1. An Approach to Academic Writing By Dr Nora Jullok School of Bioprocess Engineering Universiti Malaysia Perlis

2. Importance of an FYP thesis Explanations –Audience –Purpose and strategy –Organization –Style –Flow –Presentation –Positioning Language Foci –The vocabulary shift –Formal grammar style –Linking words and phrases –This + summary word Q&A Presentation Outline: Part I

3. Close the gap between research and teaching Answer interesting research questions Test your ability to do research FYP’s Purpose Test your ability to disseminate your findings

4. Explanations AUDIENCE An understanding of your audience’s expectations and prior knowledge audience.pdf PURPOSE & STRATEGY Audience, purpose and strategy are typically interconnected To display familiarity, expertise, and intelligence Strategy.pdf ORGANIZATION Information is presented to readers in a structured format. Organization.docx STYLE - Academic or non-academic writing FLOW -establishing a clear connection of ideas PRESENTATION -number of errors; preposition; homophones, basic grammar errors

5. Style Academic writers need: –To be sure that their communications are consistent and appropriate both for the message being conveyed and for the audience. –Know what is considered academic and what is not.

6. Cont…. Grammar check program on PC: –Find spelling errors –Basic grammar errors –Not to offer stylistic advice for academic writers.

7. Language focus: The vocabulary shift Choosing the more formal alternative when selecting a verb, noun, or other part of the speech. Verbs: English often has 2 or more choices to express an action or occurrence. For written academic style, there is a tendency for academic writers to use a single verb wherever possible.

8. Language focus: The vocabulary shift Example: –According to some biologist, coming up with clear proof of the decreasing numbers of frogs has been difficult. (Less formal style)  –According to some biologist, offering clear proof of the decreasing numbers of frogs has been difficult. (Academic style)

9. Language focus: The vocabulary shift Task Eight: Review / maintain / develop / cause / eliminate / reach / determine / investigate / decrease / constitute 1. Scientists are looking into innovative ways to combat AIDS 2. The purpose of this paper is to try to figure out what is lacking in our current understanding of corrosion and corrosion protection in concrete.

10. Language focus: The vocabulary shift Task Eight: Review / maintain / develop / cause / eliminate / reach / determine / investigate / decrease / constitute 3. Rice and aquatic products make up a major part of the diet of the people in the Mekong Delta, Vietnam. 4. Worldwide consumption of pesticides has gone up to 2.6 million metric tons..

11. 1. Generally avoid contractions (but keep in mind that in some fields it may be OK to use them). Export figures won't improve until the economy is stronger Export figures will not improve until the economy is stronger. 2. Use the more appropriate formal negative forms. not... anyno Not…muchlittle Not…manyfew 3. Limit the use of “run-on” expressions, such as and so forth and etc. This semiconductors can be used in robots, CD players, etc. These semiconductors can be used in robots, CD players, and other electronic devices. Language focus: Formal Grammar Style

12. 4. Avoid addressing the reader as you (except, of course, if you are writing a textbook or other instructional materials). You can see the results in Table 1The results can be seen in Table 1. 5. Be careful about using direct questions. In some fields they are common, while in others they are not. What can be done to lower the costs?It is necessary to consider how costs may be lowered. 6. Place adverbs within the verb. Actually, very little is known about the general nature and prevalence of scientific dishonesty. Very little is actually known about general nature and prevalence of scientific dishonesty. Language focus: Formal Grammar Style

13. 7. Consider whether you should split infinitives. We need to adequately meet the needs of those enrolled in the program. Neural networks have the ability to correctly classify new patterns. 8. Aim for an efficient use of words; Use as many words as you need to express your points; try to use no more than you really need. It may be difficult to make a decision about the method that we should use. Choosing the proper method may be difficult. Language focus: Formal Grammar Style

14. Flow Another important consideration for successful communication. Clear connection of ideas help reader follow the text.

15. Language focus: Linking Words and Phrases

16. Sentence connectors raise a small, but important, issue-namely-punctuation. A few key points: –Semicolons (;) –Colon (:) –Dashes (-) –Commas (,)

17. Language focus: Linking Words and Phrases PUNCTUATIONUse Semicolons (;)- To join 2 completely independent sentences and work much like a full stop. e.g., Air traffic delays due to high traffic volume have increased considerably over the last decade; these delays have become a major public policy issue. -Sentence connectors -Can be used to chunk longer sentences into parts. -Can be used to separate rather long items in a list. Colons (:)Use to introduce a list Dashes (-)Use to introduce a list as well with some additional information. Commas (,)Used in variety situations such as: -Conjunction (such as and, but, or) -Subordinator (such as although, if, whereas) -If there is no second clause initiator (such as thus or because), punctuation depends on the kind of clause being joined

18. Language focus: This + summary word Another to maintain flow is to use this/these +a noun to join ideas together. –E.g., UniMAP lecturers know that students need to understand the differences between formal and informal language. However, this understanding cannot usually be acquired quickly.

19. Task 18 Choose a summary word from the list to complete each sentence. Can you think of other possible summary words in addition to those on the list? Process / problem / finding / disruption / estimation / view / situation / difficulty 1. The traditional economic and consumer behavior models assume a rational, thoughtful consumer who gathers information about a good and then carefully makes a purchase. This_______has recently been challenged, particularly because of the growing number of consumer choices.

20. Have you ever experienced this?

21. 5 minutes break

22. Abstract Introduction Literature Review Materials and Methods Results and Discussion Conclusion, Recommendation References Part II: Body of the Thesis

23. Kindergarten Vs University

24. For maximum clarity and consistency, write your manuscript in this order: The ‘write’ order Methods Results Methods Results Introduction Discussion Introduction Discussion Abstract Title Abstract Title Write during the research process Write after obtaining/analyzing your results Write last

25. 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

26. Introduction Example

27. 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 Beginning

28. Introduction Providing background statistics DO cite the references Figures must be clear, not blurry Label each figure/table, eg. Figure 1.1

29. 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 Middle

30. Clearly state the aims/scope of your study State the methods you will use to carry out your aims Introduction End

31. 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 Background

32. 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 xylose- fermenting S. cerevisiae strains. Thus, focused basic research is expected to identify genes responsible for high-temperature fermentation. Research question

33. Introduction Example 1.5 Research Approach How you will answer the research question 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 cross- profiling. 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.

34. 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? Literature Review What is your hypothesis? DO cite references.

35. 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 high- temperature stress is still lacking. Literature Review Example

36. Clear subheadings Describe methods in the past tense Methods must be described in sufficient detail so that other researchers can reproduce the experiment Methods How did you carry out your work? Describe statistical tests used Include setup figures if necessary

37. 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

38. Figure 3.1 A 100 ml fermentation bottle 3.3 Fermentation conditions 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 MgSO 4, 2  g/L ZnSO 4, 10  g/mL pantothenate and 0.1  g/L biotin. Batch fermentation was carried out in a 100-mL bottle with a CO 2 outlet (Figure 3.1).

39. 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 UV- mini (Shimadzu).

40. 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. Results What did you find?

41. What does your result means? This part should answer your research question in the Introduction part. Discussion So what?

42. Restate the research question (1-2 sentence) ALWAYS provide the major/main results first Give your conclusions, based on the results Result & Discussion Beginning Answer the research question

43. Interpret the results Compare your results with those from other studies –Same or different? –Possible reasons why? Result & Discussion Middle

44. Mention possible applications, implications and speculations, if appropriate Suggest future work if necessary Result & Discussion End

45. Result & Discussion Example 0 mM furfural70 mM furfural Figure 4.1 Performance of S. cerevisiae with and without the presence of 70 mM furfural REMEMBER to have a control!

46. Result & Discussion Example

47. Tell them again what you told them, in one paragraph. Conclusion

48. 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.

49. 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, 9965- 9969. 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. References Example

50. Readers want to know ‘who’s the killer’ from the start Concise (? Words) Describe your research question Objectives/hypotheses Abstract Techniques; avoid details Most important results Concluding statement

51. Abstract Example 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.

52. Must be specific, catchy Fewest possible words that adequately describes the contents The Title

53. Common mistakes The material from the river was compared with the mountain The material from the river was compared with that from the mountain

54. Saccharomyces cerevisiae (Use the full name only for the first time) Second time onwards, use S. cerevisiae only Common mistakes

55. Reactions with the new cycler were faster. Faster than what? Reactions with the new cycler were faster than those with the old cycler.

56. 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 Abstract

57. 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 Introduction

58. 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.. Useful set phrases Results & Disc

60. Presentation Outline