1 GUIDELINES FOR MASTERS THESES IN THE DEPARTMENT OF AGRICULTURAL SCIENCES Laura Hauta-aho, Hanna-Riitta Kymlinen and Leena Lindn August 2012

2 Contents

1 INTRODUCTION ............................................................................................. 3 2 GOALS OF THE THESIS ................................................................................ 3 3 STRUCTURE OF THE THESIS ....................................................................... 4 4 CONTENT OF THE THESIS ........................................................................... 4

4.1 Title page ................................................................................................. 4 4.2 Abstract .................................................................................................... 4 4.3 Table of contents ..................................................................................... 5 4.4 Abbreviations and concepts .................................................................. 5 4.5 Introduction ............................................................................................. 6 4.6 Literature review ...................................................................................... 6 4.7 Research objectives ................................................................................ 7 4.8 Materials and methods ........................................................................... 7 4.9 Results ..................................................................................................... 9 4.10 Discussion ........................................................................................... 10 4.11 Conclusions ......................................................................................... 11 4.12 Acknowledgements ............................................................................. 11 4.13 List of references ................................................................................ 11 4.14 Appendices .......................................................................................... 12

5 REFERENCING ............................................................................................. 12 6 REFERENCES .............................................................................................. 14

6.1 Authors .................................................................................................. 15 6.2 Date of publication ................................................................................ 16 6.3 Title of publication ................................................................................ 16 6.4 Serial publications ................................................................................ 16 6.5 Monographs ........................................................................................... 17

7 TABLES AND FIGURES ............................................................................... 17 8 LAYOUT ........................................................................................................ 19 9 EXAMINATION AND GRADING OF THESES .............................................. 20 10 MATURITY TEST ........................................................................................ 20 11 BINDING OF FINAL THESIS AND SUBMISSION TO DEPARTMENT ...... 21 APPENDIX 1: SCIENTIFIC NAMES AND ABBREVIATIONS ......................... 23 APPENDIX 2: RECTORS GUIDELINES FOR HANDLING CASES OF SUSPECTED PLAGIARISM ............................................................................ 26 APPENDIX 3: EXAMPLES OF DOCUMENTING REFERENCES ................... 27 APPENDIX 4: EXAMPLES OF PRESENTING RESULTS IN TABLES AND FIGURES .......................................................................................................... 30

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1 INTRODUCTION

These guidelines were drawn up for students of the Department of Agricultural Sciences

and their supervisors. The Department came into being on 1 January 2010, following

the merger of three units: agricultural engineering, animal science and applied biology.

Each of the former units had their own writing instructions, which formed the basis for

these guidelines. Though primarily drawn up with an eye on Masters thesis writing, the

guidelines may also be used for practical assignments and similar tasks as applicable.

The draft version was submitted to the Departments teaching staff for comments in

addition to being discussed at meetings between major subject teachers and in the

departmental committee for the development of teaching. These guidelines were

compiled by Laura Hauta-aho, Leena Lindn and Hanna-Riitta Kymlinen. Any

corrections or suggestions for improvement may be sent to Laura Hauta-aho

(laura.hauta-aho@helsinki.fi) at the Departments student affairs office.

2 GOALS OF THE THESIS

When working on a thesis, one should aim at clear and accurate reporting, using

unambiguous language and a precise, academic style. The goal is that a person

unfamiliar with the topic but with the required background to understand the content

could replicate the study based on the report. The purpose of the thesis process is to

promote learning but also to demonstrate the competence acquired. Writing enhances

thinking and writing skills improve through practice.

In accordance with the standing regulations of the Faculty of Agriculture and Forestry,

the Masters thesis (with a scope of 40 credits) is to focus on a problem of scientific

relevance and importance to the Facultys areas of responsibility. The thesis should

demonstrate the students ability for scientific thinking, competence in the relevant

research methods, familiarity with the topic and proficiency in academic writing.

(Section 18)

In addition to these general goals, theses also have other objectives and subtargets. For

example, the study guide of the Faculty lists the following learning outcomes for the

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course on Scientific Writing, KTB406, illustrating various aspects of academic writing:

x The student will learn the reasoning behind the scientific style of writing through the combination of analysis of a published paper and writing a preliminary version of part of the Masters thesis in an appropriate scientific style.

x The student will understand the principles behind the structure of the scientific paper and how to apply them in the students own work.

x The outcomes will assist the student in the preparation of the Masters thesis.

3 STRUCTURE OF THE THESIS

As a minimum, the Masters thesis includes the following sections: title page, abstract,

table of contents, introduction, literature review, research objectives, materials and

methods, results, discussion of results, conclusions and list of references. In addition,

the thesis may contain a list of abbreviations or concepts, a summary,

acknowledgements and appendices all under separate headings. The goal is to write

the Masters thesis in the style of a scientific article.

4 CONTENT OF THE THESIS

4.1 Title page

The thesis title is placed at the centre of the title page, and the following information in

the bottom right corner: Name of the author, Masters thesis, University of Helsinki,

Department of Agricultural Sciences, major subject or specialist option, month and year

of completion.

4.2 Abstract

The abstract is a short, independent description of the thesis content. It answers the

following questions: what did the research focus on, why and how was it carried out,

what were the main results and conclusions? No references are cited in the abstract.

Abstracts are drawn up on specific form templates, available on the Faculty of

Agriculture and Forestry web site and in the Departments model file for Masters

theses. The abstract is placed after the title page and written using single line spacing.

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Under Further information on the abstract form, indicate the name(s) of the thesis

supervisor(s). The keywords under the abstract text are important since they are used

when archiving theses in databases. Choose four to eight words that describe the content

of your work as explicitly and comprehensively as possible. Words contained in the

thesis title are not automatically considered to be keywords, so if important, they must

be repeated in this field. Index term lists, such as Agriforest Thesaurus (http://www-

db.helsinki.fi/eviikki/Welcome_eng.html), maintained by the Viikki Campus Library,

are good sources for keywords.

4.3 Table of contents

The table of contents provides an overview of the structure of the thesis and the

relationships between the topics discussed. It contains the headings and subheadings, as

well as the number of the first page of each chapter. Headings are numbered

hierarchically (e.g., 3, 3.1, 3.1.2), and the text should be structured so it does not call for

more than three heading levels. None of the headings should be identical to the title of

the thesis, and there should always be at least two parallel subsections. No period is

added after the last or only number of the heading nor after the heading itself. The table

of contents also shows the initial page numbers for references and appendices.

The headings and page numbers in the table of contents must be identical to the thesis

content. We recommend that you use the Table of Contents function found in word

processing applications to ensure the table is easy to update when finalising your thesis.

4.4 Abbreviations and concepts Good language use is characterised by the avoidance of abbreviations. However, they

may sometimes be justified and necessary. For example, if a long foreign-language

name of an organisation or chemical compound occurs frequently, abbreviations may

make the text easier to read. Theses dealing with molecular biology often contain

complex names of genes and proteins, which are abbreviated according to international

guidelines (Appendix 1). If the thesis contains numerous abbreviations or concepts that

need to be defined, these are listed before the introduction. The list could be styled as

follows (for further examples, see Appendix 1):

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ACI American Concrete Institute

ATP Adenosine triphosphate

Central angle

4.5 Introduction

The introduction briefly describes the background of the thesis, the reasons for selecting

its topic and often the way in which the topic has been limited. If the study is a part of a

larger research project, the introduction also indicates the name and sponsors of the

entire project and all the parties involved. The purpose of the introduction is to capture

the readers attention and provide preliminary information about the matters discussed.

The section concludes with a description of the reasons for conducting the study.

Avoid an excessively long introduction. The recommended length is three to four

paragraphs or one to two pages. The introduction is usually finished towards the end of

the project when writing your conclusions, or as the very last section. The abstract,

introduction and conclusions are the most frequently read sections, and many readers

base their opinion of the entire thesis on them.

4.6 Literature review

The literature review consists of a body of text and may include tables and figures. It

introduces the theoretical framework and previous research related to the topic in a

concise and critical manner, presenting key perspectives and substantive research

findings. A system description is usually included in technologically oriented theses.

The content of the review is organised using headings, which are best structured early

on in the project. The headings provide a framework for the thesis and help you

understand the interrelations between the topics, delimit the content and search for

source literature.

The literature review requires a great deal of work. The author must have good insight

into the research field in order to pick out relevant literature that deals directly with the

topic. Source literature consists primarily of original scientific publications. Readers

must easily be able to distinguish between the thesis authors own interpretation or

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conclusions and previously published research that has passed scientific scrutiny. It may

be useful to summarise the literature at the end of the review.

If the topics of your Masters and Bachelors theses are related, you can utilise the

information compiled for the Bachelors thesis in the Masters literature review.

However, you are not allowed to directly copy text from the Bachelors to the Masters

thesis. The literature review of the Masters thesis is usually clearly more compact than

that of the Bachelors thesis.

4.7 Research objectives The goals of the Masters thesis are described under a separate heading after the

literature review. While they are already mentioned in the introduction, this is where the

objectives are explained clearly and in detail. A thesis often has a single overarching

goal, which can be divided into more detailed, numbered subgoals. The research topic

can also be defined and any research hypotheses introduced in this context. The section

on research objectives is short, often consisting of a single paragraph.

4.8 Materials and methods

This section describes your research materials and methods in such detail that the study

could be replicated on the basis of the information provided. However, every minor

detail need not be explained if it is not significant to the results. This section usually

begins with a description of the research material, followed by an account of

environmental factors essential to research, such as the cultivation site, geographical

location, soil type or substrate quality, nutrient status and weather conditions during

field experiments. The section concludes with a description of the methods used for

measurements and analyses and the statistical processing of results. This section is

commonly written in the past tense. Use the first-person singular and the active or

passive voice depending on the point of view you wish to express. The active voice, for

example, highlights the subjective choices involved in research work and is often the

recommended option in scientific journals. Whatever your choice, follow it

systematically throughout the Materials and methods section.

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The size of the research material and the method of compilation (experiments or

sampling) must be explained thoroughly. In the case of experiments, provide

information about the test subjects, number of replicates, procedures the subjects

underwent, sampling and measurements performed. In technology-related studies, the

tested theory, equations and structure of calculation applications often need to be

described. In the case of design-based research, provide information about the design

methods, principles and calculation equations and methods. Generally known and used

research methods need not be explained in detail a reference to a source in which the

method is described is adequate. However, any deviations from the source references

method or test conditions must be described precisely.

When mentioning any research equipment by name, follow it by the make,

manufacturer and country of manufacture in brackets. Also mention the manufacturer,

country of manufacture, as well as the batch number of chemicals, if there is any risk of

variation in the product quality from batch to batch. Examples:

x Nitrogen content was determined using the Dumas combustion method in a CHN-1000 carbon-nitrogen analyser (Leco Inc., St Joseph, MI, USA).

x The amylose standard was obtained from ICN (batch 14059, ICN Biomedicals, Costa Mesa, CA, USA).

Also indicate the accuracy of measurement devices and any uncertainties related to

them. This is essential for the reliability of the results and the entire study. Reliability is

not self-evident, but it and the usefulness of the results can be assessed as long as any

sources of error and their impact are known. Your supervisor will provide further advice

concerning your research topic.

Any equations and formulas used in the study are presented on their own line in the

Materials and methods section. Use the equation editor in your word processing

application to write and sequentially number equations. After this, refer to equations

with their number, similarly to figures and tables. Example:

=

, (1)

where

= density (kg/m3)

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m = mass (kg)

V = volume (m3).

The Materials and methods section concludes with a description of the methods used for

statistical analysis. No source references are needed for commonly used methods (such

as one-way analysis of variance), but if the method is new or less known, provide a

source containing a detailed description of the method. The software used for statistical

analyses is also described similarly to equipment and chemicals. Example:

Analyses of variance and correlation were performed using SPSS (version 16.0,

SPSS Inc., Chicago, IL, USA).

4.9 Results

The results are presented clearly and concisely. If the study contains any preliminary

experiments, their results should be described first. These are followed by the principal

results corresponding to the research objectives. The results are presented consistently

in the simple past tense and are not interpreted at this stage. Descriptions of materials

and methods are not repeated in the Results section, and there is usually no need for

source references in this context. Moreover, the section does not present any

conclusions or discuss the reliability of results. The statistical reliability of results is

indicated in a suitable manner, for example, using the probability (P), confidence

interval or coefficient of determination (r2).

The results are described in the body text, with the main results further highlighted in

figures and tables. The labels and texts in figures and tables must enable the reader to

interpret the results without resorting to the body text. Do not elaborate on the content

of figures and tables in the text itself; briefly describe the result and add a reference to

the figure or table in question. An example of a well-formulated presentation:

The fertilised seedlings were longer than the control seedlings (Table 1).

Avoid the following style:

The height of seedlings is depicted in Table 1.

Keep in mind that all figures and tables must be mentioned in the body text and be

placed close to the text referring to them. In addition, paragraphs must always begin

with text, never with a figure or table. Further instructions are provided in section 7.

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The author may also choose to present some of the detailed results in appendices. In this

case, only the main findings are described in the body text, and readers may turn to the

appendices for more specific numerical data. However, extensive bodies of

measurement should not be included as such. The author is expected to pick out the

relevant data and present it in a form the reader can easily interpret. It should not be left

to the reader to interpret findings based on figures or appendices.

Calculation methods and equations must be described in such a way that the reader can

replicate them, but the results can be given directly without the intermediate steps. In

the absence of equations, references to equations or examples, it may be difficult for the

reader to understand how the author arrived at the final results.

4.10 Discussion

This section examines the significance of the findings in terms of the research

objectives and in light of previous research. Comparing your results with those of others

helps you make interpretations and generalisations, as well as draw conclusions. You

should also examine the reliability and applicability of your results and make any

suggestions for further research. Subheadings are often needed in this section, and

sometimes it may be a good idea to present and analyse the results in the same chapter.

The results are usually analysed in the same order they were presented. In other words,

first deal with the main findings. However, the goal is also to discuss the results as a

whole. Use the simple past tense when describing your own research stages and results.

Also use the past tense when referring to specific source literature, as in the following

examples: Gusta et al. (1997) used a measurement method based on long-term cold

storage to study the winter hardiness of winter cereals or A measurement method

based on long-term cold storage was used to study the winter hardiness of winter cereals

(Gusta et al. 1997). Opt for the present tense when discussing explanations, evaluating

the general applicability of the results, presenting possible applications or drawing

conclusions. Aim at an objective style in your statements.

Instead of merely repeating the results, interpret them. For example, instead of writing:

Treatment 1 gave a dry matter content of 12% and treatment 2 a content of 18%. This

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was due to..., opt for: The differences between the dry matter contents of treatments 1

and 2 were caused by... Answer the following questions to help drawing up this

section.

x Did you solve the research problems or question? x Did your results support the research hypothesis? x How do the results agree with previous research? x What new information did the research reveal? x How can the results be put to use? x Did the research bring up new topics for study? x Were the research methods well suited to solving the original research question? x What type of cases can the methods be used for?

4.11 Conclusions

Start the Conclusions section by returning to your research objectives. In the Masters

thesis, conclusions cast a brief, summarised look at the objectives and results of the

writers research. Instead of repeating the results, you are expected to present a

synthesis of them. Even negative results may be valuable and significant. Do not

introduce new results or refer to figures or tables in this section. The final sentence

should be a positive one.

4.12 Acknowledgements

If the thesis is related to a research project, this is where you thank project participants,

funders and any material suppliers. You may also acknowledge any key persons and

your thesis supervisors. Write the names in full (in Finnish texts, titles and honorifics

are also written unabbreviated). When writing in English, use the abbreviations Dr. and

Prof. You can conclude this section with a personal note, thanking, for example, your

friends and family for their support and encouragement.

4.13 List of references

The list of references contains all the references mentioned in the text, organised in

alphabetical order by the authors last name. An exception to this are personal

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communications, which are not included in the list, as well as sources of information,

which have been read and consulted but are not referred to in the thesis.

Source references usually consist of four elements: author, date, title, and publication

channel or name of publisher. You can use applications such as RefWorks to manage

source references and create a list of references. The Viikki campus library arranges

courses in using RefWorks. Sections 5 and 6 provide guidelines on recommended

conventions for source documentation.

4.14 Appendices

Appendices include supporting documents, which need not be included in the body text

for the reader to follow the discussion but to which references must be made. Such

documents are often related to the compilation of material, such as maps, data collection

forms or illustrative diagrams. Tables summarising statistical analyses may also be

presented in appendices.

Appendices are numbered sequentially in the order they are referred to in the text. They

are also provided with a title preceded with the number of the appendix (e.g. Appendix

1: Title). If the appended material has not been written by the author, a source reference

must also be added to it. If the appendix includes several tables or figures, a reference to

both the appendix and the number of the table or figure should be included in the text

(e.g. Appendix 1, Table 2). Appendices come after the list of references, and page

numbering continues throughout the list of references and appendices.

5 REFERENCING

The body text itself contains source references. Along with the list of references, they

enable the reader to get acquainted with the original publication and double-check

information discussed in the thesis. References must be placed in such a way that the

reader easily sees which part of the text is based on the source. Source references

usually apply to a single sentence. If the source citation is longer, for example a full

paragraph, a reference to the source is made at the beginning of the citation.

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Information published by others can be included in the text as direct or indirect

citations. Indirect quotations are usually preferred in academic writing, meaning that the

author explains (and summarises) the source information in his or her own words.

Direct citations are justified only if indirect quotation is impractical. A short direct

citation must always be placed in quotation marks. A long direct citation must be

indented by a tab from the left margin.

Plagiarism, passing on another persons writings or ideas without an adequate source

reference, is strictly forbidden. Plagiarism is a serious violation of good scientific

practice. In accordance with the guidelines of the National Advisory Board for Research

Ethics, all suspected plagiarism cases must be investigated without delay and reported

to the faculty dean or the university rector. The Faculty of Agriculture and Forestry has

drawn up its own guidelines for suspected plagiarism (Appendix 2).

Source references consist of the authors last name and the year of publication. When

referring to long works, the page number of the reference should also be given. In the

case of two authors, separate their last names with the word and in the text and with

an ampersand (&) in brackets. When referring to a work with three or more authors, list

only the last name of the first author, followed by the abbreviation et al.. When citing

several publications at the same time, list the sources in chronological order, with works

published in the same year listed in alphabetical order by the authors last name.

References included in the same place in the thesis are separated with a comma. When

using several works by the same author published in the same year, distinguish them by

assigning letter suffixes to the year, for example, 2003a and 2003b. In the body text,

source references are placed inside brackets in either of the following ways, depending

on the sentence structure: It has been shown (Pirinen 2001, Smith & Roberts 2002,

Roberts et al. 2003, Mahosenaho 2004b) that..., but The study by Pirinen (2001)

indicated that..., while Roberts et al. (2003) found that....

If the source publication does not mention an individual author, include the name of the

organisation responsible for publication in the reference. For example, when referring to

Acts or committee reports, list the name of the responsible organisation, that is, the

Government or relevant committee. In the event that no responsible organisation is

identified, cite the source by the year of publication as well as Anon. (short for

Anonymous) or the title of the work (or the first two or three words of it).

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Unpublished, unprinted and electronic sources (such as theses, dissertations,

manuscripts, handouts and websites) are referenced in the same way as other textual

sources, using the name of the author or organisation, the year of writing and the title of

the text. For electronic sources that do not indicate the year of writing, use instead the

year in which you accessed the source online. In the list of references, the title of

unpublished and unprinted sources is followed by the type of text (for example,

Masters thesis in horticulture, manuscript or inventory list) and the place of storage (for

example, the Department of Agricultural Sciences or the Helsinki City Archives). For

online sources, indicate the URL address at which the text was accessed, the time and

date of the last update, as well as the date on which you read or printed the material.

Careful consideration should always be given to the use of online sources.

Orally obtained information and private email messages or letters are only cited in the

body text and need not be included in the list of references. The text reference consists

of the informants name, workplace (if known) and the date the information was

provided (for example, Jane Smith, MTT Finland, email message to author, 17 February

2006).

In the rare event that you must cite an original publication that you are unable to obtain

in person, you can use either of the following two options. If only the abstract is

available, clearly indicate the name of the source in which you read it (for example,

Web of Knowledge, CAB Abstracts or Horticultural Abstracts), as well as the abstract

number. If a source needs to be cited second-hand through another publication, indicate

this by the abbreviation ref., followed by the author and year of publication of the

volume cited in brackets (for example, Kaku (1975, ref. Sakai and Larcher 1987)

showed that...). Both the cited and the original publications are indicated in the list of

references in the usual manner. Second-hand references should only be used if the

original publication is unavailable. Any costs from interlibrary loans should be

discussed with the thesis supervisor.

6 REFERENCES

The references provided in the body of the text point the reader to a list of cited sources

at the end of the thesis, titled References. References in the text and the list must

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match one another so the reader can easily find the correct source of information. The

list must include all of the references used (except personal communications) in

alphabetical order by the last name of the author(s).

As a rule, sources are listed in such detail that they can be unmistakably identified and

traced. Appendix 3 provides examples of ways to document different types of sources.

The list of references typically contains the following information:

x Author(s) x Year of publication x Title x For online sources, the URL address, date of the most recent update

(if available) and the date on which the source was viewed or

retrieved (if the source cannot be downloaded or retrieved, use the

phrase available from, otherwise use retrieved from)

x Edition used (if several available) x Place of publication (publishers city) x Publisher or conference organiser x Editor(s) of collected work x Title of collected work x Page numbers of an article in a collected work, publication series or

periodical; total number of pages of non-serial publications

x Title of publication series or periodical x Number of volume x Number of issue (indicated after the volume only if page numbering

does not continue from one issue to another in series and periodicals)

x Conference name, date and venue x Type and storage location of unpublished and unprinted sources x Page numbers of articles

Any lines following the first line of a reference are indented by 57 mm.

6.1 Authors

The author is identified by the last name, followed by a comma, a space and the

initial(s) of the authors first name. If the publication has two authors, their last names

are separated with an ampersand (&). In the case of three or more authors, the names of

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the first authors are separated with a comma and the two last with an ampersand.

Publications by the same author are listed in chronological order unless they can be

arranged alphabetically by the second (and following) author(s). Publications with no

individual author are listed according to the corporate author or title of publication, and

the author is given as Anon..

6.2 Date of publication

The name of the author is followed by the year of publication and a full stop.

Publications from the same author in the same year are each identified with a lower case

letter placed after the year without a space. For unpublished works, indicate the year in

which they were produced. If the information is unavailable, indicate this as n.d., for

no date, in brackets. For reprinted works, provide the years of both the first print and

the reprint (1775, reprinted 1986).

6.3 Title of publication

The year of publication is followed by the title of the work and a full stop. Italicise any

genus or species names according to the same conventions used in the text body. Titles

are written with lower-case initials, apart from the first word. In German-language

publications, however, all nouns are written with initial capital letters. Many American

journals capitalise all of the nouns in their titles, but in the list of references these should

be replaced with lower-case letters. In non-serial publications (books and conference

proceedings) written in Finnish, only the first word has an initial upper-case letter.

However, the nouns forming the title of an English-language non-serial publication are

written with initial capitals. Examples of titles are provided in Appendix 3.

6.4 Serial publications

Serial publications are issued regularly or irregularly under a single title. They include

scientific journals, as well as report and other publication series. The title of the

publication is followed by the full name of the serial, written with initial capital letters,

except for prepositions, articles and conjunctions (for example, Journal of the Science of

Food and Agriculture).

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The name of the serial is followed by the volume number. If the volumes are

unnumbered, indicate the number and year of the issue. If the volume includes several

issues, each with its own page numbering, indicate the number of the issue after the

volume number, separated by a comma. The number of the volume is followed by a

colon, the first and last page numbers of the publication separated by a hyphen, and

finally a full stop.

6.5 Monographs

A monograph (such as a book, conference proceedings or encyclopaedia) consists of

one more volumes and forms a single entity. For monographs, indicate the edition (if

not the first), place of publication, publisher and number of pages.

Academic volumes and conference proceedings can often be referred to as collected

works, in which each chapter is written by an individual author. Use the authors name

to refer to an individual article in collected works. In the list of references, give the

author, year of publication and article title, the same way you would for serial

publications. The article title is followed by In:, the name(s) of the editor(s) of the

collected work, brackets containing the abbreviation ed. or eds., and the title of the

collected work. Lastly, indicate the place of publication, the name of the publisher, as

well as the page numbers of the chapter or article.

Conference proceedings are cited in the same way as scientific publication series or

collected works, depending on whether the publication has an editor. Conference

organisers must be specified in such detail that interested readers can easily find the

publication.

7 TABLES AND FIGURES

Tables are used to present numerical or other data in a compact, structured format. They

are often the best alternative for long lists, as well as summarised statistical analyses

and numerical test results. Figures are used to provide an illustrative description, and the

matters presented in them must always be explained to the reader in the body of the text.

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Results may not be presented as both a table and a figure. Appendix 4 contains

examples of tables and figures picked from original scientific articles.

Tables and figures are titled and numbered separately and sequentially. The titles must

provide a detailed and specific description of the content. Table titles appear above the

table, and figure titles below the figure. Any source reference, followed by a full stop, is

placed at the end of the title. Tables and figures are presented and usually referred to

in numerical order and they should be placed close to the text referring to them.

Moreover, paragraphs must always begin with text, never with a figure or table. Tables,

figures and appendices must be clear enough for the reader to understand them without

recourse to the body of the text.

Each figure, table and appendix must be referred to in the body of the text (Table 1,

Figure 1). Diagram axes must be named and their units of measurement clearly

indicated. No abbreviations, except for units of measurement, should be used in tables

and figures. However, if they are unavoidable (for example, in column headings), you

should also explain the meaning of each abbreviation in the title or legend of the table or

figure. Mean values are usually used in tables and figures that illustrate statistical

analyses. The number of observations (n) used to calculate the mean values must be

indicated, and usually a measure of variation, such as standard deviation (SD) or

standard error (SE), is also provided. Two blank lines are left above and below tables

and figures. The recommended width is the column width used in the body of the text.

Tables are a good way to depict results, especially when a graphical presentation cannot

be used. The columns are usually used for dependent variables or key statistics, while

the rows depict treatments or sample members. For large tables, you may use a font size

10 and/or a landscape layout. Horizontal lines are used under column headings and at

the end of tables, and columns are separated from one another with sufficient space.

Data in columns is decimal-aligned, the comma being used as the decimal separator (for

examples, see Tables 1 and 2 in Appendix 4).

Since figures usually make the results much easier to interpret, their use is highly

recommended. The word figure is collectively used to refer to scatter and column

diagrams, graphs, charts, drawings, photos and other types of visuals. In figures

depicting results, the sample points are connected with a dotted line only if the values

19

between the points can be deduced (continuous variable). Regression lines or other

corresponding statistical graphs should not extend beyond the measured values. The

same symbol or colour coding should be used systematically for a single treatment or

test subject throughout the thesis. Use the same font as you do elsewhere in the text.

Even though no official font size requirements have been defined for figures, avoid a

size smaller than 10 and always ensure your figures are clear and reliable.

If you plan to use a figure created by someone else, you should request permission from

the creator or publisher. If you cannot get such permission, you may draw your own

version of the figure, where applicable. In this case, the main terms must be included in

the figure or its caption in the language of the thesis. A reference to the source in which

the figure was originally published must be added to borrowed figures and figures

drawn from model. The permission obtained for a borrowed figure must also be

mentioned in the caption (e.g., Permission to publish the figure obtained from XX).

8 LAYOUT

The title of the thesis is written on the first page using capital letters, bolding and a font

size of 14 pt. Use bolding and a font size of 14 pt also for main headings. First-level

subheadings have a font size of 12 pt and they also are bolded. Second-level

subheadings have a font size of 12 pt. Do not use bolding for them. The text of the

thesis is printed on A4 size paper, using line spacing of 1.5, a clear font face and a font

size of 12 pt.

Closer line spacing can be used in tables and figures. Leave a left margin of 45 cm for

binding. The right margin is 2 cm, and the top and bottom margins 22.5 cm. For two-

sided printing, the inside margin is 4 cm and the outside margin 2 cm. Use justified

text alignment and disable automatic hyphenation in English-language theses (in

contrast to theses written in Finnish, in which hyphenation is used).

Leave one blank line between headings and text, as well as between paragraphs. Pages

are numbered with Arabic numerals, starting with the title page, but do not display page

numbers until the first page of the actual body text. In other words, no page numbers

should appear on the title page, abstract and table of contents, although they are

included in the numbering. Page numbers are placed at the top of the page and centred.

20

The thesis template provides further information on the layout. The abstract is drawn up

on a form specifically designed for this purpose and included in the template file.

Instructions on binding are provided in Chapter 11.

9 EXAMINATION AND GRADING OF THESES

It is a good idea to have at least one student peer read the thesis manuscript towards the

end of the writing process. Such peer evaluation is useful for both the feedback giver

and receiver. The manuscript is next submitted to the supervisor and thereafter to the

professor in the discipline or specialist option (unless the professor is also the

supervisor). The manuscript is then revised so it is acceptable in terms of both content

and layout. If required, have the English-language abstract checked and revised. Having

obtained permission from the supervisor or professor, the student holds a Masters

seminar presentation on the thesis topic. After this, the thesis can still be revised based

on, for example, the opponents comments.

The revised Masters thesis is submitted to the two examiners appointed by the

professor in the discipline or specialist option. One of the examiners usually comes from

the major subject department and the other one from outside the department. Masters

theses are assessed on a scale of seven Latin grades, using the matrix adopted by the

Faculty Council (http://www.helsinki.fi/af-

faculty/studies/forms/assessment_matrix_masters_thesis.pdf).

The Faculty Councils meeting schedule should be taken into consideration when

planning the completion and examination schedule for the Masters thesis jointly with

the professor in charge. The examination of Masters theses usually takes three to four

weeks, after which the professor in the specialist option proposes a grade based on the

examiners statements. The Faculty Council decides on the approval and grading of the

thesis. The thesis writer will be given the opportunity to object to the proposed grade

before it is discussed by the Faculty Council.

10 MATURITY TEST

21

In English-language Masters programmes students must also pass a written maturity

test to demonstrate their familiarity with the topic of the thesis and proficiency in the

English language.

The maturity test is arranged at a separately agreed time after or close to the completion

of the thesis. The test clearly defines the target group and style of writing to be a

popular scientific article for a trade journal. The topic deals with the students thesis or a

section of it. The maturity test is to be written at the student affairs office on a

workstation that is offline and has the spell checker disabled. The recommended length

of the written test is 4,0005,000 characters. The language will be evaluated by an

English-language revisor at the Language Centre, and the department will stand for the

costs incurred. Once the student has revised the test, the supervisor approves or rejects it

after considering the content and the revisors comments. Finally, the supervisor

provides feedback to the student in person and ensures that the approved maturity test is

entered in the Student Register.

11 BINDING OF FINAL THESIS AND SUBMISSION TO DEPARTMENT

The completed Masters thesis is to be copied and bound in soft or hard cover. The

student can freely choose the colour of the cover. One bound copy each is to be

submitted to the supervisor, the professor in the discipline or specialist option, the

departments student affairs office and the Viikki Campus Library. It is polite to submit

one bound copy to any outside sponsor of the thesis. The student may submit any

chosen number of bound theses to other cooperation partners.

All Masters theses completed at the Faculty of Agriculture and Forestry are stored in

the online HELDA archive

(http://www.helsinki.fi/library/viikki/digitalrepository/ethesis.html). The student is to

make PDF versions of the final thesis and abstract and email them to the Viikki Campus

Library (e-tutkielmat@helsinki.fi). Masters theses of the Faculty of Agriculture and

Forestry with a grade of Cum laude approbatur or higher may be published online

(http://ethesis.helsinki.fi/ohjeet/gradu.html, in Finnish), provided that the author has

given permission for publication. This is done by completing, printing and signing such

22

permission for online publication (http://www.helsinki.fi/af-faculty/studies/forms.html )

jointly with the thesis supervisor or professor in charge. If permission is granted, the

Viikki Campus Library makes the full text available online, and if not, it only publishes

the abstract. Students are encouraged to publish their work online, because the Internet

makes it easier for those interested in the topic to access the valuable information

contained in the thesis.

23

APPENDIX 1: SCIENTIFIC NAMES AND ABBREVIATIONS Names of species The first time an organism is mentioned in the text, it is called by its English name, followed by the scientific name in brackets. In the scientific name, both the genus and species are italicised and the genus capitalised. The scientific name also includes the full or abbreviated name of the authority (the person who named it). Cultivar names are written in inverted commas and not italicised. Examples:

Wild strawberry (Fragaria vesca L. Rgen) E. coli bacterium (Escherichia coli or E. coli)

Intra-specific hybrids (between two species of the same genus) have binary names, in which the species name is preceded by a cross depicting the hybrid (). The cross is the mathematical symbol for multiplication. It can be replaced by the lower-case letter x, written in Arial, size 10 pt. Examples:

Garden strawberry (Fragaria ananassa (Weston) Royer), or Garden strawberry (Fragaria x ananassa (Weston) Royer).

Abbreviations and units of measurement Abbreviations are usually avoided in theses, essays and reports. Common abbreviations (e.g., etc.) should always be written out in full. Abbreviations customarily used in a specific discipline can be used in the text, but sparingly. If specialised abbreviations, such as short forms of chemical compounds, need to be used frequently, they can be clarified in a list of abbreviations at the beginning of the thesis. If only a few abbreviations are used, however, such a list is not necessary. In this case, the name is written in full at first mention, followed by the abbreviation in brackets. Subsequently, the abbreviation can be used on its own. Genes, proteins and mutants Standard written forms are used for genes, proteins and mutants. When a gene is first mentioned in the text, its name is written out in full, followed by the abbreviated form in brackets. Abbreviations of plant genes are capitalised and italicised, those of proteins are capitalised but not italicised and those of mutants are written in lower-case letters and italicised. Examples of plant genes:

CHS, chalcone synthase gene CHS, protein coded by chalcone synthase chs, chalcone synthase mutant

As for bacterial genes, both the gene and mutant are written in lower-case letters and italicised. The names of bacterial proteins are capitalised (no italics). Examples of bacterial genes:

E. coli lacZ, -galactosidase gene LacZ, -galactosidase protein

24

lacZ, -galactosidase mutant Erwinia pel, pectate lyase gene Pel, pectate lyase protein pel, pectate lyase mutant

Gene fusions can be expressed with a colon and a dash, as in 35S:GFP or 35S-GFP. A lower-case p is used as the prefix for plasmids (pBR322) to distinguish them from promoters, which are written with a capital P (P35S). Units of measurement Two kinds of abbreviations are used for units of measurement. General-purpose abbreviations are used in public communication. SI units (defined in the International System of Units) are used in the jargons of mathematics, technology and the natural sciences, and in the contexts prescribed in the regulations for the SI system. Table 1 presents some of the most common SI units and their generally used abbreviations. Table 1. SI units and their abbreviations Unit of measurement

SI symbol

second s minute min hour h day d year a millimetre mm centimetre cm metre m kilometre km kilogram kg litre l are (100 sq. m) a hectare ha

For further information about the SI system, see: http://www.bipm.org/utils/common/pdf/si_brochure_8_en.pdf http://www.france-property-and-information.com/metric_conversion_table.htm Restriction enzymes The first three letters of restriction enzyme names are usually italicised, but the convention is changing and italics are becoming more of an alternative. Examples: SacI EcoRI BamHI.

25

Words or figures Whole numbers 110 and round numbers with a short spelling (hundred, thousand, million) are usually written out. Numbers 11 and above are expressed in figures. Figures are also used in connection with

a) several contrasting numbers (18 women and 7 men) b) abbreviations (5 kg, 7 km, 3).

N.B.! Exact, large amounts are written out in numerals: a grant of 1,000.

26

APPENDIX 2: RECTORS GUIDELINES FOR HANDLING CASES OF SUSPECTED PLAGIARISM Please read carefully the UH Rectors guidelines for handling cheating and plagiarism among students (10 pages) in this link: https://alma.helsinki.fi/download/2000000180533/Ohje_paatos_en.pdf (Alma-link)

27

APPENDIX 3: EXAMPLES OF DOCUMENTING REFERENCES

The list of references contains all the sources cited in the text, listed in alphabetical

order by the last name of the first author. The following examples show how different

types of sources are documented in the list of references.

1 Article in a serial publication Soimakallio, S., Mkinen, T., Ekholm, T., Pahkala, K., Mikkola, H. & Paappanen, T.

2009. Greenhouse gas balances of transportation biofuels, electricity and heat

generation in Finland Dealing with the uncertainties. Energy Policy 37: 80-90.

Uthayakumaran, S., Gras, P. W., Stoddard, F. L. & Bks, F. 1999. Effect of varying

protein content and glutenin-to-gliadin ratio on the functional properties of wheat

dough. Cereal Chemistry 76: 389-394.

2 Conference proceedings Stoddard, F. L. 2004. Starch granule size in wheat. In: Cauvain, S. P., Salmon, S. E. &

Young, L. S. (eds.). Using Cereal Science and Technology for the Benefit of

Consumers (Proceedings of the 12th ICC Cereal and Bread Congress, May 23 26

2004, Harrogate, UK). Cambridge, UK: Woodhead Publishing Ltd. s. 461-466.

Kymlinen, H.-R., Nykter, M. & Sjberg, A.-M. 2007. Cadmium and fatty acid

content of linseed in Finland. In: Lund, M., Larsen, T .U., Thgersen, J. O.,

Christensen, S., Brsting, C., Plauborg, F., Munkholm, L. J., Olesen, J. E., Callesen,

O., Askegaard, M., Hansen, J. G. & Hvelplund, T. (eds.). Trends and Perspectives

in Agriculture (NJF 23rd Congress, June 26-29 2007, Copenhagen, Denmark). NJF

Report 3 (2): 342-343.

3 Item in a collected work or standard ASAE S269.4. 1991. Cubes, pellets and crumbles definitions and methods for

determining density, durability and moisture content. 3 s. In: ASAE Standards

1993, s. 429-431.

Bardner, R. 1983. Pests of Vicia faba other than aphids and nematodes. In:

Hebblethwaite, P. D. (ed.). The Faba Bean (Vicia faba L.). London, UK:

Butterworths. s. 371-390.

28

4 Series of reports Uusitalo, M. 2004. European bird cherry (Prunus padus L.) a biodiverse wild plant for

horticulture. Agrifood Research Reports 62. Jokioinen, Finland: MTT Agrifood

Research Finland. 82 s.

5 Book Blackman, R. L. & Eastop, V. F. 2000. Aphids on the Worlds Crops. An identification

and information guide. 2nd ed. Chichester, UK: John Wiley & Sons Ltd. 476 s.

6 Electronic source FAO 2008. FAOstat. http://faostat.fao.org/default.aspx. Vienna, Austria: Food and

Agriculture Organization of the United Nations. Visited 12.10.2008.

FAOSTAT 2004. Means of production, agricultural machinery.

http://faostat.fao.org/site/421/default.aspx. Vienna, Austria: Database of Food and

Agriculture, Organization of the United Nations. Published 2004, visited 15.3.2006.

7 Unpublished or unprinted source Donner, J. 1998. Annalan huvila-alueen historia. Manuscript. Available at the Street and

Park Division of the Helsinki City Public Works Department. 36 pp.

8 Alphabetical ordering

As a rule, sources are listed in alphabetical order by the authors names. Publications by a

single author that cannot be listed alphabetically by the authors name are placed

chronologically from oldest to newest. Examples:

Smith, B. F. 2000 Smith, J. A. 1992 (chronological order) Smith, J. A. 1994 Smith, J. A. & Bloggs, F. B. 2003 (alphabetical order) Smith, J. A., Bloggs, F. B. & Jones, P. 1999a Smith, J. A., Bloggs, F. B., Jones, P. & Carr, S. T. 1999b Smith, J. A. & Chalmers, C. 2005 Smith, J. A., Jones, P. & Bloggs, F. B. 1998 Smithers Smyth

29

9 Example list of references Bardner, R. 1983. Pests of Vicia faba other than aphids and nematodes. In:

Hebblethwaite, P. D. (ed.). The Faba Bean (Vicia faba L.). London, UK:

Butterworths. s. 371-390.

Blackman, R. L. & Eastop V. F. 2000. Aphids on the Worlds Crops. An identification

and information guide. 2nd ed. Chichester, UK: John Wiley & Sons Ltd. 476 s.

Donner, J. 1998. Annalan huvila-alueen historia. Manuscript. Available at the Street and

Park Division of the Helsinki City Public Works Department. 36 pp.

FAO. 2008. FAOstat. http://faostat.fao.org/default.aspx. Vienna, Austria: Food and

Agriculture Organization of the United Nations. Visited 12.10.2008.

Stoddard, F. L. 2004. Starch granule size in wheat. In: Cauvain, S. P., Salmon, S. E. &

Young, L. S. (eds.). Using Cereal Science and Technology for the Benefit of

Consumers (Proceedings of the 12th ICC Cereal and Bread Congress, 23 26 May

2004, Harrogate, UK). Cambridge, UK: Woodhead Publishing Ltd., s. 461-466.

Uthayakumaran, S., Gras, P. W., Stoddard, F. L. & Bks, F. 1999. Effect of varying

protein content and glutenin-to-gliadin ratio on the functional properties of wheat

dough. Cereal Chemistry 76: 389-394.

Uusitalo, M. 2004. European bird cherry (Prunus padus L.) a biodiverse wild plant for

horticulture. Agrifood Research Reports 62. Jokioinen, Finland: MTT Agrifood

Research Finland. 82 s.

30

APPENDIX 4: EXAMPLES OF PRESENTING RESULTS IN TABLES AND FIGURES Table 1. Pearson correlation coefficients between properties of oat groats after steaming and tempering (n = 54 for moisture and temperature, n = 1080 for mechanical properties).

Moisture Temperature Height Maximum force

Number of peaks

Temperature -0.191 Height -0.274* -0.023 Maximum force -0.271* 0.012 0.290** Number of peaks 0.035 -0.101 0.089** 0.027 Final force -0.257** 0.037 0.174** 0.955** 0.022 *,** P < 0.05, 0.01, respectively

(Reference for this model table: Gates, F. K., Sontag-Strohm, T., Stoddard, F. L., Dobraszczyk, B. J. & Salovaara, H. 2008. Interaction of heat-moisture conditions and physical properties in oat processing: II. Flake quality. Journal of Cereal Science 48: 288-293) Table 2. Dough mixing and extension parameters in a set of eight lines of wheat differing in the presence of three high molecular weight glutenin subunits. Data show means of four replicates.

Genotype Mixing time (s)

Peak resistance

(N)

Resistance breakdown

(%)

Bandwidth breakdown

(%)

Extensi-bility (cm)

Maximum resistance to

extension (N)

+ + + 233 23.5 6.5 42.5 11.50 14.80 + + 170 24.6 17.0 53.0 13.85 9.83 + + 198 21.4 16.5 45.5 12.00 20.85 + + 82 16.8 26.5 43.0 2.95 5.82 + 96 23.0 20.5 50.5 9.40 11.32 + 98 20.0 22.0 52.5 8.45 6.12 + 96 20.2 27.0 29.5 2.85 13.57 91 15.6 16.5 38.0 4.10 7.50 Standard error

12 1.0 1.3 3.5 0.81 0.85

(Reference for this model table: Uthayakumaran, S., Beasley, H. L., Stoddard, F. L., Keentok, M., Phan-Thien, N., Tanner, R. I. & Bks, F. 2002. Synergistic and additive effects of the three high molecular weight glutenin subunit loci. I. Effects on wheat dough rheology. Cereal Chemistry 79: 294-300)

31

Figure 1. Effect of thidiazuron concentration (TDZ) on shoot development of Norway maple axillary bud explants in the first experiment. For each subculture, mean values with the same letter do not differ significantly at P < 0.05. Error bars show standard deviations (n = 3 5).

(Reference for this model figure: Lindn, L. & Riikonen, A. 2006. Effects of 6-benzylaminopurine, thidiazuron and type of explant on in vitro shoot proliferation of Acer platanoides L. Propagation of Ornamental Plants 6: 201-204)

a

a

ab

b

bb

bcc

b

b

b

a

a aa

a

0

0.5

1

1.5

2

2.5

3

1 2 3 4

Subculture (nr.)

Num

ber o

f nod

es

TDZ 0 M TDZ 0.01 M TDZ 0.1 M TDZ 1 M TDZ 5 M

32

Example of a drawing adapted from another source:

Figure 2. Pathways affecting flowering and stress responses as influenced by climate change in the boreal region. CBF/ DREBs (C-repeat Binding Factor/Dehydration-Responsive Element Binding factor) have a central role in cold acclimation and responses to abiotic stresses and are regulated by temperature and light. CBF activates COld-Responsive/Late Embryogenesis-Abundant (COR/LEA) genes that improve freezing, drought and salinity tolerance. Heat stress induces DREB2A that improves heat tolerance through the Heat Shock transcription Factor-Heat Shock Protein (HSF-HSP) pathway. Vernalization and CBF act in a coordinated fashion to regulate FLC (Flowering Locus C) that, in turn, regulates further downstream genes to induce flowering. Adapted from Chew & Halliday (2011). The source of the original drawing must be listed in the references: Chew, Y. H. & Halliday, K. J. 2011. A stress-free walk from Arabidopsis to crops. Current Opinion in Biotechnology 22: 281-286 (Reference for this model figure: Stoddard, F. L., Mkel, P. S. A. & Puhakainen, T. 2011. Adaptation of boreal field crop production to climate change. In: Blanco, J. & Kheradmand, H. (eds.). Climate Change Research and Technology for Adaptation and Mitigation. InTech - Open Access Publisher, Rijeka, Croatia, s. 403-430)

33

Example of an annotated photograph:

Figure 3. Photograph of the trial site after the November 2010 harvest. Numbers show replicates, letters indicate crop composition of the main plot: B = Bromus, F = fallow, G = Galega, M = Bromus-Galega mixture. Photo by the author. (Reference for this model photo: Stoddard, F.L, Univ. of Helsinki) Example of an image taken from the internet:

Figure 4. Faba bean leaves showing damage at the edges due to Sitona lineatus weevils. (Wikipedia: http://commons.wikimedia.org/wiki/File:Tuinboon_bladrandkever.jpg. Published 2005, visited 1.8.2012 (picture is in the public domain).

34

(A) (B) (C) (D) Figure 5. DNA, RNA and protein analysis of tobacco plant leaves (generation T0) transformed with the F4 ETEC fimbrial gene, faeG. Numbering from 6.1 to 6.12 refers to individual transgenic plants. C, non-transgenic control plant. (A) Schematic presentation of the plant transformation vector T-DNA regions. p35S, cauliflower mosaic virus 35S promoter; SS, apoplast-targeting signal sequence from barley trypsin inhibitor; 3nos, 3 untranslated region of the nopaline synthase gene from A. tumefaciens C58; pnos, nopaline synthase gene promoter; neo, Neomycin phosphotransferase; 3ocs, 3 untranslated region of the octopine synthase gene from A. tumefaciens C58; RB and LB, right and left borders, respectively, of the T-DNA. (B) DNA hybridization analysis indicating the copy number of the transgene faeG. A total of 10 g of HindIII-digested DNA per lane was separated in an 1% agarose gel and hybridized with a faeG PCR fragment. Kb, DNA size standard in kilobases. (C) RNA hybridization analysis showing the amount of the faeG-specific mRNA. A total of 10 g of total RNA per lane was separated in an 1% agarose gel and hybridized with a faeG PCR fragment. Kb, RNA size standard in kilobases. (D) Immunoblot analysis detecting the FaeG protein produced in the transgenic plants. A total of 20 g of total soluble protein per lane was separated in a 10% SDS-PAGE gel and immunodetected with a polyclonal anti-FaeG serum. KDa, protein size standard in kilodaltons. (Reference for this model figure: Van Molle, I., Joensuu, J. J., Buts, L., Panjikar, S., Kotiaho, M., Bouckaert, J., Wyns, L., Niklander-Teeri, V. & De Greve, H. 2007. Chloroplasts assemble the major subunit FaeG of Escherichia coli F4 (K88) fimbriae to strand-swapped dimers. Journal of Molecular Biology 368: 791-799)

1 INTRODUCTION2 GOALS OF THE THESIS3 STRUCTURE OF THE THESIS4 CONTENT OF THE THESIS4.1 Title page4.2 Abstract4.3 Table of contents4.4 Abbreviations and concepts4.5 Introduction4.6 Literature review4.7 Research objectives4.8 Materials and methods4.9 Results4.10 Discussion4.11 Conclusions4.12 Acknowledgements4.13 List of references4.14 Appendices

5 REFERENCING6 REFERENCES6.1 Authors6.2 Date of publication6.3 Title of publication6.4 Serial publications6.5 Monographs

7 TABLES AND FIGURES8 LAYOUT9 EXAMINATION AND GRADING OF THESES10 MATURITY TEST11 BINDING OF FINAL THESIS AND SUBMISSION TO DEPARTMENTAPPENDIX 1: SCIENTIFIC NAMES AND ABBREVIATIONSAPPENDIX 2: RECTORS GUIDELINES FOR HANDLING CASES OF SUSPECTED PLAGIARISMAPPENDIX 3: EXAMPLES OF DOCUMENTING REFERENCESAPPENDIX 4: EXAMPLES OF PRESENTING RESULTS IN TABLES AND FIGURES