MICROBE SAFARI

Courtesy of Linda Sherwood, Montana State University

We're going on a microbe safari
To "see" what we can't see.
Under toilets, in corners, and in my tea,
Who knows where they might be?
They might even be on me!

Oh, in the environment there are microbes galore,
Bacilli and cocci and so much more.
Look for them clinging to your teeth or your toes,
There's probably a million just in your nose.
Those microbes really know where to goes.

PURPOSE

 

INTRODUCTION

Your mother always told you to wash your hands before dinner, and she was right to do so. Everything you touch in the environment, including your body and other organisms, could be home to microorganisms. But how many microbes are there? What are they doing? What do they look like? Who are they related to? How can their activities be controlled? These are some of the questions microbiologists ask in order to understand ecosystems, disease transmission, and the interactions of microbes with other organisms.

In this exercise, you will work in a group of four to five students to develop a research project that answers a microbiological question of interest to you. You will be given great flexibility in choosing a research topic. The only limits will be time, supplies available to you, your skills in microbiology, and two stipulations that I make. The first stipulation is that your study must include measurements of microbial abundance. The second is that you characterize at least one microbe isolated in your study using the techniques you have learned in this course. Your attempts to measure microbial abundance and to characterize one or more microbes must be relevant and meaningful to the goals of your research project. Before beginning the research, your team will submit a research proposal to a review panel. After responding to the reviewers' comments, experimentation will begin. Upon completion of the project, your research team will prepare a scientific paper detailing the project. This paper will be submitted for peer review before publication in the Class Journal of Experimental Microbiology. In writing the journal article, your team will demonstrate that it:

THE EXERCISE

PREPARATION

1. Begin thinking and talking to your teammates about a possible research project.

2. Each group will purchase a notebook to use as a lab notebook. The notebook will be used by the group to record all aspects of the research project.

3. Read the handout "Writing from the Moment of Observation". This handout describes the best procedures for recording the information about a research project.

WRITE THE RESEARCH PROPOSAL

1. Along with other members of your team, determine a microbiological question of interest to all team members.

2. Devise a research plan to answer that question. Below is a list of materials you will have available to complete your research project.

 

 

AVAILABLE MATERIALS

sterile applicator sticks
sterile cotton swabs sterile H20 transparent tape microscope slides coverslips inoculating loops
microscopes

Gram stain reagents
lactophenol cotton blue
cultures of known organisms to use as experimental controls for various procedures

blue fat plates
nutrient agar plates starch plates
casein plates thioglycollate broth
Christensen's urea agar

As you develop your plan, consider the following:

3. Write a research proposal for submission to the review panel. The research proposal is due to your lab instructor by the date indicated in the syllabus. Use the following format when writing your proposal. If you do not follow this format, the research proposal will be returned without being reviewed, delaying the completion of your project.

4. Revise and resubmit your research proposal, if needed. If resubmitted, your team must respond to the reviewers' comments in the revised proposal. The revised proposal is due to your lab instructor by the date indicated in the syllabus.

IMPLEMENT THE RESEARCH PROPOSAL

Each team will work together to complete the experimental procedures and gather relevant data. The team's activities will be recorded in the team's lab notebook.

PREPARE A JOURNAL ARTICLE TO BE SUBMITTED TO THE CLASS JOURNAL OF EXPERIMENTAL MICROBIOLOGY

1. Each group will submit one article. Each team will begin writing the article in lab on the date indicated in the syllabus.

2. The article will be submitted for peer review in lab on the date indicated in the syllabus. NOTE: Attach the team's lab notebook to the submitted article.

3. The final article, ready for publication, will be submitted in lab on the date indicated in the syllabus.

4. Use the following guidelines for writing the article:

TITLE: The title is brief, but should include important descriptors of the project so that the experimental approach used can be anticipated. For instance: "The Isolation, Enumeration, and Morphological and Metabolic Characterization of Bacteria from Martian Soil."

ABSTRACT: This is a brief summary that outlines the major results reported in the article and their significance.

INTRODUCTION: In this section, introduce the reader to the research problem. This section includes a clear statement of any hypotheses being tested. Before stating the hypotheses, describe the observations and experiences that led to their formulation. For instance, if a scientist hypothesizes that Martian microbes are different than Earth microbes, an explanation or description of earlier observations or other factors that lead to its formulation should accompany the hypothesis.

EXPERIMENTAL METHODS: In this section, describe how the experiments were done and what tools, media, and reagents were used. This section should be organized to reflect the order in which results will be presented in the Results section. Standard microbiological procedures need not be described; instead, cite the lab manual or other sources. For instance, if a Gram stain was done, refer the reader to the lab manual in the text and include a complete citation for the lab manual in the reference section of the article. A common method is to number each reference, and then to insert the number for a reference in appropriate locations throughout the article.

RESULTS: Many kinds of data are presented in this section. Always try to organize data into figures or tables whenever appropriate, while still remembering that the story of the results is being told in this section. Therefore, in this section, the results are described in general terms in the text (i.e. point out major results) and the details are illustrated in the accompanying tables and figures. The construction of informative tables and figures takes practice. Consult your instructor if you have any questions.

DISCUSSION: This is often the hardest section to write so be prepared to think about, write, and rewrite this section many times before initial submission. In the discussion section, the data are interpreted and evaluated. Below is a list of the kinds of information included in this section:

REFERENCES: List any books, articles or other materials used as a resource for your paper. Many methods for citing these resources can be used. A commonly used format is illustrated in the box to the right.

Sherwood, L. S and Sherwood, J. E. (1991). The isolation, enumeration, and morphological and metabolic characterization of bacteria isolated from Martian soil. MB101 Journal of Experimental Microbiology 1: 13 - 16

Sambrook, J., et al. (1989). Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

EVALUATION This project is worth a total of 50 points. The score for the project will be determined using the attached score sheet. Submit the score sheet with the ready-for-publication draft of the article. Your individual grade will be determined after evaluating each team member's contribution, as described in the Assessment handout.


GRADING This assignment will be graded using the attached score sheet.

MICROBE SAFARI RESEARCH PROJECT - SCORE SHEET

___ Submission of Required Drafts of Research Proposal and Journal Article (3 points) a

All Required Drafts Are Submitted

Deadlines Are Met

  • Yes (1) ___
  • No (0)___

  • Always (3)b___
  • Usually (2, e.g., one draft is late)___
  • Rarely (1, e.g., 2-3 drafts are late)___
  • Never (0)

a Number of possible points.
b The numbers in parentheses indicate the mastery level.

To Score:


___Maintenance Of Lab Notebook (9 points)

Procedures Used in the Project Are Recorded

Results Obtained by the Project Are Recorded

Entries Contain Sufficient Detail for Reader to Evaluate How Competently the Experiments Were Executed and the Results Interpreted

  • All (3)___
  • Most (2)___
  • Many are missing (1)___
  • None are recorded (0)___
  • All (3)___
  • Most (2)___
  • Many are missing (1)___
  • None are recorded (0)___
  • Always (3)___
  • Usually (2)___
  • Rarely (1)___
  • Never (0)___

To Score:


___Title of Article (2 points)

Title Serves to Attract Attention of Interested Audience

Title Allows Reader to Anticipate Experimental Design

  • Yes (1) ___
  • No (0)____
  • Yes (3)___
  • No (0) ___

To Score:


___Abstract (4 points)

Outlines Major Results

Indicates Significance of Results

  • All (2) ___
  • Some (1)___
  • None (0)___

  • Clearly stated (2)___
  • Poorly stated (1)___
  • Not done (0) ___

To Score:


___Introduction (6 points)

Indicates Purpose of Research

Indicates Significance of Research

  • Clearly stated (2)___
  • Poorly stated (1)___
  • Not done (0) ___
  • Clearly stated (2)___
  • Poorly stated (1)___
  • Not done (0) ___

To Score:


___Description Of Procedures (13 points)

Descriptions Are Detailed Enough to Allow Precise Replication of Experiments

When Appropriate, Description Also Includes Information on Variables Expected to Impact Outcome or Interpretation of Experiments; These Variables Could Not be Manipulated

Each Procedure or Sets of Related Procedures Are Reported in Concise Paragraphs

Descriptive Paragraphs Are Organized to Reflect Relatedness of Procedures and/or Chronology

All Procedures Are Described in Experimental Methods

  • Yes (4) ___
  • Minor
  • omissions (3)___
  • Major
  • omissions (2)___
  • Experiment cannot be replicated (1)___

  • Yes or not applicable (2)___
  • Some (1)___
  • No (0)__

     

  • Yes (3)___
  • Some unnecessary information (2)___
  • Wordy descriptions (2)___
  • Written as a series of steps (1)___

  • Yes (3)___
  • Somewhat (2)___
  • Poorly organized (1)___

  • Yes (1)___
  • No (0)___

To Score:

___Experimental Design (13 points)

Includes Measures of Microbial Abundance

Includes Procedures That Characterize One or More Isolates

Operational Definitions Are Clearly Stated

Uses Experimental Procedures That Are Appropriate to the Purpose of the Research

Clearly Demonstrates the Use of Appropriate Controls

Completes Procedures in a Competent Manner

  • Yes (1) ___
  • No (0) ___

  • Many (2)___
  • Some (1)___
  • None (0)__

     

  • Yes (2) ___
  • Implied (1)
  • Not stated (0)

     

  • All are (3)___
  • Most are (2)___
  • Many are not (1)___
  • None are (0)___

  • Consistently (3)___
  • Infrequently (2)___
  • Never (1)___

  • Consistently (3)___
  • Infrequently (2)___
  • Never (1)___

To Score:

___Communication of Results (12 points)

Results Are Presented in Paragraphs

Order of Presentation Parallels Order of Experiments

Results Are Presented in Enough Detail for Reader to Interpret Their Meaning

When Appropriate, Well-Constructed, Properly Titled and Labeled Tables and Figures Are Used to Visually Display Results

All Results Are Reported in Results

  • Yes (2) ___
  • No (1) ___

  • Consistently (3)___
  • Infrequently (2)___
  • Never (1)___

     

  • Consistently (3)___
  • Infrequently (2)___
  • Never (1)___

     

  • Yes (or not needed) (3)___
  • Yes, but not labeled (2)___
  • Yes, but not well constructed (1)___
  • No visuals were used even though they should have been (0)___

  • Yes (1) ___
  • No (0) ___

To Score:

___Interpretation Of Data (11 points)

The Inferences Drawn Are Consistent with the Data and with Information Regarding Any Uncontrolled Variables

Expected Results Are Explained

Unexpected Results Are Noted and Possible Explanations and/or Suggestions for Further Research Are Made

Each Hypothesis Made Is Either Accepted or Rejected

A Clear Distinction Is Made Between Fact and Implication

  • Consistently (3)___
  • Infrequently (2)___
  • Never (1)___
  • Consistently (2)___
  • Infrequently (1)___
  • Never (0)___
  • Consistently (2)___
  • Infrequently (1)___
  • Never (0)___

     

  • Consistently (2)___
  • Infrequently (1)___
  • Never (0)___

  • Consistently (2)___
  • Infrequently (1)___
  • Never (0)___

To Score:

___Discussion (7 points)

Purpose and Major Findings Are Summarized

Implications of Results Are Related to Interested Audiences

Order of Discussion of the Results Parallels the Order of Experiments Described in Experiments & Methods

All Interpretations of the Data Are Reported in the Discussion

  • Most are (2)___
  • Many are not (1)___
  • No summary (0)___

  • Yes (2)___
  • No (1)___
  • Consistently (2)___
  • Sometimes (1)___
  • Never (0)___
  • Yes (1)___
  • No (0)___

To Score:

___Citation of Resources for Paper (6 points)

Bibliography Is Attached

Reader Can Locate Cited Documents, Articles, Books, and Web Sites in Library and on WWW

Sources of Factual Information Are Documented in the Text

  • Yes___
  • No___

     

  • Always (3)___
  • Usually (2) ___
  • Rarely (1) ___
  • Not at all (0) ___

  • Always (3)___
  • Usually (2) ___
  • Rarely (1) ___
  • Not at all (0) ___

To Score:


___Quality of Writing (14 points)

Overall Organization

Paragraph Structure

Sentence Structure

Proofreading & Editing

Scientific Names Are Written Properly

  • Overall presentation is logical and the main theses of the paper are easily understood (3) ___
  • Some organization problems, but the main theses of the paper are easily understood (2)___
  • Organization is so poor that the main theses of the paper are difficult to understand (1)___

  • Consistently good paragraph structure is observed (2)___
  • Poorly constructed paragraphs are frequently observed (1)___

     

  • Grammatical errors are rare (3)___
  • Grammatical errors are relatively common, but do not significantly impact readers ability to understand meaning of sentence (2)___
  • Grammatical errors are so serious and/or frequent that understanding sentences is difficult (1)___

  • No typos and spelling errors (3)___
  • Some typos and spelling errors (2)___
  • Many typos and spelling errors (1)___

     

  • Always (3)___
  • Usually (2)___
  • Rarely (1)___
  • Never (0)___

     

To Score: Sum the mastery levels and record the total as the points earned


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