Sample Honours Thesis Table of Contents

Please note: this is only an example. Each School has its own specifications, some of which are stricter than others. Furthermore, each thesis is different and will have different emphases on particular sections. CHECK with your supervisor for advice on length of sections and of the thesis as a whole.

Sample: from the School of BABS, UNSW

table of contents

ABSTRACT I

TABLE OF CONTENTS II

ACKNOWLEDGEMENTS V

LIST OF TABLES VI

LIST OF FIGURES VII

LIST OF ABBREVIATIONS VIII

1 INTRODUCTION 1

1.1 HEPATITIS C VIRUS 1

1.1.1 DISCOVERY 1

1.1.2 EPIDEMIOLOGY 2

1.1.3 PATHOGENESIS 2

1.1.4 TREATMENT 3

1.2 MOLECULAR BIOLOGY 3

1.2.1 STRUCTURE OF GENOME 3

1.2.2 GENETIC VARIATION 6

1.2.3 GENOTYPIC DIFFERENCES 8

1.3 RNA DEPENDENT RNA POLYMERASE ACTIVITY 9

1.3.1 POLYMERASE FUNCTION 9

1.3.2 MODEL SYSTEMS OF HCV REPLICATION 11

1.3.3 GENOTYPE SPECIFIC STUDIES 11

1.3.4 BIOCHEMICAL PROPERTIES 12

1.4 KUNJIN VIRUS RNA DEPENDENT RNA POLYMERASE 13

1.5 CONCLUSION 15

1.6 AIMS AND HYPOTHESIS 16

2 MATERIALS AND METHODS 17

2.1 HCV POSITIVE SERA SAMPLES 17

2.2 RNA EXTRACTION 17

2.3 CDNA SYNTHESIS 17

2.4 HCV PRIMER DESIGN AND USAGE 18

2.5 NESTED POLYMERASE CHAIN REACTION (NPCR) 21

2.5.1 REACTION AND CYCLING CONDITIONS 21

2.5.2 PCR PRODUCT PURIFICATION 22

2.6 AGAROSE GEL VISUALISATION 22

2.7 DNA SEQUENCING 22

2.8 DNA SEQUENCE AND PHYLOGENETIC ANALYSIS 23

2.9 KUNJIN VIRUS PLASMID 23

2.10 KUN PRIMER DESIGN AND USAGE 23

2.11 CLONING PCR PRODUCTS 24

2.11.1 RESTRICTION DIGEST 24

2.11.2 LIGATION 24

2.11.3 TRANSFORMATION 24

2.11.4 COLONY PCR 24

2.12