Honor’s Research Proposal for Sciences and Mathematics (HO 401 Research Proposal, etc.) Structure and Format

Overview

The following is a general overview of how most students in the Department of Sciences and Mathematics should structure their HO 401 Honors Project Proposals.

All students should consult with their Honors Advisor to make sure the project they are proposing fits well into this structure. Students are free to make adjustments to this structure as needed when suggested to do so by their advisor.

The proposed experiments should, in general, be written using the first person plural (“we will do these things”) and should be written in the future tense (“we will do these things”.)

The literature reviews sections should be written in the past tense when describing research that has already been done (“Wickner et al. [4] showed that the CUR1 gene is necessary for prion propagation.”) and should be written in the present tense when talking about general principles (“Sexual competition often leads to sexual dimorphism [3].”)

I.  Introduction

Should be like an abstract that would be submitted for a scientific paper or for a meeting. About half a page. 

Should include the following:

• Broad introductory statement describing the importance of the planned research.
• Three or four brief but related statements giving current background about planned research that is also relevant to the planned research.
• Importance and implications of planned research based on the what is already known about the topic.
• Summary statement summarizing your hypotheses and how the experiments that you are proposing will address the hypotheses.
• Provide citations, in the departmental format, for all information and assertions.

This will be the hardest section to write, because it is both succinct and a summary of the rest of the proposal. You should probably write this part last. You should write the sections that this will summarize before you write the summary itself.

II.  Background

Should be a review of the literature that is directly relevant to your proposed project. One to two pages.

• Relevant literature
  • Summarize published literature relevant to the proposed research. Be sure to provide citations in the departmental format.
• Previous research
  • Provide one or two paragraphs describing recent findings that justify the proposed research project.  If the findings have been published, cite the work using the departmental format.  If the findings are unpublished, state this in parentheses (unpublished data).

III.  Proposed Research

Should be the bulk of your proposal. Details of what you are actually proposing, the how’s and why’s.

• Introduction
  • What hypothesis or hypotheses are you testing?
  • Describe one or two aims for the proposed research and describe how they will test your hypotheses.  For example if there are two aims (approaches) that you plan to use to solve your experimental problem, state in the introductory sentence “There are two aims for the research to be conducted by myself in the laboratory of a named research advisor (or with the guidance of a named mentor)”
  • The next two sentences should be introduced with the subheading (Aim 1—in bold) and succinctly state the broad approach and goal of each aim, followed by how it fits into one of your hypotheses.
  • For example, [Aim 1.  We plan to use polymerase chain reaction (pcr) to remove or disrupt genes that are adjacent to the transposon insertions. If our hypothesis is true, this will prevent IcsA secretion.”]  Aim 2.  The second aim should be treated in the same fashion as in Aim 1 above. Write in the first person plural (“we”) and in the future tense (“we will”).
• Aim 1.
  • Here, you should restate aim 1 and describe in detail the approaches that will be taken to address its goals. A rationale should be given to the readers.  A specific scientific approach should be defined.  The predicted outcomes of the research should be addressed. Do not give step-by-step directions for protocols. Just mention the protocol itself and explain why it is being used and what you hope it will reveal. What outcomes do you predict and, if those outcomes actually happen, what will you be able to conclude? If the outcomes do not happen, what you will you conclude?
• Aim 2.
  • The second aim should be treated in the same fashion as Aim 1.
• Summary paragraph.
  • Such summary paragraph should repeat the overall purpose of conducting the experiments and the importance and implications of the predicted results.

IV. References

A numbered list of all the references cited anywhere in your proposal.

Only include references you actually cited in your text. Provide all the information for each reference stipulated by the departmental style for references and use the departmental format. 

Reference Format

See some sample research articles from PLoS Biology for examples on how to lay out and format your references:

• Small Heat Shock Proteins Potentiate Amyloid Dissolution by Protein Disaggregases from Yeast and Humans
• Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies
• CULLIN-3 Controls TIMELESS Oscillations in the Drosophila Circadian Clock
• Using Grizzly Bears to Assess Harvest-Ecosystem Tradeoffs in Salmon Fisheries
• Structural and Functional Loss in Restored Wetland Ecosystems

References should be listed at the end of your essay. There should be a left-justified sub-heading of “References” before your reference list begins.

References should be listed in numerical order by the citation number used to identify them in the text.

All authors should be listed by initials and surname, unless there are more than five authors, in which case only list the first five authors followed by “et al.” Separate different authors with commas. Do not separate surnames and initials with commas. Do not use “and” before the last author.

The full title of the reference should be listed. Do not put the title in quotes.

Use the accepted abbreviations for journal titles. Do not use periods after the abbreviations in the title. For instance, the official abbreviation for the Journal of Biological Chemistry is J Biol Chem, not J. Biol. Chem. Note that some journal titles aren’t abbreviated (e.g., Nature), but most are.

If you don’t know the accepted abbreviation, try looking up the article in PubMed. The PubMed citation will give the journal title in the form of its accepted abbreviation. However, do not just copy the entire PubMed citation. They use a different style than we do; just use PubMed to determine the accepted journal abbreviation (and, if needed, information on the authors, year, title, volume, and pages — just reformat them to fit our departmental style.)

If PubMed does not list the article or journal you are referencing, the CAS (Chemical Abstracts Service) provides an alphabetical list of biology and chemistry journals along with their official abbreviations. Try looking for the journal there. Just remember, do not include the periods in the abbreviations even though the CAS list does.

The second and third lines of a reference should be indented to line up with the beginning of the text on the first line.

Journal Articles

Here is the generic format for journal articles:

1.   Author1 AB, Author2 CB, Author3 DE (year) This is the article title. J Interesting Results 55: 100-110.

For journal articles, start with the authors’ names last name first, followed by initials not separated by any commas and without periods after each initial. Use commas only to separate the different names. Do not put an “and” before the last name. If there are five or less authors, use all the authors’ names. If there are more than five authors, list the first five, followed by “et al.” The “al.” always has a period after it even if it does not end the sentence but the “et” never does.

After the authors names, give the publication year in round brackets. No period before or after the year.

Then give the journal title. Accepted abbreviations should be used for journal titles, but do no put periods after each abbreviated word in the title. Put a period after the article title. Give the volume number of the journal, but do not give the issue number or date. After the volume number, put a colon and give the beginning and end pages of the article, but do not use “pp” or “pg”.

For journal articles that are available both online and in print (hard copy), always format your reference as if you had obtained the article from the print version of the journal. So, even if you go online to read a Nature article, you still format it so the citation includes the journal volume and page numbers, and you do not include the URL or the date accessed. If your online copy of the journal article does not provide the information you need in your citation, look the article up in PubMed. The PubMed listing will give the volume number, the page numbers of the print copy, etc. Use that information in your citation (you will change its formatting slightly, but use the info itself), even if your online copy wasn’t formatted that way. You do not need to provide the DOI information.

For journal articles that are only available online, the online journal will still provide both a volume number for the article and page numbers for the article. Format your reference in the same style as for an article from a print journal with authors, year, title, journal name, volume and page numbers. Do not put the URL or the date accessed info. If you are unsure what volume and page numbers to use for an online article, look the article up in PubMed. The PubMed listing will give the volume number, the page numbers to use. Use that information in your citation (you will change its formatting slightly, but use the info itself), even if your online copy wasn’t formatted that way. You do not need to provide the DOI information.

Here are two examples of how to format references that are journal articles:

5.   Redecker D, Kodner R, Graham LE (2000) Glomalean fungi from the Ordovician. Science 289: 1920–1921.

6.   Weismann D, Hartvigsen K, Lauer N, Bennett KL, Scholl HP et al. (2011) Complement factor H binds malondialdehyde epitopes and protects from oxidative stress. Nature 478: 76-81.

Web Pages

Here is the generic format for web pages:

6.   Author AB (year) Web page title <http://www.sciencewebpages.com/this web page> Accessed 2013 Sept 23.

For web pages that ARE online journal articles, treat the article as if it were a regular journal article, as described in the Journal Articles section above.

For web pages that are NOT online journal articles, you need to provide, if known, the author’s name, space, the date of last revision in parentheses, space, title of document, space, the URL in angle brackets, space, and very importantly the date (year month day, in that order) when you viewed/read the page, period. This last information is the “date of access” and is formatted “Accessed year month day.”

It is sometimes, but not always possible to find the web page author(s), document title, and date of last revision. Look at the top and at the very bottom of the page for the author(s) and revision date; look at the title on the top of your browser window, or sometimes even in the URL itself, for the document title. If some of the information (such as author) just is not available, leave it out and go to the next item in the list of information to include in the reference. If the date of last revision is not available, leave it out and go to the next item of information to include in the reference. But ALWAYS include the page URL and the date accessed.

This style of formatting web page citations is a modified version of the basic format suggested by the Council of Scientific Editors (CSE).

If you can find all the information the formatting of your citation will be some variation of this:

7.   Daneholt B (2006) Advanced Information: The 2006 Nobel Prize in Physiology or Medicine: RNA Interference. <http://www.nobelprize.org/nobel_prizes/medicine/laureates/2006/advanced.html> Accessed 2023 May 28.

If you cannot find an author, your reference listing might look like this:

8.   (2006) Press release: The 2006 Nobel Prize in Physiology or Medicine: RNA Interference. <https://www.nobelprize.org/prizes/medicine/2006/press-release/> Accessed 2028 May 28.

If you cannot find either the author or the date of last revision, you reference listing might look like this:

9.   What is Epigenetics? < https://www.cdc.gov/genomics/disease/epigenetics.htm> Accessed 2023 May 28.

Books

Here is the generic format for entire books, from books where the same author or authors wrote the entire book.

10. Author1 AB, Author2 CD (year) This is the book title. City: Publishing company. p xxx.

For information taken from books, give the authors of the book — last names first followed by their initials without periods. Only put commas between different authors’ names. Follow this with the year published in round parentheses. Then put the title of the book, followed by a period. Give the city where the publisher is located (usually available on the copyright page), colon, name of the publishing company, followed by a period. Put a lower-case p and give the EXACT page number where the information you are citing can be found in the book, followed by a period. Do NOT give the total number of pages for the book, just the pages that provided the information you are citing.

If the information you are citing is from a chapter in a book where every chapter is by different authors, use the format described in the section on Chapter in a book, directly below.

Here is an example of how to format a book in your reference list.

11. Chase JM, Leibold MA (2003) Ecological niches: Linking classical and contemporary approaches. Chicago: University of Chicago Press. p. 212.

Chapter in a book

Here is the generic format for a chapter in a book where each chapter was written by different authors:

12  Author1 AB, Author2 CD (year) This is the chapter title in Editor1Name E, Editor2Name F, editor(s). Book Title. City: Publishing company. pp xxx-xxy.

If your source is a chapter in a book, where each chapter is written by different authors, first give the names of all the authors — last names first followed by their initials without periods. Only put commas between different authors’ names. Follow this with the year published in round parentheses. Then give the title of the chapter, followed by “in” followed by the name or names of the book’s editors. For the editors give their last names first followed by their initials without periods; separate different editors with commas only, no “ands”. Put a period after the editors’ names. Then give the book title, ending with a period. Then give the city where the publisher is located, followed by a colon, followed by the name of the publisher, ending with a period. Finally, use lower-case “pp”, period, followed by the range of pages of the chapter, first page number to last.

Here is an example of how a chapter in a book looks in the reference section:

13. Simberloff D (1997) Eradication. In: Simberloff D, Schmitz DC, Brown TC, editors. Strangers in paradise: impact and management of nonindigenous species in Florida. Washington (D. C.): Island Press. pp. 221–228.

You might want to look through the PLoS Biology archives to find an article similar in theme or content to the report you are writing, to give you a better idea of how to deal with some of the formatting issues you will be encountering.

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Written by: Ross E Whitwam
Last updated: 28 May 2023.