S14-Final Laboratory Report Instructions

S14-Final Laboratory Report Instructions

Note to the instructor: There are numerous formats for writing laboratory reports and the instructor should review the following guidelines and modify them to suit their needs. Even if the instructor chooses to give the students the guidelines belowas written, the instructor will need to provide students with guidelines for how to format the references.

Introduction

For the last five weeks, youhave collected a variety of data related to theASYMMETRIC LEAVES1 (AS1) and ASYMMETRIC LEAVES2 (AS2)genes in Arabidopsis. These data needs to be assembled into a report. The final version of the report should resemble a primary scientific literature article. As examples,review Semiarti et al. 2001(1) and Byrne et al. 2002 (2). Your report should clearly explain how the specific mutations you identified in the AS1 and AS2 genes cause changes in protein structure that lead to the as1 and as2 mutant phenotypes. Below are the sections required for the report and instructions for how they should be written.

Title

Titles are a short phrase that clearly tells the reader what to expect from the report. A title such as “AS1 and AS2 of Arabidopsis” is too vague. Thetitle needs to provide some indication about what youdiscovered about AS1 and AS2. The author’s name should also be clearly listed.

Abstract

Write this last! An abstract is a summary of the entire paper. The abstract should have the following brief statements: short summary of the function of AS1 and AS2, the scientific reason for why the experiments were done, an overview of the generalmethods used, and the main outcome. Although abstracts are short, they are probably the hardest of all sections to write.

Introduction

The introduction needs to include the following background information: Arabidopsis as a model genetic system, basic leaf development, the AS1 gene and the AS2 gene, central dogma, and levels of protein structure.When writing an introduction, the author starts by explaining the broadest topics first and ends with the most specific topics. The statements in the introduction must be supported by at least 5primary literature articles. By definition, primary literature contains data that the authors collected themselves.The primary literature articles must be properly cited, meaning that the main point of the primary literature article is usedto support a statement in your laboratory report and the citation itself is properly formatted (see below).

Materials and Methods

This section is notwritten as a laboratory protocol. Instead the important points of the protocol are written in complete sentences that accurately state how the experiment was carried out (incubation temperatures, DNA isolation buffer used, sequence of PCR primers, etc.). Look at the AS2 paper (1)as a guide for what the materials and methods section should look like.

Results

This section presents and describes the data. This section contains figures with figure legends and also a narrative that explains the data to the reader. This section does NOT contain an analysis of the data; just present the data in this section. You need to transition the reader into this section. The first paragraph should be briefly state the goals of the overall work and an overview of how the data was collected.

Here arethe data that need to be included in the results section:

1) High-qualitypictures of the as1, as2 and wild type Arabidopsis plants that clearly show the leaf phenotypes.

2) Leaf petiole length graphs with appropriate statistics.

3) Sequence alignments of the AS1 and AS2PCR products amplified using DNA isolated from wild type,as1 and as2 plants. The mutation needs to be clearly labeled.

4) Protein sequence alignment comparing wild type and mutant AS1 and, separately, a protein alignment of wild type and mutant AS2.

5)A figure that clearly shows the protein structure of the mutant AS1, normal (wild type) AS1 and the superimposed normaland mutant AS1 proteins.

6) A figure that clearly shows the protein structure of the mutant AS2, normal (wild type)AS2 and the superimposed wild type and mutant AS2 proteins.

All figures must have figure legends and should be described in the narrative of the results section.

Discussion

Discuss what the results mean. The main goal of this section is to analyze the data while clearly articulating how mutations in the AS1 and AS2 genescause changes in protein structure and how these mutations lead to the as1 and as2 mutant phenotypes. You shouldalso discuss the implications or significance of these results (although don’t merely repeat the introduction) and how you might expand or clarify the results based on the limitations of computational modeling.

References

You need at least five primary literature article properly cited for each report. Properly cited means that the main point of the primary literature articlesupports what is being cited in the lab report. In addition, the citations must be properly formatted. The instructor will provide guidelines that detail what specific format will be used for citing references.

Works cited

1. Semiarti E, Ueno Y, Tsukaya H, Iwakawa H, Machida C, Machida Y. 2001. The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana regulates formation of a symmetric lamina, establishment of venation and repression of meristem-related homeobox genes in leaves. Development 128:1771–1783.

2. Byrne ME, Simorowski J, Martienssen R a. 2002. ASYMMETRIC LEAVES1 reveals knox gene redundancy in Arabidopsis. Development 129:1957–1965.

Rubric for grading the lab report-points will be assigned according to the guidelines above.

Section / Points possible and explanation / Points received
Title and name / 1 pt total
0.5 pts-Title is descriptive.
0.5 pts-Author’s name clearly stated.
Abstract / 6 pts total
2 pts-A short summary of the function of AS1 and AS2.
1 pt-An overview of why the experiments were done.
1 pt-A succinct overview of the methods.
2 pts-Main finding is clearly stated.
Introduction / 6 pts total
1 pt-Arabidopsis and its use as a model system.
1 pt- Basic description of leaf development.
1 pt-Clear description of the central dogma and protein structure.
2 pts-Clear background information describing the AS1 and AS2 gene.
1 pt-The introduction is well organized.
Materials and Methods / 5 pts. total
3 pts-DNA isolation, PCR, bioinformatics and molecular modeling are included in the materials and methods.
2 pts-The descriptions of the materials and methods are clear, succinct and accurate.
Results / 18 pts total
3 pts-The first paragraph provides the reader context for why and gives an overview of how the experiments were carried out.
1 pt-Nice pictures of the as1, as2 and wild type Arabidopsis plants.
1 pt-Leaf petiole length graphs with appropriate statistics.
1 pt-Sequence alignments of wild type DNA sequence compared to the mutant sequence of AS1 and AS2 genes. The mutation needs to be clearly labeled.
1 pt-Protein sequence alignment comparing wild type and mutant AS1 and, separately, a comparison of wild type and mutant AS2.
1 pt-A figure that clearly shows the protein structure of the mutant AS1, wild type AS1 and the superimposed wild type and mutant.
1 pt-A figure that clearly shows the protein structure of the mutant AS2, wild type AS2 and the superimposed wild type and mutant.
3 pts-All 6 figures must have descriptive figure legends.
6 pts-All 6 figures are clearly described in the narrative of the results section.
Discussion / 6 pts total
2 pts-There is a clear description of how mutations in the DNA change the structure/function of a protein which results in the mutant phenotype.
2 pts-The data is referred to and is used to support the relationship between DNA, protein structure/function and phenotype.
2 pts-The significance of the work is presented and there are suggestions for how the work could be expanded or clarified.
References / 4 pts total
1 pts-At least five primary literature papers are cited.
2 pts-The in text and reference page citations are properly formatted.
1 pts-The main point of each primary literature article is referred to in the narrative.
Grammar and format / You will not receive points for this, but you could lose points for this.
Plagiarism / You will be reported to the Dean of Students and potentially receive a 0 on the lab report. .

Total points 45