Grading:

Exam 1- test concepts, experimental approaches/methods, and their application. 100

Exam 2- 100

Journal presentation (50), participation in discussion (25), homework (25). 100

Final paper-Review (total 100)
a. [10] Identify & ask an important general question in biology.
b. [30] Review the literature
c. [10] Identity specific questions still unresolved.
d. [10] Propose working hypotheses. Pose specific questions;
e. [30] What approaches would you use to answer the questions. Describe the methods [including cell biological approaches and interpret the expected results
f. [10] Significance of the study. What are the broader implications? How will it advance the thinking in the field?


 Format of Paper/Proposal:

1. Topic : You are asked to design a few original experiments that should answer a currently unsolved question related to topics covered in this course. We are interested in the mechanistic aspects of a process. How does a process work? How is that process regulated? Please do not be comprehensive, choose a specific area of interest.
The proposal should not be the same as any paper or project that you have worked on before or plan to start. You can discuss with faculty, or students, but the basic idea must be your own.

2. Proposal should include the following:

i. Title
ii. Abstract (~250 words)
iii. Review of the literature in the selected topic (bulk of report is here)
Note- the emphasis is on key papers that defined the field.
Use models, figures or tables to illustrate/summarize the messages.
iv. Identify a few key questions, then focus on one specific area.
a. statement of the problem or question
b. Material: model system chosen and reasons for the choice (e.g. yeast, fly, animal cell)
c. Experiment: experimental design should include method e.g. western blot, microarray, specify antibody or probe. Buffer or conc details are not needed
d. expected results and interpretation of the results
e. Significance: a brief discussion of the significance of solving the problem.

3. Length ~5-8 pages single spaced (excluding figures and references. Total: Not to exceed 10 pages). Double space between paragraphs.
Use headings/subheadings to separate sections.

4. Format: References: Include key references (limit <20):
using the following format: with full author, title, and journal vol and page numbers.
e.g. Journal.
Bramhill D. (1997) Bacterial Cell Division. Annu Rev. Cell Dev Biol. 13: 395-424
Salyers AA and Whitt DD (1994) Antibiotics: mechanism of action. In “Bacterial Pathogenesis” ch. 8, pp 97-110. ASM Press.

Legend: Figure, table, or model must be accompanied by a legend.

5. Grading of proposal will be based on significance of problem, feasibility of experimental design, originality, creativity, and whether approaches proposed answer the questions directly.
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Suggested Format:

II.  Project summary (<250 words) –a description of the research, the objective, technical approach, and expected results.
III Project Description:
1.  Background.  Introduce topic and select area of emphasis.  What are some important unresolved questions?  E.g.
     A  .  “WHAT IS THE GENERAL QUESTION?”
      How does the hormone ethylene induced expression of an enzyme?
 What do we know about this process?  Review key findings in the literature.
 What do we not understand yet?  [Identify major questions only]
 What is/are the working model/s?

.  B.  WHAT IS THE WORKING HYPOTHESIS/MODEL YOU WANT TO TEST?
[should be testable, show Model fig]
 e.g. Hormone binding to a receptor initiates a cascade of events leading to phosphorylation of an effector.
 Focus on a few specific questions within the model.

2.  Specific aims:  Select and list a few specific aims
WHAT ARE THE SPECIFIC QUESTIONS?  Articulate the Specific Aims to answer these questions
a. What proteins interact with the receptor?
b.  Is the protein(s) phosphorylated by ethylene interaction?
c. What is the function of the downstream component?

3. Approach and Methods for each aim:  How would you approach the problem, and how would you do it (methods)?  Controls.

4. Expected Results and their significance
What significant advances would you have made?

IV.  References: Include key references (limit 20-30):
using the following format: with full author, title, and journal vol and page numbers.
e.g. Journal.
Bramhill D. (1997)  Cell Division.  Annu Rev. Cell Dev Biol. 13: 395-424
Salyers AA and Whitt DD (1994)  Antibiotics:  mechanism of action.  In “Bacterial Pathogenesis” ch. 8, pp 97-110.  ASM Press.
V.  Figures, tables, models are encouraged.  Put at end of text or within text.  Include a clear legend.


U.S. Department of Health and Human Services
Public Health Service

Individual National Research Service Award
Application PHS 416-1

Jan 2002.  Taken from:   http://grants.nih.gov/grants/funding/416/section_1.htm#background

Item 30b. Research Training Proposal. This section should be well formulated and presented in sufficient detail that it can be evaluated for both its research training potential and scientific merit. It is important that it be developed in collaboration with the sponsor, but it is to be written by the applicant.

Include sufficient information to permit an effective review without reviewers having to refer to the literature or any previous application. Brevity and clarity in the presentation are considered indicative of an applicant’s approach and ability to conduct a superior project. Sections (1) through (4) of this item are not to exceed 10 pages including all tables and figures. Follow the format below:

   1.Specific Aims. State the specific purposes of the research proposal and the hypotheses to be tested.

   2.Background and Significance. Sketch briefly the background to the proposal. State concisely the importance of the research described in this application by relating the specific aims to broad, long-term objectives. For competing  continuation applications, be sure to summarize your progress under your current award.

   3.Research Design and Methods. Provide an outline of:

          Research design and the procedures to be used to accomplish the specific aims;

          Tentative sequence for the investigation;

          Statistical procedures by which the data will be analyzed;

          Any procedures, situations, or materials that may be hazardous to personnel and the precautions to be exercised; and

          Any courses planned which support the research training experience.

     Potential experimental difficulties should be discussed together with alternative approaches that could achieve the desired aims.


Journal Presentation and Discussion
Sp 2000, Sze/Song
 Scientists communicate their new findings by their publications and by their oral presentations at meetings and seminars.  Significant papers address important fundamental questions in biology and introduce us to new concepts, new working models, and novel findings.  They stimulate discussions and often generate ideas for future experiments.  The purpose of journal discussions is not only to learn new information and ideas but also to learn how research is conducted and how one evaluates the quality of the work.  Active participation is strongly encouraged to stimulate independent thinking.  [You will be evaluated for presentations and for participation during the semester.]

Preparation
1.  Read the paper(s) provided and make notes regarding each section.
 I.  Introduction:
  What is the purpose of the study?
  What do we know about the problem?
  Is the question significant?
  What are the specific questions asked?
  What is the working hypothesis?
 II.  Approach and Methods:
  What approaches are used to answer the question(s)?
  [Discuss only approach, understand the principles of the methods used]
III. Results  (combine with Methods)
Briefly state the specific aim of each experiment.
  Describe briefly the method for each expt, followed by   what results were obtained,
  then interpret the data.
  Are the results convincing?  What are alternative approaches?
 IV.  Discussion
  What were the major findings and what are the conclusions?
Are the conclusions supported by the results?  Do the results support the working hypothesis or model?
What new questions arise from these studies?
Propose experiments to test your questions and ideas.
  Bring your questions and see if you can resolve it during the discussion.

2.  Be prepared.  Any one of you may be called on to present any one of the sections above during the discussion.  So bring your notes to class.  Try to get the main points first.  Understand details later.

Suggestions re. Presentation
1. Introduction: [as above]  use model figures to convey basic concepts and current general knowledge quickly
2. Each Experiment/ Fig:
Start with goal of expt,  [what is the question?]
Present essential points of Method /approach, so we know how expt was conducted
Present Result; and interpret the results.
Give take home message of the expt.
Pose next question, and move to next expt. and result.
3.  Summary: conclusions.  What are new questions?  How would you approach these?

Useful WEBsites:

Journals online in the UMd library
http://www.lib.umd.edu/UMCP/ETC/EJNLS/subject.php3?subject=Life_Sciences

NSF postdoctoral fellowships:
https://www.fastlane.nsf.gov/servlet/fastlane.pdoc.DisplayProgramType

NIH postdoc fellowships
http://grants.nih.gov/grants/funding/416/phs416.htm

High Impact Journals with Cell Biology
Primary Research Journals:
Cell
Current Biology
Development
EMBO Journal
Journal Cell Biology
Journal of Biological Chemistry
Journal of Cell Science
Molecular Biology of the Cell
Nature
Nature Cell Biology
Proceedings National Academy of Sciences
Science
The Plant Cell

Reviews
Annual Review of Cellular and Developmental Biology
Trends in Cell Biology
Trends in Neurobiology
Trends in Microbiology