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

  Office & Office Hours:

 Foster Hall 337D
 Wed 12:00-1:00 pm
 (&  by  appointment)

646-5217
eserrano@nmsu.edu

OPTICAL SOCIETY OF AMERICA

• COURSE DESCRIPTION
• PREREQUISITES
• TEXTBOOKS
• LECTURES & READING ASSIGNMENTS
• SCHEDULE OF TOPICS, EXAMS & ASSIGNMENTS
• CONFOCAL LAB TIMES

• 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
• Sept 2 Bio 591 Oral presentation topic due
  
• Oct 7  Bio 550 Confocal Proposal due
  
• Oct 28  Bio 591 Lab report due
• Dec 2 Bio 550 Lab report due
  
• Final Exam Thurs Dec 11 3:30 

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

Biology 591,  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 this course and Biology 550 (Confocal Practicum) 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).

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.  The confocal video and supplementary readings from Imaging Neurons are in  Biology Foster 234.

SCHEDULE OF PRESENTATIONS AND LECTURES

DATE	MAIN TOPICS	CLASS ASSIGNMENTS /  RESOURCES
>>BIO 591: AUG 19 - OCT 21
Aug 19	Class Overview Introduction to Confocal Microscopy	BioRad 1024 Video Lab tour of Fluorescence Imaging Facility
Aug 26	BioRad 1024 System and Access Safety Concerns & FIF User Compliance Fundamentals of Fluorescence Sample Preparation	Readings from  CBACM Ch 1  Introduction to Confocal Microscopy Ch 14 Setting up a Core Facility 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 2	Selection of Fluorescent Probes 1	First training session: Operation of Olympus microscope: CLASS  HANDOUT NOTE: MONDAY GROUP MEETS SAME TIME ON WEDNESDAY Select and submit topic for presentation (use  list for ideas) Readings: CBACM Ch 5 Multicolor LSCM Ch 7 Immunohistochemistry Handouts from Imaging Neurons in  Foster 234 Appendix 3 Care and Cleaning of Optical Equipment Appendix 4 Safety and Cautions Fluorescence basics review
Sept 9	Selection of Fluorescent Probes 2 Lasers Online BioRad Web exercise Fluorescent probe database	Second training session: Introduction to Lasersharp (bead scan) CLASS  HANDOUT Readings CBACM Ch 4 Accurate Imaging Ch 6 Lens Selection Handouts from  Imaging Neurons Chapter 12 Practical Limits to Resolution Appendix 3 Lenses, Filters, Spectra
Sept 16	Optics, Lenses, and Resolution Lab discussion	Third training session: Introduction to Metamorph COMPUTER TUTORIAL This exercise will use the TE2000 in the Serrano lab. Schedule time with Amanda. Exercise link : color wheel, resolution, monitors and printers
Sept 23	Digital Image Processing Software: Metamorph,   Image J, etc Lab discussion	Fourth training session: Bead and tissue scan  CLASS HANDOUT You have 4 weeks to complete this exercise.  Refer to lab schedule  (part 2) for times. Access the following web sites and browse contents NIH Image Imaging Programs (Keck - Univ of Washington)
Sept 30	Discussion Student Presentations (Bleu,David)	Fourth training session: Bead and tissue scan HANDOUT You have 4 weeks to complete this exercise.  Refer to lab schedule  (part 2) for times.
Oct 7 CONFOCAL PROPOSAL DUE FOR BIO 550: PRACTICUM	Discussion Student Presentations (Carolina, Jason )	Fifth training session: Bead and tissue scan HANDOUT You have 4 weeks to complete this exercise.  Refer to lab schedule  (part 2) for times. CONFOCAL PROPOSAL DUE FOR BIO 550: PRACTICUM
Oct 14	Fall Break	NO CLASS
Oct 21 SCHEDULE CONFOCAL LAB HANDS ON EXAM WITH SERRANO	Discussion Student Presentations (Debra, Lori) SCHEDULE CONFOCAL LAB HANDS ON EXAM WITH SERRANO	Fifth training session :  Bead and tissue scan HANDOUT You have 4 weeks to complete this exercise.  Refer to lab schedule  (part 2) for times. Readings Handouts from  Imaging Neurons Appendix 1 Glossary
Oct 28 WRITTEN ASSIGNMENT DUE
Dec 11	Final Exam  3:30-5 pm
BIO 550:  OCT 28- DEC 2
Oct 7	CONFOCAL PROPOSAL DUE FOR BIO 550: PRACTICUM
Oct 28	Discussion
Nov 4	Discussion
Nov 18	Discussion
Dec 2	Presentation (4)
FINALS WEEK TBA	Presentation (3)

CONFOCAL LAB TIMES Part 1	TEAM
Monday     9:15 - 10:45 am Except Sept 1 rescheduled to Sept 3	Yellow     Jason, Lori Jo, David
Monday     3:30 - 5 pm Except Sept 1 rescheduled to Sept 3	Green::   Carolina, Debra
Tuesday    9:00- 10:30 am	Blue:       Bleu, Jose, Laura
CONFOCAL LAB TIMES Part 2	TEAM
Monday     9:00 - 10:30 am	RED        Laura, Jose
Monday     2:30 - 4:00  pm	YELLOW  Jason, Debra
Monday     4:00 - 5:30 pm	BLUE       LoriJo,  David
Tuesday     9:00 - 10:30 am	GREEN    Bleu, Carolina

 

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.

BIO 591: 500 PTS

In class participation : (100 pts)  Based on your contribution to class discussion, attendance, and evidence of preparedness for class. 

Presentations: (100 pts)  Based on your 30  minute oral presentation Suggested topics:

PMT technology

tunable lasers

scanning disk confocal imaging

FRET

fluorophore colocalization 

vital imaging

fluorophore physical chemistry and synthesis

ion imaging

fluorophores for membrane and compartments

image reconstruction and processing

multi-photon imaging

see text for more ideas....





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

Assignments (200 points) You will be required to complete assignments related to the lab exercises.   These assignments will be announced in class and  will be posted on this web site.  Due Oct 28, 2003

BIO 550: 500 pts


CONFOCAL PROPOSAL: (150 pts)   The term paper will consist of a proposal for a confocal study suitable for a practicum.   Topics should be selected in consultation with the instructor.   Details of what should be included in the proposal and how to organize the proposal  will be posted here: INSTRUCTIONS .  Due Oct 7, 2003

In class participation : (100 pts)  Based on your contribution to class discussion, attendance, and evidence of preparedness for class.


Presentation: (100 pts)  Based on your 30 minute oral powerpoint presentation of your project


Lab Report  (150 pts)  You will submit a brief report summarizing your practicum findings. INSTRUCTIONS Due Dec 2, 2003

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

A     90-100%
B     80-89%
C     70-79%
D     60-69%
F     < 60%
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:  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. Dan Howard.  Hisoffice 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!"