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Bio 446 / Bio650

Neurophysiology Lab

Fall 2023

Tuesday - 12:30 to 1:20 PM Lecture
Thursday - 12:30 to 3:20 PM Lab
Multidisciplinary Science Bldg.
725 Rose Street, Room 155B.
This is the red brick and stucco building directly across the street from Biology (Thomas Hunt Morgan Building), right next to the UK clinic parking garage.

  

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Fall 2023:
Instructor: TA:

Dr. Robin L. Cooper
RLCOOP1@email.uky.edu
Office: Biology, rm 226
Tel: 257-5950
Office Hours: email for appt.
WWW Home page (go to)

No TA this year

 

work together

 
Jump to on this page:

Course outline (go to)

Syllabus MS word & PDF for Bio 446

Syllabus MS word & PDF for Bio 650

 Course schedule & experiments (go to)

COURSE OUTLINE

Development of the course:

Cooper, R.L., Titlow, J. and Majeed, Z.R. (2012). Introduction of a new neurophysiology laboratory for students at the University of Kentucky. Annual Meeting of Society for Neuroscience. New Orleans, LA., USA. (ppt)

Why comparative neurophysiology is of interest [ pdf ]

FREE NEUROPHYSIOLOGY TEXT BOOK ON LINE (use for a review of basic concepts)
http://nba.uth.tmc.edu/neuroscience/m/s1/index.htm

Free background information on neuron morphology, conducting electrical, ionic bases of resting & action potential, and Synapse structure

Schedule
Presentation schedule & topics:

Class Photo

TBA

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Lithium project:

Movie by Kaitlyn Brock here download

Paper 1; Paper 2; Paper 3; Paper 4; Paper 5 ( all are PDFs)

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Zinc project:

Movie by Elizabeth Elliott here download

Paper 1; Paper 2; Paper 3; Paper 4; Paper 5; Paper 6; Paper 7; Paper 8; Paper 9; Paper 10

Paper 11; Paper 12; Paper 13; Paper 14; Paper 15; Paper 16 ( all are PDFs)

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TOPICS AND READINGS-TENTATIVE SCHEDULE
Please note that this is a tentative schedule and may be modified depending on how the course is progressing. All changes will be announced in advance, and students will be well aware of them-particularly regarding what is going to be included on exams.

Week, Topics, Student-driven In-class Activities

Week 1:

Tuesday: Learn about equipment (extracellular & intracellular amps, microscopes, electrode puller). Solutions and laboratory tools. Animal care. Lab notebooks & reports.

SEE these movies before class: How to analize PD nerve activity MOVIE Download

Likley the effects of Fe3+ on neuronal function for Thursday's class

- Learn to record from proprioceptors (extracellular) in the crab leg and relate to joint positions. Research paper discussion. (see this lab PAGE- Joint receptors in a crab)

Class data sets:

For past class projects and publications - Articles and resources

Week 2:

www.pubmed.gov

Read over abstracts for Zn2+ and Li+ project... see emails for links.

Week 3:

Thursday- experiments with plants

Movie for a lab protocol in recordings (Movie MP4) Youtube Link: https://youtu.be/sEdBDbmVQ_s

.......................................................MS word and PDF

Week 4:

 

- We will start on the bread board to learn about OHM's law and electrical conduction .................................(see this lab Page- Neuron model )

Might still be working on MRO of crayfish.

- Crayfish - proprioception. The MRO preparation (Lab web page) (also how to move segment ... movie by Alex Stanback) (Here....MPEG or window media)

But, if finished then we start intracellular recordings.

- Measure membrane potentials in crayfish abdomen muscles and plot Rp vs [Na]o graphs and Rp vs [K]o graphs. (see this lab PAGE- RP, K, Na)

Making a cheap electrode holder (500 mB movie file from an IPHONE- need to download and then watch. Also on YOUTUBE https://www.youtube.com/watch?v=7FFNriDjLc0)

... helpful material 2 slides on a ppt or the PDF

? Midterm exam will be posted here or emailed to class.

Week 5:

- Measure facilitation and depression in tonic and phasic neuromuscular junctions in crayfish abdomen muscles. We will learn how to stimulate motor nerves and record EPSPs/IPSPs. (see this lab PAGE- EPSPs)

- Quantal analysis of synaptic transmission: Crayfish NMJ record quantal responses..(see this lab PAGE- quantal analysis )

- 5-HT action on NMJ model page 68 or 53 of document --Wu's dissertation)

 

Power point on optogenetics PPT,

Introduction to the leech nevous system: Titlow, J., Majeed, Z.R., Nicholls, J.G. and Cooper, R.L. (2013) Identifiable neurons in the central nervous system of a leech via electrophysiology and morphology, sensory field maps in skin and synapse formation in culture: Student laboratory exercises. Journal of Visualized Experiments (JoVE). (81), e50631, doi:10.3791/50631. http://www.jove.com/video/50631/intracellular-recording-sensory-field-mapping-culturing-identified

Learn how to dissect the leech ventral nerve cord and obtain intracellular recordings from identified neurons. Current injections and threshold measures. Record in situ synaptic connections. Investigate the ionic currents making up the action potentials. (see this lab PAGE- Leech ganglion lab)

So cool brain circuits : https://www.youtube.com/watch?time_continue=44&v=Pn4dksaAvok

-Mapping skin receptive fields on the leech while recording from neurons. Dye fills. (see this lab PAGE- Leech Skin lab)

- Learn how to forward fill neurons from the crab leg proprioceptors (CoCl2, 4-Di-2 ASP) as well as stain with methylene blue. (see this lab PAGE- Staining of Joint receptors in a crab)

- Learn to record from tension receptors in the crab leg related to muscle length and contraction as well as human muscle EMG. (see this lab PAGE- tension nerve recordings)

- EEG Human lab (go to lab EEG lab page)

- Earthworm preparation to learn about conduction velocity and refractory periods ................................(see this lab Page- Earth worm experiments)

- Introduction to the leech nevous system and practice dissection. Staining of leech ganglia.

- Learn how to remove and culture leech neurons for forming synapses in culture. (see this lab PAGE- Leech neuron culture lab)

-Catch up on experiments and analysis day. Graph data, catch up on homework and literature gathering. Plot I V curves and use Ohms law to determine Rm with crayfish skeletal muscle.

Sensory recordings from the cockroach cerci. (see this lab PAGE- cockroach cerci )

Vision: crayfish caudal photo receptor in crayfish.

..................(see this lab PAGE- Crayfish photoreceptors lab)

No class. Work on your own out of lab for write ups.

- Make up any labs needed. Make sure lab report is going along OK. Pass out take home exam.(Exam 2)

- (Finals week) Turn in final exam and reports.

Required Texts
None. Handouts and www based content.

Supplementary Materials
Readings from the primary literature will be assigned on occasion. These articles will be posted on Blackboard for you to download and print.

Lab report write ups

Now for the individual projects........you can use your own set (your own group) of data for write ups but this has to be your own thought process and analysis and interpretation of the data. Discission is independent as well.

The paper grading rubric HERE

The write up for a lab exercises will need to be as if you were planning to submit it to a journal for peer review by other research scientist. The format will be as that described for the Journal of Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology. Go to the www and look up information for authors on this journal's home page.

http://www.elsevier.com/wps/find/journaldescription.cws_home/525464/description#description

then go to guide to authors

http://www.elsevier.com/wps/find/journaldescription.cws_home/525464/authorinstructions

Then go to how to list your references and see format for references. Also you can open up a past article on the journal's web site and see how they formatted them.
So try a demo cover letter as well.

Sample Cover letter to paper-1; Sample paper-1; when published-PDF-1 by Undergrads in Bio395.

Sample cover letter to paper-2; Sample paper-2;...when published-PDF-2 by Undergrads in Bio395.

Course Description
The course will focus on the experimentation in primarily neurophysiology with some emphasis in muscle physiology. Generation of receptor potentials in sensory neurons will be measured as well as action potentials in axons. Pharmacological experimentation of ionotropic and metabotropic receptors subtypes and second messengers signaling will be conducted. The key role of ion channels and transporters in regulation of the membrane potential will be covered in great detail. The concept of electrochemical equilibrium will be introduced and quantitative description of the equilibrium membrane potential will include discussion of Goldman and Nernst equations and their applications. The mechanisms of action potential generation, as a result of synaptic and receptor stimulation within a neural cell, will be measured in terms of voltage gated ion channels.
The mechanisms of neuron-neuron communication through electrical and chemical synapses will be examined in live preparations. The function of gap junction ion channels will be examined and measured at electrical synapses. The complex intracellular mechanisms controlling neurotransmitter release at the chemical synapses will be examined. The proteins participating in the SNARE complex, involved in the synaptic vesicles fusion, as well as the molecular machinery involved in synaptic vesicles recycling will be emphasized along with quantal analysis of synaptic transmission. The historical introduction of the quantal hypothesis and its experimental conformation will be covered. Synaptic plasticity will be covered up to the latest discoveries in the field.

Course Objectives
By the end of this course, you should:
1. Have a conceptual understanding of the information processing in the nervous system.
2. Understand the molecular mechanisms that enable signal transmission in the nervous system in terms of receptor potentials, synaptic potentials and action potentials.
3. Know what are the cellular specializations and the molecular machinery involved in the neuron-neuron communication at the state of the art level.
4. Develop a basic knowledge of the sensory processing.
5. Be able to understand and critically analyze research papers in the field of Neuroscience.
6. Be able to develop new ideas and suggest future research directions in the field of Neuroscience.
The overall objective of the course is to develop insightful understanding of the neurological processes at molecular and cellular level by experimentation. The course will complement other courses offered within the new Neuroscience Major we are establishing on campus.

All exams are required of all students.

There will be class room presentations in front of the whole class by the students as a means of going over the exams and quizzes as well as presenting your research report. If you have anxiety issues for classroom presentations please see the disability office at UK and obtain an official letter that you need out of giving a class room presentation, otherwise you are expected to be able to talk in front of the class.

If you are unable to take an examination as scheduled, it is your responsibility to contact me before the exam. There will be no make-up exams; students with excused absences will have their point total for the course pro-rated. Unexcused absences from an exam will result in a score of zero for that test. Homework and problem sets that are turned in late will be marked down a point each day they are late, and they must be turned in before those that were turned in on time are returned.

Quizzes
Quizzes will be assigned to each topic. The quizzes score will be used as an extra credit toward your exam score.

Attendance
Required for all laboratory sessions.

Format
In this course, you will learn the fundamentals of neural processing through a variety of activities, including lectures, problem sets, independent/group study, and in-class exercises. Please note that you are responsible for all the material in the assigned chapters, including figures, summaries, and "boxes," regardless of whether it is covered in lectures. Thus, you will be responsible for covering some material from the text or readings on your own.

Canvas/Class Communications
Course announcements, assignments, lecture outlines and additional materials will be posted online using Canvas. Exams and homework dates will remain fixed. Updates to this syllabus (regarding topics and reading) will be posted; please check periodically. You will also receive important course announcements via your UK e-mail account. If you do not use your UK e-mail account, you need to activate it. It is strongly recommended that you check your e-mail regularly. I may send messages-sometimes with attachments-to the class using this medium. You should also feel free to e-mail me if you have any questions or problems. Feel free to call me as well, if you prefer a more personal communication. I am also available during the office hours. If you would like to meet with me at another time, please don't hesitate to e-mail or to call, and I can schedule a time to meet.

Honesty and Civility
You must abide by UK's Code of Conduct which prohibits:
1. Academic dishonesty and impropriety, including plagiarism and academic cheating.
2. Interfering or attempting to interfere with or disrupting the conduct of classes or any other normal or regular activities of the University.
We take plagiarism and other forms of cheating very seriously. If you have any questions as to whether something is plagiarism, please ask me, or, if that's not possible, assume that it is and don't do it!

Disabilities
Any student who needs accommodation because of a disability should contact me privately to discuss the specific situation as soon as possible. The Office of Disability Resources and Services. They can coordinate reasonable accommodations for students with documented disabilities.
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