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Primary Journal Article: Analysis of BRCA1 mutants
BRCA1 paper draft (20 pts) and Final Paper (100 pts.)
* Introduction, Materials and Methods, Results, Figures and Legends, and Literature Cited sections for peer review are due the week of October 31 (20 pts.)
* Title, Abstract, and Discussion sections are due the week of November 14 for workshopping. *Final paper containing all parts of a primary journal article is due the week of November 28 (100 pts).
As you wrote your papers describing the outcomes of the catalase kinetics and photomicroscopy labs, you gained experience presenting, describing, and analyzing the data you obtained in a lab experiment. This final lab report will also allow you to present data and analyze your experimental outcomes, but now you will also integrate information from other primary journal articles and will describe your experimental methods so that your paper describes your entire BRCA1 research project in the format of a complete scientific journal article.
As we mentioned when introducing your earlier papers and discussed again during your Journal Club lab, the format for a primary journal article is not identical from journal to journal. Although the exact format is not universal, the sections we discussed earlier in the semester are found in some form or another in all primary journal articles and will be included in your final BRCA1 paper. These sections include:
Results (with figures and figure legends) Discussion:
Materials and Methods:
This primary journal article will be completed in three parts:
1. To build toward a complete journal article, you will write a draft paper that contains Introduction, Materials and Methods, Results, Figures, and Literature Cited sections based on your research experiments performed to identify whether novel mutations in the BRCT domain of BRCA1 result in a cancerous phenotype. Desсrіptions of these sections are included below and will be discussed in lab. Your paper containing these sections will be reviewed by your peers in lab during the week of October 31 so that you can receive constructive feedback to be used in synthesizing your final paper.
2. Following your independent experiments, you will write a draft containing the additions to your figures and results sections, as well as the Title, Abstract, and Discussion section. Desсrіptions of these sections are included below and will be discussed in lab. Your paper containing these sections will be reviewed by your peers in lab during the week of November 14 so that you can receive constructive feedback to be used in synthesizing your final paper.
3. Your final paper will include all the sections found in a primary journal article and will also be based upon your BRCA1 research project. The report should contain these sections in the order indicated above and in the format described for your earlier papers and in this handout. This paper is due the week of November 28.
Note: Again, we cannot emphasize strongly enough the importance of constructing your paper using YOUR OWN WORDS AND IDEAS. Copying material from other sources is plagiarism, even if you cite the source. Incidences of plagiarism will be dealt with through the appropriate University procedures. If you are struggling with the material or struggling with synthesizing the material to generate a cohesive paper, please come and talk to one of your instructors. We will be more than happy to help you work your way through this assignment in an effort to familiarize you with the reading and writing of scientific literature.
When generating your journal article, please use the format for each section that is described below. Some of the desсrіptions below are new to you. You have seen others in the handouts accompanying your earlier writing assignments. Please read each section carefully to aid in your synthesis of a paper that conforms to our expectations and to the expectations of a typical journal publishing work in the biosciences. In addition, you can utilize Chapter 9 of Jan Pechenik’s Short Guide to Writing about Biology (copies are in the Biol 182 lab, on reserve in Cooley Science library, and available for purchase in the bookstore) to help you with each section.
Desсrіptions of sections in a Primary Journal Article:
The Title should describe or summarize your results from the experiments you are reporting in the paper. Remember, a simple indication of the technique you used is not a suitable title for a primary journal article. Indicate your most significant results.
Example: Nucleotide triphosphates are required for microtubule assembly. Abstract
The Abstract should be a brief desсrіption of the important findings being reported in your paper. Using only a single paragraph, the Abstract should provide readers with enough information that they basically understand the question you have asked, what techniques you used to address the question, the results you obtained, and the significance of these results. Because of the space limitation, most authors present their abstract by using only one or two sentences to address each of these topics. Further desсrіption of the development of a typical abstract is provided below:
The first sentence is usually a general overview of the field in which the experiments were performed.
Example: The generation of microtubule filaments involves the assembly of tubulin monomer subunits into a long, linear array of molecules.
The second sentence can say something specific about the aspect of the field that the experiments sought to address (i.e. the question being asked).
Example: The mechanism by which these monomers assemble is unclear.
Each subsequent sentence should describe an experiment performed to address the issue mentioned above, and should report the result obtained from the experiment. One or two sentences are usually included for each experiment. If many experiments were performed, the desсrіption of the experiment is often removed and only the result is present. This allows for all results to be presented in a short abstract.
Example: To determine if GTP is involved in monomer assembly, tubulin monomers were incubated in presence of a non-hydrolyzable GTP analog. Microtubules failed to assemble in the presence of the GTP analog.
If your results are significant, you should conclude the abstract with a sentence indicating how this set of experiments has contributed to our understanding of cell function.
Example: The failure of microtubule assembly to take place indicates that GTP hydrolysis is necessary for tubulin polymerization.
The Introduction may be the most difficult part of a research paper to write. It is often much more difficult for an author to read the work of others (often dozens of papers) and summarize the current state of knowledge in a field in a couple of paragraphs than it is to write an entire paper describing the experiments one has just performed.
The Introduction usually begins with a paragraph providing a general overview of the area of molecular biology the paper will address. This paragraph often cites a review article as its reference source. Subsequent paragraphs in the Introduction then describe the findings of others that relate directly to the experiments and conclusions about to be reported in the body of the paper. These paragraphs usually contain a reference or two for each sentence, indicating that these sentences are a desсrіption of the reported results of others. The final paragraph of the Introduction is often a very brief desсrіption of the findings reported in the paper. A good, concise Introduction section is typically only 3 – 5 paragraphs in length. (*See the Humphreys et al. paper you read for Journal Club for an excellent example of a concise, well-written Introduction.)
When writing this section, you must read the papers you cite (not just read the title or abstract, and especially not just refer to someone else’s summary of the paper in their own introduction!). Then be sure to provide that one or two sentence summary of the paper in your intro. What about it pertains to the question you are asking in your experiment? What background does it provide for the reader so that they better understand why you’re doing the experiment you’re performing?
For this paper, be sure to refer back to the bibliography you generated in lab to help you find papers that are relevant to our topic and can help you write an excellent introduction.
Written in sentence form, the Results section describes the results of the experiment that you performed. In the Results, simply state what you found, without interpretation or elaboration. Remember that your Results section should be a desсrіptive report of your observations. Describe what you saw on your yeast plates. What were the relative sizes of the colonies? What quantitative data did you collect? Were the values significantly different? There is no need to point out every datum, but do point out trends you may want to focus on later in the Discussion portion of the paper. Remember to refer directly to the figures as you write the results section (e.g. “We found that XXXX (Fig. 1).”) Take the time to describe your results carefully.
Remember that the first sentence or two of this section often states why the experiment was performed and what technique was used (e.g. In order to examine the role of microtubules in chromosome movement, we treated cells with the microtubule destabilizing drug colchicine immediately prior to entry into mitosis.). The remainder of the Results describes what was observed as the experiment was performed. The last sentence describing the Results should
summarize in a single sentence what you observed. Do not include an interpretation of why you observed these results here – the interpretation is to be saved for the Discussion section.
Please write this section using a past tense active voice. (Use phrases like, “We treated . . .”, “We observed . . .”, “Cells exhibited….” See example above.)
The figures are presented to serve as the raw data for a reader to see in order to make his/her own interpretations of your results. Make sure your figures include both your experimental data and any controls you have run. Each figure should be described by a single figure legend, placed underneath the figure. This legend should begin with a title sentence that summarizes the data in the figure. The remainder of the figure legend should carefully describe what is presented in the figure. Your figures should be understandable by a reader of your paper who does not refer to the text of the Results section. Thus, the figure legend can sometimes get quite long. Don’t hesitate to be desсrіptive. In addition, the figures should be clearly labeled to indicate what is present in each panel. The labels can be as simple as numbers or arrows, but should be clearly described in the figure legend. The legend should begin with a short title placed under the figure. The text in the figure legend should very briefly describe how the experiment was performed and may briefly indicate the results obtained. An interpretation or discussion of these results is not included in the figure legend.
**Take a careful look at some figures from the primary journal articles you have read in order to get a good idea of the information included in a figure legend and to see how figures are labeled. Other authors’ papers are excellent sources of ideas for how to effectively depict your data in figure form!
For this paper, your Results section will include both an examination of the colony sizes you obtained for your yeast transformed with each plasmid, as well as the data you collected from your DNA sequence analysis. Thus, you might envision having (eventually) three figures (which may have more than one panel each):
Figure 1: Presentation of relative colony size for yeast with each plasmid. Figure 2: Visual representation of your sequence data.
Figure 3: Presentation of the data from your independent experiment.
The Discussion usually begins with another sentence describing what experiments were attempted and why they were performed (similar to the first sentence of the Results). The second sentence often describes what results were actually observed. The remainder of each
paragraph expounds upon the significance of the results. What do these results mean? How do your control samples influence your interpretation of your results? Integrate your observations with the findings of others to generate a nice “story” about your BRCA1 mutations and phenotypes in yeast. (Remember to carefully cite the papers you use in these comparisons.) Make certain to include not only your insights into why you obtained the results that you did, but also your thoughts on how these results influence our understanding of BRCA1 function or activity in eukaryotes. Remember, this section reports your insights into the data you obtained. Generate some insightful analyses! Finally, conclude your discussion with a brief desсrіption of what you would do next. Be creative!
Remember not to fall into the trap of using this section to describe what you perceive as your own procedural errors. We began this experiment without knowing what “should” happen, and you should not write this section as though you had some specific result in mind when you began the project. Write as if the data you collected are as accurate as possible, and discuss those data in the context of the primary literature. Be concise, be accurate, but be persuasive in this section. Convince the reader that your interpretation of the data is the correct one.
Materials and Methods
This is where you describe how you went about testing your hypothesis. You must provide enough detail so that another investigator could duplicate your study simply by reading your desсrіption. Chances are your study will not be duplicated exactly, but may be modified by another investigator in order to answer related questions or test similar hypotheses.
Because the Materials and Methods section is used only as a resource by readers, most journals now place this section at the end of the paper. Place the Materials and Methods section after the Discussion section in your paper.
The Materials and Methods section is often divided into subsections that represent different sets of experiments. “Yeast transformation” and “DNA sequencing” may be two appropriate subheadings for the set of experiments you performed. Protocols described in detail in other papers and certain procedures, such as routine lab activities like mixing solutions or weighing materials, need not be described exhaustively. If you have used another source for your protocol, cite the source of the procedure and then describe the procedure briefly. Please note that we have given you information on how to cite some of these procedures. You may not cite the lab handouts for this section.
Again, we highly recommend referring to the papers you have read for examples of published Materials and Methods sections (as well as all other sections of your paper!) for additional insights.
Make certain to cite within the text of your paper any material you use that comes from a published source. Your citation will contain the author’s last name followed by the date, all enclosed in parentheses (Jones 1998). If two authors published the paper, include both of their names (Jones and Smith 1999). If more than two authors are on the publication, use the Latin et al to indicate the additional authors (Jones et al. 2000).
When listing the full citations in the References section at the end of the paper, make certain to list all authors, last name first followed by first initials, then the year of publication in parentheses, followed by the article title, journal name, volume number, and page numbers. The authors should be in alphabetical order, not in the order of when you cited them.
Jones PJ (1998) Microtubules mediate chromosome movement during mitosis. J Cell Biol 145: 123 – 135.
Jones PJ, Smith AB, and Doe JD (2000) Colchicine treatment results in chromosome loss in Xenopus laevis oocytes. Science
255: 123 – 127.
*Remember that citing a paper does not give you authorization to copy the author’s words or ideas. Use the sources you are citing to obtain information that you can integrate into your ideas regarding BRCA1 function. DO NOT PLAGIARIZE.
Do not include other sources that were not cited, even if they are relevant and you read them from beginning to end. Only include those you have cited in the text. Remember, and ideas that are not your own MUST be credited to the author.