
b. Increase, cation influx, depolarization
c. Decrease, anion influx, depolarization
d. Increase, anion influx, depolarization
e. Decrease, cation influx, hyperpolarization
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f. Increase, cation influx, hyperpolarization
g. Decrease, anion influx, hyperpolarization
h. Increase, anion influx, hyperpolarization
5. The auditory system is extremely responsive, in terms of speed, when interpreting high
frequency sounds. In brief terms, explain why hair cells can emit signals more rapidly than
many other neural systems when responding to stimuli (sound).
Their response uses rapid mechanical mechanisms rather than slower chemical release.
6. Hair bundles do not simply respond to sound waves, but also amplify the signal emitted by
wave energy. This amplification process utilizes a unique “twitch” process in which a
physical link between ____________ of one hair cell and an adjacent hair cell mechanically
force movement that increases ion flow and thus amplifies the neural signal.
a. The membrane
b. Sodium/potassium pumps
c. Calcium channels
d. Dendrites
e. The nucleus
7. In the Youtube video, movement of the three bones of the middle ear is described as pivoting
on an axis that is due to ___________________.
a. A viscous fluid that bathes these bones
b. A series of ligaments that hold the bones in place
c. A series of muscles that respond to and amplify movement of the bones
d. Four small bones that encase the three bones of the inner ear
e. A single axis bone that passes through the malleolus
8. From the Hanover College resource page, viewing the “Sound Basics” link, set the frequency
(left side of screen) to 400 Hz and note how many compressions occur on the screen (time
duration 625.00). Change the frequency to 800 Hz and note how many compressions now
occur over the same duration. Click on the “play” button to listen to the differences in tone
for the two frequencies.
Number of compressions: 400 Hz = ______________ 800 Hz = ____________________
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9. From the Hanover College resource page, view the “the ear” link. Start the sound and slowly
move the frequency from low to high. Describe what happens to the hair cell containing
membrane within the cochlea as sound waves change from low frequency to high frequency.
a. Membrane movement shifts from apex only to base only
b. Membrane movement shifts from base only to apex only
c. Membrane movement shifts from entire length of membrane to base only
d. Membrane movement shifts from entire length of membrane to apex only
e. Membrane movement is consistent regardless of the frequency change
10. From the Hanover College resource page, view the “the ear” link. Start the sound and slowly
move the amplitude from high to low. Describe what happens to the hair cell containing
membrane within the cochlea as sound waves change from high amplitude to low amplitude.
f. Membrane movement shifts from apex only to base only
g. Membrane movement shifts from base only to apex only
h. Membrane movement shifts from entire length of membrane to base only
i. Membrane movement shifts from entire length of membrane to apex only
j. Membrane movement does not shift, but does change in size
11. Generate a useful, concise question from the background reading for this Chapter.
12. Generate a useful, concise question from the cyber laboratory exercise for this Chapter.
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Chapter 8 : Working Memory
Introduction:
Background reading:
Background video viewing:
ERIN resource:
Authors: Albert Compte, IDIBAPS, Barcelona, Spain
Topic / Subtopic: F. Cognition and Behavior / F.01. Learning and Memory
Resource Type: Simulation
Educational Level: 2 Intermediate undergraduate
Publication Date: 2012
Listing Date: February 22, 2013
http://wm.crm.cat/en/
This website gives an overview of behavioral, anatomical, and computational aspects of working
memory. A major feature is an interactive computer model. The example here is tuned
persistent delay activity in the prefrontal cortex of non-human primates observed during
oculomotor delayed-response tasks. Some parameters in the simulation of the network model can
© Terence Bazzett
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be changed interactively to study how the strength of inhibition and excitation in the microcircuit
affect the capacity of the model to store information in working memory.
Student quiz questions:
1. According to the cyber lab exercise, the first researcher to study working memory was
William James which he named primary memory.
2. According to the cyber lab exercise, which of the following brain structures would not show
increased oxygen consumption during the delay period of the delayed matching task?
a. Dorsolateral prefrontal regions
b. Superior frontal gyrus
c. Superior frontal junction
d. Visual cortex
e. Parietal anterior cortex
3. From the cyberlab exercise titled, “network memory during working memory trial” set the
excitatory and inhibitory stimuli at equal levels of very low intensity (far left side of the bar
for both). Count and report below the number of action potentials that occur in the response
period of the third (bottom) neuron recording when these inputs are both set at the lowest
level.
Number of action potentials during response period ___4-5____
Now increase the inhibitory input to the highest possible level (far right of the bar) while
leaving the excitatory input at the lowest possible level (far left of the bar). Count and report
below the number of action potentials that occur in the response period of the third (bottom)
neuron recording when excitatory input is at this lowest level and inhibitory input is at this
highest level.
Number of action potentials during response period _zero__
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Chapter 9 : Sleep
Introduction:
Background reading:
Background video viewing:
ERIN resource:
Authors: D.T. Max, National Geographic
Topic / Subtopic: E. Homeostatic and Neuroendocrine Systems / E.08. Biological Rhythms and
Sleep
Resource Type: Article - News, Image - Diagram, Image - Photograph
Educational Level: 1 Introductory undergraduate, 2 Intermediate undergraduate
Publication Date: 2010
Listing Date: March 8, 2012
http://ngm.nationalgeographic.com/2010/05/sleep/max-text
The Secrets of Sleep From birth, we spend a third of our lives asleep. After decades of research,
we’re still not sure why. Includes a feature article, photographs, and interactive diagrams.
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Chapter: Transduction of Sensory Input – Visual
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