PLANT MOLECULAR BIOLOGY- Spring 2009                                                               last updated: 01/25/2009
 
COURSE WEB SITE: http://maize.lehman.cuny.edu/
 

SCHEDULE (*note exceptions!) *MON, 3-4:45 pm Davis Hall 223

Jan 26 Lecture 1: Protein Structure & Function (1-3)

Quinlan et al (2007)
Feb 2 no class
Feb 9

 

 Lecture 2: DNA Structure/DNA Replication (4: 101-6; 131-7 and 9:372-5) 

PCR Protocols

454 Sequencing technology  434 Life Sciences Co.

Pyrophosphate sequencing

 

 
Feb 16 College closed
THURS, Feb 19 Interlab meeting: Davis 223, 3-4 pm, Dr. Louis Bradbury, "Defining a role for a new enzyme in the carotenoid biosynthetic pathway."
Feb 23  Lecture 3: Gene Structure, Transcription, and Translation (4:108-115;118-131)
Mar 2 Lecture 4: Cell Culture and Viruses (4.7; 6.7) (Read 6.1-6.6 as review in cell biology)
Mar 9 Lecture 5: Recombinant DNA Techniques (9) 

pBluescript info

 
Mar 16 Lecture 6: Transgenic organisms (9)  

Plant Metabolic Engineering (reading)
Mar 23 MIDTERM EXAM (lectures 1-6)
Mar 30 Lecture 7: Gene structure &
transposable elements (10) Last date for approval of end of semester presentation manuscripts.
Apr 6 Lecture 8: Transcription
initiation (11) 
Apr 13
no class- Spring Recess
Apr 20 Lecture 10: Gene control in development (11, p. 471-2;15.1; 15.3; 15.4; 22.2) ABC model; model update

 
Apr 27

 

 

 Lecture 9: Transcription termination, splicing and post-transcriptional control (12)
May 4

(E. Wurtzel) Research seminar on "Using genomic approaches to solving global vitamin A deficiency"

reading:

1. Matthews, P.D. and Wurtzel, E.T. (2007) Biotechnology of food colorant production in Food Colorants: Chemical and Functional Properties. (Carmen Socaciu, Editor) CRC Press. pdf

2. Li, F., Vallabhaneni, R., and Wurtzel, E.T. (2008) PSY3, a new member of the phytoene synthase gene family conserved in the Poaceae and a key regulator of abiotic-stress-induced root carotenogenesis. Plant Physiology 146 (3): 1333-1345 supplementary material online.
 
3. Li, F., Vallabhaneni, R., Yu, J., Rocheford, T., and Wurtzel, E.T. (2008) The maize phytoene synthase gene family: overlapping roles for carotenogenesis in endosperm, photomorphogenesis, and thermal stress-tolerance. Plant Physiology 147:1334-1346  supplementary material online.

Deadline-email presentation files and pdfs
May 11 presentations
tba FINAL exam based on primary literature readings

 

COURSE WEB SITE: http://maize.lehman.cuny.edu/ Databases/ Info Genomics Tools
CUNY Plant Sciences PhD Program  NCBI METHODS/RESOURCES
Wurtzel home page MEDLINE Lehman Library

 

 

MOLECULAR BIOLOGY- (Professor Wurtzel)
Lehman College Academic Calendar      
Office hours: Contact Dr. Wurtzel by electronic mail (e-mail) wurtzel@lehman.cuny.edu
    Send an e-mail message to ask brief questions or to request an appointment for additional help. Also, see Dr. Wurtzel after class to make appointments.
TEXTS:
1. Molecular Cell Biology, Sixth Edition (Lodish, Berk, Kaiser, Krieger, Scott, Bretscher, Ploegh,Matsudaira,), W.H. Freeman, NY 2008. 
2. Companion web site for many text resources: http://bcs.whfreeman.com/lodish6e/
OTHER RESOURCES:
1. Access the Lehman Molecular Biology server for up to date info on this course: http://a32.lehman.cuny.edu/ The syllabus is hyperlinked to useful ancillary reading materials and information resources. Information will be added and updated throughout the semester.
2. Current Protocols in Molecular Biology CDROM- available in Biology Computer Lab in Davis Hall 223, second floor (see posted hours for availability).  
3. Recommended additional reading on plant molecular biology: Biochemistry and Molecular Biology of Plants by Buchanan, Gruissem, Jones 2000.
4. Background texts. Go to the NCBI Bookshelf.
 
COURSE REQUIREMENTS: 
 
EXAMS: One midterm and a cumulative final.
 
PRESENTATIONS: Students will prepare and present a PowerPoint presentation of a recent (less than one year) primary literature journal article. See syllabus for when to email your presentation and pdfs. Presentations will be in alphabetical order during the designated sessions. See PRESENTATION INSTRUCTIONS below.
GRADING POLICY: Grades will be based on (approximate %): Midterm and Final Exam (60%);  PowerPoint slide presentation of recent journal article (10%) and its in-class slide presentation (30%) +/- other factors (class participation, effort, preparation, and attendance). 

 

PRESENTATION INSTRUCTIONS: Students must prepare a Microsoft PowerPoint presentation based on two recent articles in plant molecular biology chosen from primary journals (with impact factor of at least 3.0) and present it to the class within 30 minutes and include no more than 30 slides including the title slide. Review articles are not permitted but may be used to provide background information only.

Step 1: Find an article to present. Use articles from "primary" journals such as: Science; Nature; Cell; The Plant Cell; Plant Physiology; Proceedings of the National Academy of Sciences, USA;  Here is also a link to a long list of journals; other freely accessible journals Also check this useful journal site from CSHL : LINK  Lehman Library access to journals on the Internet ; MEDLINE ; National Center for Biotechnology Information (NCBI): Gene Map >98

Step 2: Get approval: Submit PDF files of the articles to Dr. Wurtzel for approval (at least four weeks prior to presentation: see deadline date in syllabus). This can be sent by e-mail.

Step 3: Prepare a presentation written in your own words! Prepare a maximum of 30, and no less than 25 slides. Name the file with your last name and course number and semester. Make images and type as large as possible to fill the screen. Keep words to a minimum. The presentation will consist of the following slides.

   A. "TITLE" which should include the following- title of paper; journal, volume, page numbers, year; authors and institution; your name and email link. This slide should also hyperlink to a PDF file of the paper; the filename should be the first author followed by publication year (ie. wurtzel_2003.pdf).
   B. General background- why the topic is of interest and other information to understand the research.
   C . Introduction of the research (Hypothesis and Specific Aims)
   D. Data for at least 4 key experiments. The experiments you will describe should be chosen with care. Make sure that they are the key experiments in the paper.
   E. Summary of results of the other experiments
   F. Conclusions 
   G. Future Directions

Step 4: One week before presentation: Bring the PowerPoint presentation file (named with the format: "yourlastname_Spring2009.ppt") and journal article pdf file (named with the format: "lastnameforfirstauthor_2009.pdf") to class on a CD or flash drive. You must check your presentation on this day; no changes to the slide presentation can be made after this session.

Step 5: Presentation: You will have 30 minutes to present your presentation to the class followed by a three minute student discussion period. The time limit is strict; practice beforehand using the timer in PowerPoint (Go to "SlideShow....Rehearse Timing")! Begin your presentation by giving the article title and journal. Go through each slide, pointing to the slide, but making contact with the audience (do not prepare slides for just reading)  Describe the key experiments in detail, summarize the other experiments, and go over the conclusions made in the paper. (Do not present a separate methods section of all methods used in the paper; instead, precede each experiment with methods as appropriate). You should also mention future directions of the work. The other students are expected to participate and ask questions.