Biom 509 Introduction to Neurobiology

Spring 2017

MW 1:00 – 2:00 rm B116 DCW
F 8:00 - 9:00 rm 243 Fitz Hall


Survey Monkey Class Evaluation
(Please disregard the references to Squire, Young, and Perves in #4)


Paper Presentation Groups


Hypothesis paper presentations


General Topic





Reading assignment

Gross & Cellular Neuroanatomy


Quickquiz 1

W 18 Jan

Neurons & Glia

1.4 – 1.8


Quickquiz 2

F 20 Jan

Gross Brain Anatomy

1.9 – 1.12



M 23 Jan

Brain Dissection I

Fig 1-8 Blumenfield



W 25 Jan

Brain Dissection II

Fig 1-8 Blumenfield

Nervous System Development


Quickquiz 3

F 27 Jan

Cell Fate Determination

7.1 – 7.4


Quickquiz 4

M 30 Jan

Axon Guidance and Pathfinding

5.1 - 5.6, 7.5 – 7.6


Quickquiz 5

W 1 Feb


7.9 – 7.14


Quickquiz 6

F 3 Feb

Synapse Maturation and Refinement

5.7 – 5.16, 7.13 - 7.15



M 6 Feb

Adult Neurogenesis

Box 11.2


Integrative test 1

W 8 Feb

Paper 1: Development Methods Questions




Quickquiz 7

F 10 Feb

Ion Channels

2.4, 2.14 – 2.16, 12.6, (13.20 – 13.21)  M2.8


Quickquiz 8

M 13 Feb

Cellular Potentials quant

2.5 – 2.7, 2.9 – 2.12  M2.5  M2.7


Quickquiz 9

W 15 Feb

Subthreshold Events

2.8, 2.13, 3.24 – 3.25  M2.6


Quickquiz 10

F 17 Feb

Sensory Transduction

4.1 – 4.8, (4.9 – 4.23), 6.22 – 6.24 M4.1 M6.2


Quickquiz 11

M 20 Feb

Spinal reflexes

1.9, 8.2 – 8.3


Integrative test 2 Key2

Quickquiz 12

W 22 Feb

Vesicular Release

 3-1 – 3-9  M3.1  M3.2

Student Research Day



F 24 Feb



Synaptic transmission



M 27 Feb

Paper 2: Electrophysiology Intro



Quickquiz 13

W 1 Mar

Synaptic Plasticity

3.10, 10.4 – 10.8, 10.15 – 10.16


Quickquiz 14

F 3 Mar

Norepinephrine & Dopamine

3.11, 3.18 – 3.22


Quickquiz 15

M 6 Mar

Serotonin, Adenosine & Histamine

3.11, 3.18 – 3.22


Integrative test 3

W 8 Mar

Paper 3: GPCRs Intro




Quickquiz 16

F 10 Mar

Acetylcholine & GABA

3.11, 3.12 – 3.14, 3.17

Spring Break




12 – 19 Mar





Quickquiz 17

M 20 Mar

Glutamate and Glycine

3.11, 3.15 -3.16


Integrative test 4

W 22 Mar

Paper 4: Neurotransmitters I Intro



Quickquiz 18

F 24 Mar

Neurotrophic Factors




M 27 Mar

Peptides & Non-conventional Transmitters



Quickquiz 19

W 29 Mar

Gene Expression

3.23, Box 3-4




Quickquiz 20

F 31 Mar

Reward & Addiction




M 3 Apr

Paper 5: Substance Abuse , Intro



Quickquiz 21

W 5 Apr

Behavioral Testing I

10.23 – 10.25, 13.27 – 13.29


Quickquiz 22

F 7 Apr

Behavioral Testing II

10.23 – 10.25, 13.27 – 13.29,


Integrative test 5

M 10 Apr

Paper 6: Behavioral Testing Intro


Neuro-degenerative Disease


Quickquiz 23

W 12 Apr

Neurodegenerative Disease I

8.9, 11.1 – 11.8


Quickquiz 24

F 14 Apr

Neurodegenerative Disease II

8.9, 11.9 – 11.14



M 17 Apr

Paper 7

Neurodegenerative Disease Suppl Discussion





W 19 Apr

Paper 8: Connectome a b c d Intro

13.15 – 13.19,  M13.2

Student Paper Presentations


M 24 Apr – F 5 May





Luo, L. Principles of Neurobiology, Garland Science 2016

Free on-line student resources can be accessed by registering with Garland Science at:



Quickquiz questions will be taken directly from figure legends in the assigned reading (excluding suggested readings listed in parentheses).


Integrative Tests

Integrative tests are meant to integrate material presented in the preceding unit.  They will be posted on-line on the specified date and will be due by the following class.  You are free to use the text or your notes, but not to discuss the questions with other class members.


Assigned Papers


1. Sultan, et. al. (2015) Synaptic integration of adult-born hippocampal neurons is locally controlled by astrocytes. Neuron 88:957-972


2.  Midorikawa, M., Sakaba, T., (2015) Imaging Exocytosis of single synaptic vesicles at a fast CNS presynaptic terminal Neuron 88:492-498


3. Gantz, S.C., et al. (2015) Depression of serotonin synaptic transmission by the dopamine precursor L-DOPA Cell Reports 12:944-954


4.  Kim, J-I., (2016) Aldehyde dehydrogenase 1a1 mediates a GABA synthesis pathway in midbrain dopaminergic neurons.  Science 350:102-106








8a Nano-Connectome 

Bartol, T., et al. (2015) Nanoconnectomic upper bound on the variability of synaptic plasticity.  eLife e10778.


8b. Cellular Connectome

Hammer, S., et al (2015) Multiple retinal axons converge onto relay cells in the adult mouse thalamus. Cell Reports 12:1575-1583


8c. Brain-Wide Connectome

Gong, H., et al (2016) High-throughput dual-color precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level. Nature Communications 7:11142.


8d. Functional Connectome

Vassal, F., et. al. (2016) Combined DTI tractography and functional MRI study of the language connectome in healthy volunteers:  Extensive mapping of white matter fascicles and cortical activations. PLOS ONE 10.1371

Principles of Neurobiology Biomed 509 - spring 2017 UNM


Class time: Monday, Wednesday, Friday 1:00 – 2:00


Course director: Don Partridge (rm 209 Fitz Hall, 272-8815,


Registration: Principles of Neurobiology (Biomed 509) meets one selective requirement for all first year Biomed Sci graduate students.  All other graduate and undergraduate students wishing to enroll must obtain permission from the course director.


Textbook: Reading assignments are given in Luo, Principles of Neurobiology, 2016 Garland Science.  A textbook adds important breadth and an alternative dimension to the material covered in lecture and we strongly recommend that you purchase the textbook.  Other material may be assigned by the faculty during the course and will be put on reserve in the Medical Library.


Quickquizzes:  Class sessions marked Quickquiz will begin with a one or two multiple choice questions based solely on the figures in the indicated section in Luo, Principles of Neurobiology.  Students will answer these questions on their mobile devices at the beginning of class with the Socrative Student app.  (Note: Since the quizzes are posted online, they can also be answered during legitimate absences from class.  They will be available from about 5 minutes before until 5 minutes after start of class.  Absent students will be trusted to not refer to the text in answering quickquiz questions.)


Integrative tests: Each unit will wrap up with a take home test due at the next class session that integrates material from that unit.  Use of notes and texts is appropriate for completing these tests.


Assigned paper discussions: There will be 8 class discussions of assigned papers that are related to each of the blocks of material in the course.  Groups will be pre-assigned and given a specific aspect of the paper to present, although all students are required to come to class prepared to discuss the whole paper.  Groups will be expected to prepare an approximately 10-minute PowerPoint presentations in advance of class.  Every member of the group is expected to contribute equally to preparing the presentation.  On the rare occasion when it is necessary for one member to miss the presentation session, they are to send the course director a short written description of what they contributed to the group effort.


Oral presentations and paper:  Reading and interpreting the scientific literature, formulating your own ideas based on this information, and presenting your ideas to others are essential skills for any scientist.  The final assignment for this course is intended to provide experience in developing these skills.  Many aspects of your scientific career (including the qualifying exam and grant writing) are based on hypothesis formation.  While hypothesis formation is usually followed by designing experiments to test the hypothesis, this assignment is directed only at the aspect of making and supporting a hypothesis.

Paper and oral presentation deadlines  

Fri, 10 Feb:  Choose an area of neuroscience related to the topics of this course and based on this topic, a neuroscience faculty member will be assigned to the student. 

Fri., 24 Feb:  It is the student’s responsibility to meet with this faculty member by to discuss a hypothesis.

Mon., 3 Apr:  A draft of the paper must be turned in to the faculty member.

Mon., 24 Apr:  The final paper must be turned in to the course director.

Mon., 24 Apr to Fri, 5 May:  Fifteen-minute oral presentations with a 5-minute question period will be scheduled.



            • Quickquizzes 25%

• Integrative tests 25%

            • Participation in in-class paper discussions 20%

            • Paper and oral presentation:

Oral presentation - 15%

Hypothesis: Was the hypothesis clearly stated and well established

Knowledge: Did the student demonstrate an understanding of the material

Delivery: Was the presentation well organized and presented

Questions: Were the questions answered in a thoughtful manner

First draft - 5%

Clearly stated hypothesis

Relevance of hypothesis established

Convincing support of the hypothesis

Hypothesis adequately critiqued

Final paper - 10%

Clearly stated hypothesis

Relevance of hypothesis established

Convincing support of the hypothesis

Hypothesis adequately critiqued

Suggestions from first draft incorporated

Technical aspects (bibliography, figures, etc.)

Neurobiology (Biomed 509)

Written and oral presentation requirements of Presentation


Paper logistics:

•This paper should be no longer than 10 double-spaced typed pages. 

•The following divisions are suggested:

introduction (1/2 - 1 page): State your hypothesis in one succinct sentence and briefly explain what it means.

            background (1 - 2 pages): Give enough background to establish why your hypothesis is                            relevant.

            discussion (4 - 6 pages): Use evidence from the literature to support your hypothesis.

            critique (1 -2 pages):  Discuss possible weaknesses of your hypothesis.


•The bibliography must include: author(s), title, journal, volume, inclusive pages, and date.  Citations in the text should be by number or first author’s name. 

•A small number of figures will generally add to the clarity of the paper.  Published figures must be properly referenced.


Object of the paper:

Papers will be graded on the thoroughness of research, clarity of writing, and persuasiveness of the support for the hypothesis.  This paper is to be focused on the stated hypothesis.  Material that does not serve to explain or support this hypothesis should not be included in the paper.


Scientific hypotheses:

Laboratory experiments, grant proposals, dissertation proposals, and the qualifying exam are designed to support a stated hypothesis.  In his System of Logic, John Stuart Mills gives the following long-winded, but quite accurate, definition of a hypothesis:

“an hypothesis is any supposition which we make in order to endeavour to deduce from it conclusions in accordance with facts which are known to be real; under the idea that if the conclusions to which the hypothesis leads are known truths, the hypothesis itself must be, or at least is likely to be true.”

Two essential points about hypotheses are (1) that they are a statement of a supposition and (2) that they are testable and capable of being proven either true or false.  Your hypothesis must meet these two criteria.  The object of your paper will then be to establish that your hypothesis is a statement of a reasonable supposition, and to propose the outcome of tests of your hypothesis based on evidence from the scientific literature.


Examples of acceptable hypotheses:

We would like your hypothesis to be as original as possible, but we realize that you are unlikely to be familiar enough with the literature of neuroscience to devise an entirely original hypothesis.  At this stage, we are looking more for the clarity of your hypothesis and your ability to support it than we are for originality.  The following are a range of examples of acceptable hypotheses:

• Parkinson’s disease results from loss of neurons in the substantia nigra.

• Excitotoxicity causes cell death in Parkinson’s Disease.

• Selective block of NMDA receptors will prevent excitotoxic loss of substantia nigra neurons.