Tues 
   4:00-6:00 pm
   Foster Hall 110

  Instructor: Dr. Elba E. Serrano
  Associate Professor of Biology
  Ph.D., Stanford University
  Neuroscience/Biophysics

  Office & Office Hours:

 Foster Hall 337D
 Wed 12:15-1:15 pm
 (&  by  appointment)

646-5217
eserrano@nmsu.edu

OPTICAL SOCIETY OF AMERICA

• COURSE DESCRIPTION
• PREREQUISITES
• TEXTBOOKS
• LECTURES & READING ASSIGNMENTS
• SCHEDULE OF TOPICS, EXAMS & ASSIGNMENTS
• PRACTICUM SIGNUP

• GRADING SYSTEM
• FINAL GRADES
• EARNING GRADE POINTS
• GRADE SCALE
• ATTENDANCE

• POLICIES AND PROCEDURES:
• LATE ASSIGNMENTS
• SYLLABUS MODIFICATION
• STUDENTS WITH DISABILITIES
• CODE OF CONDUCT
• OTHER

• IMPORTANT DATES
• Nov 1 Practicum written assignments 
• Nov 15 Term paper 
• Final Wed Dec 11 3:30 

• WEBSITES FOR STUDENTS
• CELL AND ORGANISMAL BIOLOGY
• SCHOLARSHIPS & FINANCIAL AID
• INTERNSHIPS & JOBS

Biology 550,  Principles of Confocal Microscopy,  covers the fundamental principles and applications of confocal microscopy.  The class format includes lectures, student presentations, and a lab practicum. Slides sets will be provided for the hands-on portion of the course.  Students will learn to operate the BioRad 1024 in the Fluorescence Imaging Facility.  Upon completion of the course, participants will have the tools to develop an experimental protocol for a confocal imaging study in an area of research interest and will have the foundation for more intensive studies of confocal and fluorescent imaging technology.  Students who successfully complete the course may petition to be independent users of the BioRad 1024 confocal microscope in the NMSU FIF.

* Cell Organismal graduate students receive Tier II credit for the course.

Recommended:  Molecular Cell Biology (Bio 520), Instrumental Methods (Chem 471),  and Optics (Physics 470).

Students committed to professional careers in microscopy are encouraged to purchase the Handbook by Pawley.

Lectures will highlight key concepts from the texts, journals, and web pages.   Students are responsible for mastering the concepts in the readings whether or not they are discussed in class by the instructor.  The instructor is available to discuss material from lectures and readings during scheduled office hours and by appointment. . SCHEDULE OF PRESENTATIONS AND LECTURES

DATE	MAIN TOPICS	CLASS ASSIGNMENT
Sept 3	Introduction Basics of Confocal Microscopy Sample Preparation Fluorescence BioRad 1024 System
Sept 10	Safety Concerns & FIF User       Compliance BioRad 1024 System Access Confocal Optics  Resolution Fluorescent Probes	Readings from  Imaging Neurons  Appendix 3 Care and Cleaning of Optical Equipment Appendix 4 Cautions Ch 1  Microscopy and Microscope Optical  Systems Chapter 11 Confocal Microscopy: Principles and Practice  Chapter 12 Practical Limits to Resolution Select topic for pesentation (use  list for ideas) Access the following web sites and browse contents Molecular Probes BioRad Order Bio-Rad fluorophore poster Order Molecular Probes Product CD and or book
Sept 17	Practicum Preparation Student Presentations (3)	Practicum Week Lasersharp Manual Use fluorescent probe database Flourescence basics review Readings from  Imaging Neurons  Appendix 1 Glossary Appendix 3 Lenses, Filters, Spectra
Sept 24	Practicum Discussion Student Presentations (3)	Practicum Week
Oct 1	Practicum Discussion Lasers Fluorescence Energy Resonance     Transfer  (FRET ) Student Presentations (3)	Practicum Week Imaging NIH Image Imaging Programs (Keck - Univ of Washington) Readings from  Imaging Neurons  Ch 18 Lasers Ch 55 FRET
Oct 8	Practicum Discussion Image Processing: Metamorph,      Image J, etc Calcium and Proton Imaging Student Presentations (3)	Imaging NIH Image Imaging Programs (Keck - Univ of Washington) Readings from  Imaging Neurons  Ch 30 Calcium Indicators Ch 31 Quantitative Calcium Fluorimetry Ch 32 Calcium Indicator Calibration
Oct 15	Spinning Disk Scanners Multi-Photon Microscopy	Readings from  Imaging Neurons  Ch 17 Principles of MP Microscopy

 

GRADING SYSTEM

Earning Grade Points:  Grades will be calculated by adding the total points earned on all assignments and presentations.  A total of 500 pts may be earned during the course. YOU MUST TAKE THE FINAL EXAM.

In class participation : (70 pts)  Based on your contribution to class discussion and evidence of preparedness for class. 

Presentations: (70 pts)  Based on your contribution to class discussion, presentations, and evidence of preparedness for class.  Suggested topics:

PMT technology

tunable lasers

scanning disk confocal imaging

FRET

fluorophore colocalization 

vital imaging

fluorophore physical chemistry and synthesis

ion imaging

image reconstruction and processing

see texts for additional ideas

journal articles that address applications of confocal imaging to research topic of interest

Exams:  (100 pts) There will be one final exam during finals week.

Term paper: (150 pts)   The term paper will consist of a proposal for a confocal study.   Topics should be selected in consultation with the instructor.   Details of what should be included in the term paper and how to organize the term paper  will be posted here: INSTRUCTIONS .  The term paper will be due Nov. 15, 2002

Assignments (110 points) You will be required to complete assignments related to the lab practicum.   These assignments will be announced in class and  will be posted on this web site. 

Grade Scale: The grade scale may be curved at the end of the semester at the discretion of the instructor.

A     450-500 pts
B     400-449 pts
C     350-399 pts
D     300-349 pts
F     < 300 pts
S     (Satisfactory) requires a C-

S/U Option: Students must meet all requirements of the course.  A grade of C- is required  to receive an S in the course.

Attendance Students are responsible for all material covered in class as well as any previously unannounced assignments that are given out in class.  Therefore  students are expected to attend all classes.  Contact the instructor BEFOREHAND if you will be unable to attend class.
 

 

POLICIES AND PROCEDURES

Late assignments. 10% of the total points will be deducted for each week the assignment is late. Assignments will not be accepted if handed in more than 2 weeks after the due date

Syllabus Modification: The instructor reserves the right to modify this syllabus during the semester as considered necessary to enhance the quality of the instruction, to meet the needs of students in the class and to achieve course objectives. Any changes to the syllabus (or to the course schedule) will be announced in class and you are responsible for being aware of them.

Students with Disabilities:

• If you have, or believe you have, a disability and would benefit from any accommodation(s), you may wish to self-identify by contacting the Services for Students with Disabilities (SSD) Office located at Garcia Annex [phone 646-6840; TTY 646-1918] to register.
• If you have already registered, please make sure that your instructor receives a copy of the accommodation memorandum from SSD within the first two weeks of classes.
• It will be your responsibility to inform either your instructor or SSD representative (in a timely manner) if the services or accommodations provided are not meeting your needs.
• If you have a condition that may affect your ability to exit safely from the premises in an emergency or that may cause an emergency during class, you are encouraged to discuss any concerns with the instructor or with the SSD Coordinator.
• Feel free to call Ms. Elva Telles, EEO/ADA & Employee Relations Director, at 646-3333 with any questions about the Americans with Disabilities Act (ADA), and/or Section 504 of the Rehabilitation Act of 1973.  All medical information will be treated confidentially.

Code of conduct::   Please see the “Student code of conduct” in the current “Student Handbook”.  Pay particular attention to the sections on Academic Misconduct and Plagiarism. The penalty for plagiarism or other forms of academic misconduct (as defined in the Student Code of Conduct) is failure of the course: no exceptions.

OTHER:

GUIDELINES FOR CLASS DISCUSSION:  During the semester, different  opinions may be voiced in the class. You may strongly disagree with some of these, or you may find them amusing. Outbursts can be misinterpreted and are counterproductive to meaningful and thoughtful debate. Therefore, it is important that you exercise self-discipline and self-control, and treat all members of the class with the courtesy  you are entitled to receive in turn. The key words are respect and courtesy. Thank you!

XEROX and/or BACKUP all assignments before submitting them to the instructor.

SAVE xeroxes of all graded assignments and exams from this course at least until you have received your final grade.

WITHDRAWALS:  It is your responsibility to withdraw from the course.
.
DEPARTMENT OFFICE:     The Biology Department office is in FOSTER HALL 234, 646-3611.  The department secretaries are Ms. Gloria Valencia and Ms. Reta Akers.

DEPARTMENT CHAIR:     The Biology Department chair is Dr. Laura Huenneke.  Her office is in FOSTER HALL 234 (X63611).

Scholarships and Financial Aid

• "This 2001 Colleges, College Scholarships, and Financial Aid page is designed to offer college bound students, parents, and counselors easy access to information on: colleges and universities throughout the United States, free college scholarship and financial aid searches, SAT and ACT test preparation tips, and more." http://www.college-scholarships.com/
• "The mission of Scholarships.com is to assist students in obtaining scholarship awards for college using the Internet and to help them in exploring the many financial aid opportunities available to students as well as to parents. We provide information and resources necessary to discover the many local, state and national scholarship and grant opportunities available, in addition to the many Federal and private loan options for funding a college education" http://www.scholarships.com/
• "FastWeb is the nation's recognized leader in helping students make the decisions that shape their lives: choosing a college, paying for college and finding jobs during and after college.  And it's all free" http://www.fastweb.com/fastweb/content/aboutus/index.ptml?


Internships and Jobs
 

• Research and training at NIH (undergrads, grads, postdocs, faculty)
• Best Bets for Internships Abroad: http://www.cie.uci.edu/iop/internsh.html.   There are literally 100s of opportunities for internships abroad. This  page contains links to related web sites, and listings of some of the more well-known programs. The most helpful resources are noted with gold stars.
• JobWEB's Job Searching Engine: http://www.jobweb.org/search/profiles/    JobWEB provides a nationwide search engine that allows you to limit the search to internships exclusively.

Internship Programs.com  http://www.internshipprograms.com/home.asp  "The largest internship community on the Internet!"