The nicholls state university department of biological sciences masters degree thesis handbook



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THESIS

THE NICHOLLS STATE UNIVERSITY

DEPARTMENT OF BIOLOGICAL SCIENCES

MASTERS DEGREE THESIS HANDBOOK

Revised Fall, 2013

This handbook is prepared for use by students preparing to complete requirements toward the Master of Science in Marine and Environmental Biology at Nicholls State University.

Requirements herein have been established by University Graduate Studies and the Department of Biological Sciences Graduate Committee.
Purpose of the Thesis

Demonstration of scientific proficiency and literacy through the reporting of original research and scholarship.



General Characteristics of the Thesis

  • Comprised of disciplined writing and data presentation, as a scientific journal

  • May describe more than one topic or investigative strategies

  • Reports all or most original data during student’s master’s degree training

  • Reviews work that led to degree

  • Reviews work that supports original findings

  • Clarifies problem researched: why selected, how answered, and what learned

  • Includes literature of background, supporting, and similar studies

  • Includes conclusions and synthesis

  • Abstract occasionally published separately

Specific University and Department Requirements for

Thesis Development and Review

  • Must abide by Nicholls State University Graduate Studies Thesis Policy and Guidelines (revised in 2011), available from the Office of Graduate Studies (http://www.nicholls.edu/graduate)

  • Thesis committee consists of a minimum of three members, approved by the Graduate Coordinator, with a minimum of two members from the Department of Biology and at least three members being University approved Graduate Faculty.

    • Complete Approval of Committee Members form (see specific format)

  • Thesis Proposal

    • A formal proposal describing the scientific problem to be addressed during the graduate study, the methods to be employed, and a prospectus of results

    • Powerpoint presentation of thesis proposal to committee members is required

    • Strongly recommended to be completed before research begins, following selection of major professor and committee

    • Requires approvals of all committee members, then submitted to Graduate Coordinator

  • Final Examination

    • Consists of committee oral examination on research and classes and a public oral defense, which must be publicly announced two weeks prior to date of thesis defense

    • Requires completion of Final Examination Report for a Thesis (see specific format)

    • Deadlines: see current university calendar for specific dates

      • Final date to submit a thesis for thesis committee approval typically eight days prior to first day of finals

      • Final date for filing a committee approved thesis with the School of Graduate Studies typically the last class day of the semester

Content of a Thesis Manuscript

  • Title page (see specific format)

  • Certificate

  • Acknowledgements

  • Abstract

  • Table of Contents

  • List of Tables

  • List of Figures

  • List of Abbreviations

  • Body of Thesis (see specific format)

  • Literature Cited

  • Appendices

  • Biographical Sketch (200 word limit)

  • Curriculum Vitae

Formatting for Writing a Master’s Thesis

  • Font: Times New Roman, 12 point

  • Margins: 1.5” left, 1” right, top, and bottom

  • Page Numbering: Centered on bottom of page. Numbers should be Roman numerals for first section and begin Arabic numbering at the Introduction section

  • Graphics: All photos, figures, tables, etc. must appear on own page in black and white or grayscale

  • Must be word processed

  • Citations: Must follow name-date style of the Council of Biological Editors. See CBE website (www.councilscienceeditors.org).

Printing a Master’s Thesis

  • All must be printed on a white, 25% minimum cotton, acid free paper

  • The Certificate, should be printed on same paper and appear in all printed copies of the thesis

  • Printing supplies are the responsibility of the student unless otherwise noted by major professor

  • A minimum of seven copies are needed; yourself, committee members (typically three), library, Office of Graduate Studies, Department of Biology. Additional copies can be made for the student’s personal use or additional committee members

  • All Copies are bound at Ellender Memorial Library. Cost of binding is the responsibility of the student unless otherwise noted by major professor.

Certificate Format

Fill in your thesis title and your name in the paragraph. List your committee chair and type member names and titles. This form is inserted as part of the thesis and needs to be printed on the same paper type (white, 25% minimum cotton [rag] paper [acid-free]). The student has the committee sign the form before being bound.


CERTIFICATE

This is to certify that the thesis entitled “__Thesis Title___” submitted for the award of Master of Science to Nicholls State University is a record of authentic, original research conducted by __Your Name__ under our supervision and guidance and that no part of this thesis has been submitted for the award of any other degree, diploma, fellowship, or other similar titles.


APPROVED: SIGNATURE: DATE:

Name and Title _____________________ ______________

Committee Chair


Name and Title _____________________ ______________

Committee Member

Name and Title _____________________ ______________

Committee Member

Name and Title _____________________ ______________

Committee Member
Title Page Format

The following lines or clusters of lines should appear with single line spacing, center justification, and separation of equal line spacing across the length of the page. For example:

Title of Thesis

-About eight lines-

A Thesis

-About eight lines-

Submitted to the Graduate Faculty

of Nicholls State University

in Partial Fulfillment

of the requirements for the Degree

Master of Science in Marine and Environmental Biology

-About eight lines-

By

Your Name



Your previous degree(s), institution(s) granting degree(s), year(s) granted

-About eight lines-



Semester of Thesis Completion
Two Acceptable Forms of Thesis Body

Traditional Style: Typically used for the majority of thesis publications when the research encompasses one large study

    • Abstract

    • Introduction

    • Materials and Methods

    • Results

    • Discussion

    • Conclusions

Chapter Style: Typically used when reports from thesis research are journal published prior to completion of final thesis manuscript, or when research is comprised of multiple smaller studies.

    • Introduction

    • Literature Review

    • Chapter One

      • Abstract

      • Introduction

      • Materials and Methods

      • Results and Discussion

      • Literature Cited

      • Table and Figures

    • Chapter Two

      • Abstract

      • Introduction

      • Materials and Methods

      • Results and Discussion

      • Literature Cited

      • Table and Figures

    • Chapter Three, etc.

    • Complimentary Studies

    • Conclusions


Guide for Writing the Major Thesis Sections

  • Title: The title is the first thing people look at when trying to decide if a paper is worth the time to continue reading. If the title does not grab their attention, they are unlikely to read any further. The title should accurately reflect a paper’s content. The best titles are usually short (a dozen words or less) and crisp.

  • Abstract: The abstract is the second thing a person looks at when trying to decide if reading a paper is worth the time to continue reading. Most of the time an abstract is the only section read and needs to provide all the necessary information from the study. The abstract should include:

  • Problem studied or hypothesis tested: Identify the problem or hypothesis and explain why it is important. Indicate new data, concepts, or interpretations.

  • Pertinent methods: State methods used to achieve the results summarized in the results (keep the methods brief unless a new or greatly improved method is reported).

  • Results: Emphasize the most important results, positive or negative.

  • Conclusions: Summarize the major conclusions reached from your data.

  • Purpose/Significance: Explain how, when, where, and by whom data or interpretations can be applied.

  • Literature citations, footnotes, abbreviations and acronyms (unless used more than five times) should not be put into an abstract.

  • Introduction: An introduction should set the context/stage for the work performed. The introduction should establish the purpose and importance of that work and demonstrate the authors’ awareness of the most pertinent (and recent) literature, including review articles. However, some literature might be reserved for the discussion section if it is more appropriate. Lastly, the introduction should clearly state the objectives of the study.

  • Methods: Methods should be brief and include:

  • A description of the study site

  • Sampling dates and durations

  • Sampling schemes

  • Research or experimental design

  • Data analyses (including statistical probability of error used).

Write the method section in active voice. Previously published descriptions of equipment and procedures may be cited by reference, unless they are in a source of limited availability. Identify new or modified methods and explain them in detail. The method section can be tedious to read, but it is better to be overly explicit than to omit details needed by a reader to evaluate the data or repeat the study. Clarity of expression is as important in the methods section as it is elsewhere in the paper. If the experimental protocol and equipment are particularly complex, they can be displayed in a table or figure. Similarly, the numerous variables needed for some mathematical model or equation may be listed and defined in a table. The methods section can be broken into subheadings to keep different aspects of the experiment organized. These subheadings can be used in the results as well to connect the experiment with the methods.

  • Results: Present results in a clear, simple, concise, and organized fashion (use subheadings if necessary). Avoid overlapping text with information in tables and figures; do not explain analyses that should have been described in the methods section. Reserve comments on interpretation of results for the discussion section. Display data in tables if precision is important and in a figure if trends are observed. Although long lists of raw data are undesirable (they can be included in an appendix), basic data should not be refined to the degree that a reader can not verify the analyses or use the information for other purposes. Statistical testing is an important part of most analyses, but it should not obscure biological insight. Always try to describe the magnitude of the biological effect in addition to the results of statistical analyses. For example, terms such as “fewer” or “smaller” tell us little, and stating that something was “statistically different (P < 0.01)” without giving the actual difference conveys little meaning to the reader.

Most importantly, the statistical designs and models used should be appropriate for the study.

  • Discussion: The discussion provides an opportunity for interpreting data and making literature comparisons. The value of a paper can be greatly enhanced by a good discussion. Begin the discussion by synthesizing your results with regard to your objectives and then relate your work to other literature and research. Do not repeat results in this section, and comment on only the most important results. The quality of a discussion is inversely related to redundancy, wordiness, and unfounded speculation. The work of others, when cited, should be attributed carefully and accurately. Transitions from evidence to intuition need explicit identifications.

  • Conclusion: This section gives a chance to relate the results and major findings to their use in various political, social and technical arenas.  In addition, if appropriate, proposals for further actions in research, management and politics are made.  Highlight the important shortcomings of your work that could be addressed by further research, or to indicate directions that further work could take. 


Format of Literature Cited in a Master’s Thesis

  • Journal Article

Single Author

Author, A.B. Date. Article title. Journal Name. Volume(Issue):Pages


Hamilton, J.B. 2005. Distribution of anadromous fishes in the upper Klamath River watershed prior to hydropower dams—a synthesis of the historical evidence. Fisheries 30(4):10-19.
In-text citation:

(Author Year) (Hamilton 2005)

Anadromous fishes, such as Pacific Salmon, spend most of their lives in salt water and migrate up freshwater rivers to spawn and die (Hamilton 2005).

Multiple Authors

Oren Z. and Y. Shai. 1996. A class of highly potent antibacterial peptides derived from pardaxin, a pore-forming peptide isolated from Moses solefish Paradachirus marmoratus. European Journal of Biochemistry. 237:303-310.

or

Perron, G.G., M. Zasloff, G. Bell. 2006. Experimental evolution of resistance to an antimicrobial peptide. Proceedings: Biological Sciences. 273 (1583):251-256.


In-text citation:

(Author and Author Year) (Oren and Shai 1996)

Amines added at the C-termini of peptides increased alpha-helical content of peptides 25-80% (Oren and Shai 1996).

or

(Author et al. Year) (Perron et al. 2005)



All P. flourescens lines showed a highly significant increase in growth at high antibiotic concentration (Perron et al. 2006).


  • Book

Organization or Author A.A., Author B.B. Year. Title of book. Edition. Place of publication: publisher. Pages
Schlesinger W.H. 1997. Biogeochemistry: an analysis of global change. 2nd ed. San Diego (CA): Academic Press. 588 p.
In-text citation:

(Author Year) (Schlesinger 1997)

Subsidence is a natural process that is expedited by anthropogenic activities, such as fluid withdrawl, and contributes to coastal land loss (Schlesinger 1997).



  • Thesis/ Dissertation

Author A. Year. Title of thesis [degree and type of thesis]. [Place of publication]: Name of University. City, State (only if needed to locate city)
Freeman, S. 1990. Molecular systematics and morphological evolution in the blackbirds. Ph.D. dissertation, University of Washington, Seattle.

In-text citation:

(Author Year) (Freeman 1990)

Blackbirds from the northern range express the gene rarely (Freeman 1990).



  • Government Report

Government publication: author(s) or agency; year; title; agency; city; state, country (only if needed to locate city). type and number of publication
EPA (U.S. Environmental Protection Agency). 1986. Quality criteria for water. EPA, Washington, D.C. Report 440/5–86–001

or

Schick R.S., Edsall A.L., Lindley S.T. 2005. Historical and current distribution of Pacific salmonids in the Central Valley, CA. Santa Cruz (CA): US Department of Commerce, National Marine Fisheries Service, Santa Cruz Laboratory. Report nr NOAA Technical Memorandum NMFS-SWFSC-369.


In-text citation:

(Organization Year) (EPA 1996)

92-95% of isolated were confirmed as E. coli (EPA 1996)

or


(Author Year) (Schick et al. 2005)

Salmons’ range has decreased substantially (Schick et al. 2005) but efforts are being made to bolster local populations.





  • Conference Proceedings

Editor/Author A. Year. Title of paper. Paper presented at: Title of conference. Number and name of conference; date; Place.
Bartlett D. and J. Smith, editors. 2005. GIS for coastal zone management. Paper Presented at: CoastGIS ’01 Conference; 2001 June 18-20; Halifax, Canada.
In-text citation:

(Author and Author Date) (Bartlett and Smith 2005)

Subsidence is monitored by GIS imaging throughout coastal Louisiana (Bartlett and Smith 2005).



  • Website

Author. Title of document [Internet]. Date of publication. Place (State): Publisher; [cited Year Mon date]. Available from: URL
Smith, J.O. Birds commonly observed flying (Internet). 2008. New Jersey: Ornithological Society of North America; (cited 2011, January 21). Available from: www.osnabirds.org.

In-text citation:


(organization copyright date) (OSNA 2008)
Some birds have even been observed leaping from trees and not crashing back down to earth (OSNA 2008).
List of Abbreviations and Formatting Issues

  • Numbers, Variables, and Statistical Elements

  • Longitude and latitude: l48°N, 78°W (no periods).

  • Percentages and degrees: use symbols (15%, not 15 percent).

  • Fractions: may be spelled out (one-half, one-third) unless used with units of measure (0.5 mm or 0.5 years).

  • Decimal point: insert 0 before a decimal point (0.4, not .4).

  • Dates: day, month, year (e.g., 6 October 1987).

  • Numbered lists: for the most part, avoid the use of numbered lists in the text. “We used x, y, and z to take soil samples” rather than “We used three techniques to take soil samples: (1) . . . , (2) . . . , and (3) . . . .

  • Insert a space between numbers and the unit of measure (6 m, 14 mL).

  • Define all variables used in an equation.

  • With the exception of Greek letters, italicize all single-letter variables in equations. Do not italicize variables with more than one letter (e.g., “RU” meaning reproductive units as opposed to RU, in which R and U are separate interacting variables).

  • Complete words used as a variable should be lowercase (e.g., species). Each letter in multiple-letter abbreviations that are not complete words should be capitalized (e.g., acceptable, AMF for area of managed forest; unacceptable, PATCH for patch area).

  • Do not italicize Latin words or abbreviations such as i.e., e.g., et al., etc.


  • Abbreviations

p, probability

df, degrees of freedom

χ2, chi-square

FST, genetic variance contained in a subpopulation relative to the total genetic variance

CI, confidence interval or credible interval

SE, standard error

SD, standard deviation, e.g., mean (SD) = 44% (3) or mean of 44% (SD 3). Do not use ±.

mg L-1, milligrams per liter

m, meter


m s-1, meters per second

s, second(s)

min, minutes(s)

hr, hour(s)

d, day(s)

wk, week(s)

mo, month(s)

yr, year(s)

ln or loge, logarithm (base e)

log10, logarithm (base 10)

approx., approximately

cal or J, calorie (Joule)

max., maximum

°C, Celsius

t, metric ton

coeff., coefficient

min., minimum

CI, a≤ x ≤a, confidence interval

CL, x ± a, confidence limits

Jan, Feb, etc., month names



R, correlation, simple

>, more than/greater than



R2, determination, multiple

R2, multiple correlation

r2, determination, simple

no., number (of items)

diam, diameter

ppt, parts per thousand

ppm, parts per million

ppb, parts per billion

dbh, diameter, breast height

N, S, E, W, NE, NW, etc., directions

%, percent

eq(s), equation(s)



N, population size

n, sample size

x, sample mean (of x)

g, gram

ha, hectare

ht, height

temp, temperature

vs., versus

kcal, kilocalorie

V, volt

LC50, lethal concentration, 50%

vol, Vol., volume: liquid, book

LD50, lethal dose, median

wt, weight

<, less than

sex: ♀ female, ♂ male (in tables, figures, hybrid crosses)



T, Wilcoxon test

lim, limit

L, liter



  • Prefixes

giga (109) G

mega (106) M

kilo (103) k

milli (10-3) m

micro (10-6) µ

nano (10-9) n

pico (10-12) P
Useful Websites

Integrated Taxonomic Information System (ITIS): www.itis.gov

NSU Department of Biological Sciences: www.nicholls.edu/biology/

NSU Ellender Memorial Library: www.nicholls.edu/library/

Biological Journals and Abbreviations: http://home.ncifcrf.gov/research/bja/

Council of Biology Editors (CBE): http://www.councilscienceeditors.org


Approval of Committee Members Format

Type names and titles. Present to committee members for signatures and submit completed form to Graduate Coordinator for approval.


Department of Biological Sciences

Nicholls State University

Master of Science in Marine and Environmental Biology
APPROVAL OF COMMITTEE MEMBERS

Candidate Date                                                 


Committee Members:
Name Chair Signature                                                

Title                                                          


Name Signature                                                

Title                                                          


Name Signature                                                

Title                                                          


Name Signature                                                

Title                                                          


Approved:
                                                                                                                           

Coordinator of Biology Graduate Program Date


Master’s Thesis Proposal Approval Format

Type names and titles. Present to committee members for signatures and submit to the Graduate Coordinator prior to beginning your research (http://www.nicholls.edu/biology_

graduate/policies-and-forms).
Nicholls State University
Master of Science in
Marine and Environmental Biology
Master’s Thesis Proposal

Submitted by Your Name


and approved by Committee Members

_______________________________ Date_______________



Advisor, Position

_______________________________ Date_______________



Committee Member, Position

_______________________________ Date_______________



Committee Member, Position

_______________________________ Date_______________



Committee Member, PositionFinal Examination Report for Thesis Format

Type names and titles of your thesis committee. The student has the committee sign the form at the end of the oral exam and gives it to the Graduate Coordinator. Should be printed on official Nicholls State University letterhead (http://www.nicholls.edu/biology_graduate/policies-and-forms).



Graduate Studies

FINAL EXAMINATION REPORT FOR THESIS

Candidate: ________________ Student ID: ________________


College of Arts and Sciences

The candidate has successfully passed the final examination of the research:


Name: Signature____________________

Title:
Name: Signature____________________

Title:
Name: Signature____________________

Title:


Approved:
_________________________ _______________

Aaron Pierce, Ph. D. Date

Graduate Program Coordinator
_________________________ _______________

Quenton Fontenot, Ph. D. Date

Head, Department of Biological Sciences
_________________________ _______________

Dr. John Doucet, Ph.D. Date

Dean, College of Arts and Sciences
_________________________ _______________

Dr. DesLey Plaisance, Ph.D Date

Director of Graduate Studies

Report of Thesis Defense Results Format

Type names and titles of your thesis committee. The student has the committee sign the form at the end of the oral exam and given to the Graduate Coordinator. Should be printed on official Nicholls State University letterhead (http://www.nicholls.edu/biology_


graduate/policies-and-forms).

The Graduate School

NICHOLLS STATE UNIVERSITY

COLLEGE OF ARTS AND SCIENCES

Department of Biological Sciences

Report of Thesis Defense Results


TO: Director of The Graduate School Date___________________


FROM: Dr. Aaron Pierce, Coordinator of Graduate Studies in Marine and Environmental Biology
Student ______________________________________________ _______________________

First Name Middle Last Name ID .#


On this date_____________________ has completed the graduate Thesis Defense for the:
( ) Master’s Degree
It has been determined by the committee members named below that the student has:
( ) Passed without dissenting vote(s)
( ) Passed with one or more dissenting votes
( ) Failed
COMMITTEE:
Name: ___________________________ Signature_______________________________

Name: ___________________________ Signature_______________________________

Name: ___________________________ Signature_______________________________

Name: ___________________________ Signature_______________________________



Application for Graduation Form

Obtain an original form from the Dean’s office. Fill out the form and get your committee chair’s signature. Then get the department head’s signature and return it to the Dean’s office. DO NOT USE THIS PHOTOCOPIED FORM.





Marine and Environmental Biology Master’s Degree Checklist

Committee selection.


  • During first semester, form a committee (three to five members).




  • Committee must have a minimum of three approved Graduate Faculty.




  • Two members must be from Nicholls graduate faculty.




  • Fill out, sign, and have committee sign Approval of Committee Members form



Proposal.


  • Written research proposal presented to committee members for review during second semester.




  • Hold a formal proposal defense meeting for committee.




  • The accepted proposal and the Approval of a Thesis Proposal form should be signed by committee members.




  • Submit signed proposal and Approval form to Biology Graduate Coordinator.


Research.


  • Register for the thesis research course in the major department.


Thesis.


  • Thesis Policy and Guidelines and all departmental requirements have been followed regarding format (margins, font, style manual, etc.), included pages and their order, paper weight, etc.







  • Submit thesis to committee at least two weeks prior to scheduled defense (to be discussed next).



  • All corrections of thesis are made and submitted to the committee for approval. The deadline is in the University calendar as “Final date to submit a thesis for approval.”



Final Exam.


  • Student schedules a meeting for defense of thesis. Present will be committee and will be open to public.




  • Oral comprehensive exam will be given to the student in private after presentation to public.




  • Thesis is successfully defended.




  • Final Examination Report for a Thesis is signed by committee and dean.



  • Have committee members sign Report of Thesis Defense Results and turn in to Biology Graduate Coordinator.




  • Thesis signature page is signed by committee members.


Submission of Thesis.


  • Submit approved thesis in final form to the Director of Graduate Studies for signature. The deadline is in the University calendar as “Final date for filing an approved thesis.”




  • Copy completed thesis for binding. A minimum of 7 copies must be submitted; yourself, committee members (typically three), library, Office of Graduate Studies, Department of Biology. Additional personal copies may be submitted.




  • Copies are taken to Danny Gorr (x4676) on the third floor of the Library for binding. An account will be opened with the bindery in the name of the student.




  • Complete Thesis Duplication Release Form from Library



  • Receive and pay invoice received from the bindery. Payment will be made directly to the bindery.




  • When the bound thesis is received by the Library, the student will be notified.





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