How to Write an Effective
FYP Thesis
By
Dr Ku Syahidah Ku Ismail
School of Bioprocess Engineering
Universiti Malaysia Perlis
Presentation Outline
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Importance of an FYP thesis
Thesis Body
Common mistakes
Useful set phrases
Q&A
FYP’s Purpose
• Close the gap between research and
teaching
• Answer interesting research questions
• Test your ability to do research
• Test your ability to disseminate
your findings
Thesis writing
• You are writing a story
(Beginning  Middle  End)
• Tell them what you are going to tell them
• Must be easy to read and easy
to understand
• Minimize confusion – maximize
understanding
• English check
Body of the Thesis
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Abstract
Introduction
Literature Review
Materials and Methods
Results and Discussion
Conclusion, Recommendation
References
Have you ever experienced this?
The ‘write’ order
For maximum clarity and consistency, write
your manuscript in this order:
• Methods
• Results
• Introduction
• Discussion
• Abstract
• Title
Write during the research process
Write after obtaining/analyzing your results
Write last
Writing the Introduction
Why is this study interesting?
What has been studied
previously?
What is your
research
question?
How are
you going to
answer it?
The proportion
Introduction Example
Introduction Beginning
• Provide background information to put
your work into context
• DO NOT write a comprehensive literature
review of the field – remember you have a
Literature Review chapter!
• DO cite reviews that readers can refer to if
they want more information
Introduction Providing background statistics
DO cite the references
Figures must be clear, not blurry
Label each figure/table, eg. Figure 1.1
Introduction Middle
• What is the rationale/reason for your
study?
• Explain how you addressed the problem
(1-2 sentence)
• DO NOT state results from your study.
Introduction End
• Clearly state the aims/scope of your study
• State the methods you will use to carry out
your aims
Introduction Example
Ethanol derived from biomass sources is one of the
options for renewable energy which is currently gaining
prominence globally. Lignocellulosic biomass, which
consists of lignin, cellulose, hemicelluloses, and various
extractives (Jeffries and Jin, 2000) is becoming one of
the essential resources for bioethanol production since it
does not compete with food supplies. There are about
73.9 teragrams of crop residues in the world that could
produce 49.1 gigaliters of ethanol per year (Kim and
Dale, 2004). Besides glucose, the pentose sugar xylose
is the major carbohydrate component of hemicellulose
and is the carbon source of interest.
Introduction Example
Previous work done
Significant advances in improving strain performance for bioethanol
production have been developed in the past few decades since wild-type
S. cerevisiae is not capable of utilizing xylose as a carbon source. This
has been practiced by overexpressing the genes from S. stipitis
encoding xylose reductase (XR) and xylitol dehydrogenase (XDH).
Ethanol production was enhanced by overexpressing the endogenous
XK gene encoding xylulokinase (Chu and Lee, 2007; Jeffries and Jin,
2000; Kim et al., 2011). On the other hand, genetic engineering
strategies that have addressed yeast tolerance to elevated temperature
are rare (Benjaphokee et al., 2012; Prasetyo et al., 2011). To date, there
have been no reports on the improvement of thermotolerance of xylosefermenting S. cerevisiae strains. Thus, focused basic research is
expected to identify genes responsible for high-temperature
fermentation.
Research question
Introduction Example
1.5 Research Approach
In this work, industrial S. cerevisiae strains that are able to tolerate
temperatures up to 38C were isolated. In addition to the competency of
withstanding high temperature, the ability to ferment xylose was conferred to
the thermotolerant strains through genetic engineering. The performance of 8
genetically modified industrial strains and 1 genetically modified lab strain
fermenting xylose at 38C were highlighted and the expression of genes
differentially regulated at high temperature that might lead to the
thermotolerance phenotype was characterized. This was done by comparing
the levels of gene expression between the best and poor strains by crossprofiling. An intense search for specific genes resulted in a list of genes
commonly expressed by the top 3 ethanol producers. Therefore, the
differentially expressed genes were identified, and then hypothesized
whether they are involved in tolerance to high temperature.
How you will answer the research
question
Literature Review
• How does your research relate to the
past?
• What were the earlier studies?
• How did this lead to more recent studies?
• How is your work different?
• What is your hypothesis?
• DO cite references.
Literature Review Example
To elucidate the mechanism underlying the orchestration of gene
expression under certain stress conditions, we used a high-throughput
measurement technology, performing transcriptomics extensively with a
DNA microarray system. A number of researchers have investigated the
primary gene networks that control the following; adaptation to high sugar
stress (Erasmus et al., 2003), the mechanism of alcohol tolerance
(Hirasawa et al., 2007; Hong et al., 2010; Li et al., 2010a), the adaptation to
cultivation in molasses medium in fed-batch culture (Shima et al., 2005),
genes response during glucose and xylose co-fermentation (Sedlak et al.,
2003), the heat shock response (Boy-Marcotte et al., 1999) and adaptation
to high pressure environment (Fernandes et al., 2004). Most of the previous
gene profiling work on thermotolerant S. cerevisiae has focused on glucose
as the carbon source (Boy-Marcotte et al., 1999; Shahsavarani et al., 2011;
Ye et al., 2009). However, the transcriptome of recombinant S. cerevisiae
cultivated on xylose is different (Van Vleet and Jeffries, 2009). Thus, the
understanding of how the cells produce ethanol from xylose under hightemperature stress is still lacking.
Methods How did you carry out your work?
• Clear subheadings
• Describe methods in the past tense
• Methods must be described in sufficient
detail so that other researchers can
reproduce the experiment
• Describe statistical tests used
• Include setup figures if necessary
Materials and Method Example
3.1 Microbial strains and media
Escherichia coli NovaBlue (Novagen, Inc., Madison, WI)
was used as the host strain for recombinant DNA
manipulation. E. coli was grown in Luria-Bertani medium
(10 g/L peptone, 5 g/L yeast extract, and 5 g/L sodium
chloride) containing 100 mg/L ampicillin. S. cerevisiae
strains were routinely cultivated at 30ºC in synthetic
medium [SD medium; 6.7 g/L yeast nitrogen base
without amino acids (Difco Laboratories, Detroit, MI), 20
g/L glucose] supplemented with appropriate amino acids
and nucleotides, and in YPD medium (20 g/L peptone,
10 g/L yeast extract, 20 g/L glucose).
Materials and Method Example
3.3 Fermentation conditions
Figure 3.1 A 100 ml fermentation
bottle
Fermentation medium consisted of
0.5% (v/v) corn steep liquor (CSL)
(Sigma-Aldrich, Tokyo, Japan), 5 g/L
urea, 50 g/L xylose, 1 g/mL
pyridoxin-HCl, 1 g/mL thiamine-HCl,
1 g/L MgSO4, 2 g/L ZnSO4, 10
g/mL pantothenate and 0.1 g/L
biotin. Batch fermentation was carried
out in a 100-mL bottle with a CO2
outlet (Figure 3.1).
Materials and Method Example
Figure 3.2 Experimental setup
Temperature was controlled by placing
the bottles in a water bath equipped
with a magnetic stirrer (Figure 3.2).
Fermentation temperature was set to
38C with stirring at 500 rpm. Samples
were taken at 0, 4, 8, 12, 24 and 48 h of
fermentation. The xylose, ethanol,
xylitol and glycerol concentrations were
determined by high-performance liquid
chromatography (Shimadzu, Kyoto,
Japan) with a refractive index detector.
The eluent used was MilliQ water with a
flow rate of 0.6 mL/min. The column
used was a Shim-Pack SPR-Pb
(Shimadzu) with the oven temperature
set to 80C. Cell growth was monitored
by determination of optical density at
600 nm using a spectrophotometer UVmini (Shimadzu).
Results What did you find?
• Use subheadings
• Use past tense to describe results
• BUT refer to figures and tables in the
present tense
• DO NOT replicate data among figures,
table and text.
Discussion So what?
What does your result means?
This part should answer your research
question in the Introduction part.
Result & Discussion Beginning
• Restate the research question (1-2
sentence)
• ALWAYS provide the major/main results
first
• Give your conclusions, based on the
results
• Answer the research question
Result & Discussion Middle
• Interpret the results
• Compare your results with those from
other studies
– Same or different?
– Possible reasons why?
Result & Discussion End
• Mention possible applications, implications
and speculations, if appropriate
• Suggest future work if necessary
Result & Discussion Example
0 mM furfural
70 mM furfural
Figure 4.1 Performance of S. cerevisiae with and without the presence
of 70 mM furfural
REMEMBER to have a control!
Result & Discussion Example
Conclusion
Tell them again what you told them, in one
paragraph.
Conclusion Example
The performance of 8 genetically modified industrial strains with enhanced ability
to consume xylose was tested in fermentation at elevated temperature. Using a
cross-profiling strategy, the 3 best ethanol-producing strains at 38C were found
to have the same reaction towards high temperature by strengthening their cell
walls and manipulating expression of metabolic pathway genes. FLO genes were
highly induced under high temperature conditions with the yeast strains, probably
as a defense mechanism to protect the cells from high temperature. Most genes
which showed substantial up-regulation during the heat stress condition were the
same genes that enhance ethanol tolerance. So far, it seems that the genetically
modified industrial xylose-utilizing yeasts have a similar mechanism for tolerating
heat stress as other microorganisms. However, many details such as the
interactions between the genes and the roles of certain regulated genes remain
to be discovered. This report serves to provide additional details on global gene
profiling in the interest of producing a robust microorganism for high-temperature
ethanol production. The direction of future hemicellulose conversion research
would be much simplified by the development of such a robust biocatalyst.
References Example
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Alepuz, P.M., Cunningham, K.W., Estruch, F., 1997. Glucose repression affects ion
homeostasis in yeast through the regulation of the stress-activated ENA1 gene. Mol.
Microbiol. 26, 91-98.
Bajwa, P.K., Phaenark, C., Grant, N., Zhang, X., Paice, M., Martin, V.J.J., Trevors,
J.T., Lee, H., 2011. Ethanol production from selected lignocellulosic hydrolysates by
genome shuffled strains of Scheffersomyces stipitis. Bioresour. Technol. 102, 99659969.
Benjaphokee, S., Koedrith, P., Auesukaree, C., Asvarak, T., Sugiyama, M., Kaneko,
Y., Boonchird, C., Harashima, S., 2012. CDC19 encoding pyruvate kinase is
important for high-temperature tolerance in Saccharomyces cerevisiae. N.
Biotechnol., 166-176.
Bester, M.C., Jacobson, D., Bauer, F.F., 2012. Many Saccharomyces cerevisiae Cell
Wall Protein Encoding Genes Are Coregulated by Mss11, but Cellular Adhesion
Phenotypes Appear Only Flo Protein Dependent. G3 (Bethesda, Md.). 2, 131-141.
Boy-Marcotte, E., Lagniel, G., Perrot, M., Bussereau, F., Boudsocq, A., Jacquet, M.,
Labarre, J., 1999. The heat shock response in yeast: differential regulations and
contributions of the Msn2p/Msn4p and Hsf1p regulons. Mol. Microbiol. 33, 274-283.
Abstract
• Readers want to know ‘who’s the killer’
from the start
• Concise (? Words)
• Describe your research question
• Objectives/hypotheses
• Techniques; avoid details
• Most important results
• Concluding statement
Abstract Example
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Production of ethanol from xylose at high temperature would be an economical
approach since it reduces risk of contamination and allows both the saccharification
and fermentation steps in SSF to be running at elevated temperature. Eight
recombinant xylose-utilizing Saccharomyces cerevisiae strains developed from
industrial strains were constructed and subjected to high-temperature fermentation at
38C. The best performing strain was sun049T, which produced up to 15.2 g/L
ethanol (63% of the theoretical production), followed by sun048T and sun588T, both
with 14.1 g/L ethanol produced. Via transcriptomic analysis, expression profiling of
the top three best ethanol producing strains compared to a negative control strain,
sun473T, led to the discovery of genes in common that were regulated in the same
direction. Identification of the 20 most highly up-regulated and the 20 most highly
down-regulated genes indicated that the cells regulate their central metabolism and
maintain the integrity of the cell walls in response to high temperature. We also
speculate that cross-protection in the cells occurs, allowing them to maintain ethanol
production at higher concentration under heat stress than the negative controls. This
report provides further transcriptomics information in the interest of producing a
robust microorganism for high-temperature ethanol production utilizing xylose.
The Title
• Must be specific, catchy
• Fewest possible words that adequately
describes the contents
Anything wrong with this title?
“Characterization of Bacteria Causing
Cancer by Gas Chromatography”
Common mistakes
The material from the river was
compared with the mountain
The material from the river was
compared with that from the mountain
Common mistakes
• Saccharomyces cerevisiae (Use the full
name only for the first time)
• Second time onwards, use S. cerevisiae
only
Common mistakes
Reactions with the new cycler were
faster.
Faster than what?
Reactions with the new cycler were
faster than those with the old cycler.
Useful set phrases Abstract
• These results shows …
• To test whether (past tense), we
performed…
• To examine if (past tense) we (past tense)
• We used XX to YY. Using this approach,
we identified ZZ.
Useful set phrases Introduction
• Previous studies have shown that..
• The topic of XX has recently been
reviewed (insert reference).
• To determine whether…
• The purpose of this study was..
• Therefore, we tested the hypothesis..
• In this study, we sought to extend our
observations and specifically test the..
Useful set phrases Results & Disc
• The results are summarized in Table 1.
• Figure 2a shows the effect of X on Y.
• Group X showed higher/lower levels of Y
than the control group.
• In the current study, it is shown that..
• Taken together, this results suggest..
• The data supports the idea that XX..
• Our study is limited by..
Presentation Outline