MOLECULAR BIOLOGY                                                            last updated: 05/07/2012
BIO 420 prerequisites: CHE 234-235, BIO 238 and either BIO 400 or CHE 444 (Organic Chemistry, Genetics, Biochemistry).

LECTURES: MON, 10-11:40 AM pm Davis 223* *unless different room/day/time noted

Instructor: Dr. E. Wurtzel

See Blackboard for weekly course study questions

LABS: TUES, 10-1:40 PM, Davis 124* *unless different room/day/time noted
LAB MANUAL to be available on BlackBoard

Instructor: Rena Quinlan

Jan 30 Lecture 1: Protein Structure & Function (1-3)  

Begin weekly course study questions.

31  Introduction and lab tour

Davis Hall 223

Feb 6 Lab #5A: Bioinformatics and Internet Tools  (Medline Searching, Molecular Biology Tools)

Class will take place in Davis Hall 223

Info at CSH  


Lab #5B: Bioinformatics and Internet Tools (continued)

Davis Hall 223





Lab #5C: Bioinformatics and Internet Tools (continued) Independent projects

Davis Hall 223





Lab #1: Basic Techniques- Measurements

lab handout in class     appendix for lab

27  Lab #2:Plasmid DNA preparation 28


Lab #3: Restriction digestion and gel electrophoresis Semilog paper: 10 division 
Mar 5



Lecture 2: DNA Structure/DNA Replication (4.1; 4.5; 5: 187-188) 

DNA sequencing VIDEO

Animation on DNA Sequencing

Animation on PCR

PCR Protocols

454 Sequencing technology

Next generation sequencing_review

Pyrophosphate sequencing


6 Lab #4: Cloning and Transformation

Semilog paper: 12 division

12 Lecture 3: Gene Structure, Transcription, and Translation (4.2-4.4; 7.1) 13 Lab #6: Polymerase Chain Reaction 

Recommended Reading: Chapter 1 ("Optimization of PCRs") in PCR Protocols. A Guide to Methods and Applications (Innis et al., editors). Academic Press 1990.     (PCR animation) 

19 Lecture 4: Cell Culture and Viruses (4.7; 9.5) (Read 19.1-19.6 as review in cell biology) 20 Lecture 5: Recombinant DNA Techniques (5)  Davis 223

pBluescript info

26 Lecture 6: Transgenic organisms (5) 27

Lecture 7: Gene structure &
transposable elements (6) 

Davis 223

April 2 COURSE REVIEW for midterm- bring questions! 3 MIDTERM EXAM (lectures 1-6)

The exam will be based on course study questions!

Davis 223






16 Lecture 8: Transcription
initiation (7) 

DEADLINE! to submit articles for presentations

17 Lab #9A:SDS-PAGE   


23 Lecture 9: Transcription termination, splicing and post-transcriptional control (8) 24 Lab #9B: Western Blotting and immunodetection


30 Lecture 10: Gene control in development (21.2-21.4; 22) ABC model; model update May 1 Set up for (lecture) presentations- bring journal article pdf and PowerPoint  file plus hard copy of article to class. 

Research presentation "Discoveries for obtaining sustainable agricultural solutions to global vitamin A deficiency"

reading:  link Read Cuttriss et al. (2011).

8 PowerPoint Presentations of journal article- Davis 223

Lab posters for presentation:

Bring hard copy for presentation and PowerPoint  file for submission to instructor.

15 Meet with lab instructor for final evaluations- Davis 223
May 21

FINAL exam  10 AM- noon

Research Tools: Plant Genomics
Bioinformatics- NCBI (DNA, etc)
Bioinformatics- Proteomics, etc.
Comparative genomics: Phytozome
Cyanobacterial genomics: Cyanobase
Eukaryotic Ortholog Database
Genomics links
Genomics tools and resources
MAGI 454 database etc
Maize GDB: Genetics/Genomics
Maize genome (industry)
Plant GDB resources for comparative genomics
Plant Gene Nomenclature Rules
Plastid Proteome Database
Arabidopsis subcellular proteome database
Promoter Analysis:
          Cis-acting elements database
          TransFac Database
Arabidopsis coexpression networks: ATTEDII
Arabidopsis Coexpression Data mining tools
Rice Genome (Indica) (China)
Rice Genome (Japonica) (Syngenta)
Rice Genomics (US)
Rice: International Rice Functional Genomics Consortium
Rice Coexpression analysis-Rice ArrayNet
TIGR- misc genomic sequencing
Research Tools: Information
Dictionary1  Dictionary 2
Journals: Botanical  Free access
              PubMed: Literature Database
              Library resources at CUNY
NCBI BOOKSHELF: background textbooks on molecular biology, genetics, etc.  
Patents  US Patent Application Database  
             US Patent & Trademark Database


Cold Spring Harbor DNA Learning Center  METHODS/RESOURCES Journal of Visualized Experiments Register to get alerts on RESEARCH Opportunities: ASPB Diversity Bank 
COURSE WEB SITE: CUNY Plant Sciences PhD Program  Wurtzel home page Research opportunities at Lehman (link to faculty)
MOLECULAR BIOLOGY- (Professor Wurtzel)
Office hours: Contact Dr. Wurtzel by electronic mail (e-mail):
    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.
Lab instructor: Rena Quinlan
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:
1. Access the Lehman Molecular Biology server for up to date info on this course: 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 -internet access- available in the library.  
3. Background texts. Go to the NCBI Bookshelf.
EXAMS: One midterm and a cumulative final.
PRESENTATIONS: Students will prepare and present a PowerPoint presentation of a recent (less than one year old) primary literature journal article. One week before you present, submit a copy of your presentation on CD or on flash drive together with the journal article (pdf) used for the poster. Presentations will be in alphabetical order during the designated sessions. See PRESENTATION INSTRUCTIONS below.
LAB poster PRESENTATION: Students  should choose one lab or related labs and present the data in poster created using PowerPoint. You must submit the PowerPoint file containing all the pages of the poster and print out a copy for a 5'oral presntation in class. See instructions below.
LAB notebook: Students will be required to keep a lab notebook with lab methods and results. These will be checked weekly.
GRADING POLICY: Grades will be based on (approximate %): Midterm and Final Exam (50%); Lab grade (30%); PowerPoint slide presentation of recent journal article (10%) and its in-class slide presentation (10%) +/- other factors (class participation, effort, preparation for lab experiments, and attendance). ****Late material will not be accepted! No makeups for exams or labs! 
Grading will be based on lecture (70%) and lab (30%): 
70% Lecture- comprised of:
                 Midterm and Final Exam (50%)
                 PowerPoint slide presentation of recent journal article (10%) and its in-class slide presentation (10%)
30% Lab-comprised of:
                Lab notebook  (5%)
                      Lab poster and presentation (15%)
                      Preparation for lab experiments, collaboration, and attendance (10%).

PRESENTATION INSTRUCTIONS: Students must prepare a Microsoft PowerPoint presentation based on one recent article chosen from a primary journal and present it to the class within 15 minutes. Review articles are not permitted.

Step 1: Find an article to present. The journal must be "peer-reviewed" and have an impact factor of at least 3. The article must have been published within the past year. and should not be a "review". Use articles from "primary" journals such as: Science; Nature; Cell; Plant Physiology; The Plant Cell; Proceedings of the National Academy of Sciences, USAHere 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.

Step 2: Get approval: Submit a PDF file of the complete article to Dr. Wurtzel for approval (see syllabus for deadline). This can be sent by e-mail. Please send only one article at a time for approval. See this link for an example of what a PDF file should look like. Once the paper is approved, provide a hard copy version to Dr. Wurtzel.

Step 3: Prepare a presentation written in your own words! BIO 420: prepare a maximum of 12, and no less than 8 slides. BIO 642: prepare a maximum of 24, and no less than 16 slides. Name the file with your last name and course number and semester (ie. wurtzel_BIO420_Spring2011.ppt) 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. 
   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. BIO 420: Data for at least 2 key experiments. The experiments you will describe should be chosen with care. Make sure that they are the key experiments in the paper.
       BIO642: Describe all key experiments (>4). 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 (see date on syllabus): Bring the PowerPoint presentation file (named with the format: "yourlastname_Spring2011.ppt"), the article pdf and a hard copy of the journal article to class. All presentations will be collected by the course assistant onto one CD. 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 15 minutes (BIO 420) or 30 minutes (BIO642) to present your presentation to the class followed by a 5 minute (BIO 420) or 10 minutes (BIO642) 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 2 (BIO 420) or >4 (BIO642) 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.

Here is a link on how to make an effective presentation:

You tube video: Susan McConnell: Designing effective scientific presentations

LAB POSTER and presentation Instructions: Students  should choose one lab or related labs and present the data in a "poster" created using PowerPoint. You must submit the PowerPoint file containing all the pages of the poster.  Each of the pages should also be  printed out and taped to the lab wall for a 5 minute presentation on the designated day. To prepare the poster, use PowerPoint to create separate "slides" (using page format of 8.5 in x 11.5 in) for the following pages. Please refer to the video links below on tips to make an effective poster. Your poster should include the following pages.

1. Title (includes title and author).

2. Abstract

3. Introduction

4. Methods

5. Results (include data from the lab- such as restriction enzyme digest or western blot)

6. Discussion (of your results- what do the results mean? If the experiment did not work, what else would you try? What are other methods that could be used for this analysis?

7. Summary.

8. References.

9. Acknowledgments. (Where was this project conducted and in what course? Who were the instructor(s) that helped to train you?______________________________________________________________________________________________________________

Here are some links on effective ways to make a scientific poster-

You tube videos-

Tips for Creating a Scientific Poster

Making an academic research poster using Power Point

How to make a Great Scientific Poster to Present at Research Symposium of College of Optometrists

Written Directions- How to Make a Great Poster (ASPB)