SOLES Honours Projects in 2021 - School of Life and Environmental Sciences - The University of Sydney
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SOLES Honours Projects in 2021 School of Life and Environmental Sciences
Table of Contents
Biochemistry and Molecular Biology 3
Biology 16
Cell and Developmental Biology 27
Ecology and Evolutionary Biology 33
Genetics and Genomics 42
Marine Science 49
Microbiology 52
Quantitative Life Sciences 58
2Biochemistry and Molecular Biology Honours Projects 2021
Title Description Name Surname Contact
This project will use a selection of
molecular biology techniques (eg
PCR), biochemistry (eg protein
Investigating the expression, characterization,
mechanism of crystallisation) and genetic https://www.sydney.edu.au/science/about/o
Alyson Ashe
transgenerational manipulations (eg CRISPR) to ur-people/academic-staff/alyson-ashe.html
epigenetic inheritance characterize genes involved in
transgenerational epigenetic
inheritance using the model organism
C. elegans.
Antibiotic resistance is an increasing
problem globally and this project aims
to develop a new class of broad
Developing new
spectrum antibiotics by targeting a
antibiotics by targeting
never exploited interaction in bacteria. Ann Kwan https://www.kwanlabusyd.com/
specific molecular
Techniques you will use include
interactions in bacteria
protein chemistry, structural biology,
peptide evolution and microbial
assays.
Hydrophobins are fungal proteins that
naturally assemble at interfaces to
form robust coatings. This project
focuses on the expanding the
Engineering of
functionality of hydrophobins through Ann Kwan https://www.kwanlabusyd.com/
hydrophobins
“smart” engineering to produce a
coating that promote the adhesion
and growth of osteoblasts in 3D-
printed bone implants.
Identifying metabolites Radiotherapy is used commonly to
that change with treat cancers but often the clinical Ann Kwan https://www.kwanlabusyd.com/
radiotherapy schemes benefits and side effects may not be
3apparent for months or years. This
project uses mass spectrometry and
NMR experiments to identify and
quantify metabolites that may act as
early predictors of treatment success.
Porphyromonas gingivalis is a
“keystone” pathogen in chronic
periodontitis which affects a quarter of
Developing specific the world’s population. This project
inhibitors that target aims to develop “Trojan horse” Ann Kwan https://www.kwanlabusyd.com/
periodontal diseases inhibitors against a set of proteins that
steal haem (and analogues) from the
host and are associated with
virulence.
We are building 3D tissue
components in the Charles Perkins
Centre. Our biomaterials have been
used in human clinical trials. We seek
Accelerated wound
Honours students interested in Anthony Weiss https://www.weisslab.net/
repair
researching the scientific basis and
building the next generation of
biomaterials for organ and tissue
augmentation and repair.
CRISPR genome editing is now being
used to develop novel plant products
worldwide. Australia recently passed
regulations that enable the
Gene editing to commercialisation of products
https://www.sydney.edu.au/science/about/o
improve the flavour of produced with CRISPR SDN-1 Brian Jones
ur-people/academic-staff/brian-jones.html
food crops induced mutations. The Honours
projects in our lab centre on metabolic
engineering with CRISPR/Cas9 to
produce novel market-oriented plant
products.
Genomics of We have a discovery of a gene
reproductive biology - pathway that might impact seasonal Claire Wade
2 students reproductive biology in the canine.
4The goal of the wider project is to
characterise our ability to manipulate
seasonal reproduction in mammals
via this pathway. This may have
important global benefits in food
security.
Insulin resistance is a major
physiological problem that is
associated with an inability of insulin
to regulate glucose and lipid
Molecular Mechanism https://www.sydney.edu.au/science/about/o
metabolism. We now know that David James
of Insulin Resistance ur-people/academic-staff/david-james.html
metabolism is central to many
diseases and how it is regulated in
health and disease is a major
question.
Using advances in mass
spectrometry-based proteomics this
Role of Protein
project aims to uncover how https://www.sydney.edu.au/science/about/o
Phosphorylation in David James
phosphorylation affects the function of ur-people/academic-staff/david-james.html
Cellular Function
proteins and cells in both healthy and
diseased states.
Dissecting the The aim of this pathway is to
architecture of the understand how the insulin signalling https://www.sydney.edu.au/science/about/o
David James
Insulin Signaling pathway regulates metabolic ur-people/academic-staff/david-james.html
Pathway homeostasis.
Insulin regulates many aspects of
metabolism including a process called
Insulin Mediated
lipolysis that involves the release of https://www.sydney.edu.au/science/about/o
Regulation of David James
fatty acids into the circulation. Here ur-people/academic-staff/david-james.html
Lipolysis
we will shed light on the mechanism
by which insulin regulates lipolysis.
By exploiting the vast genetic
landscape of an outbred mouse
Genetics of Healthy population we aim to explore the https://www.sydney.edu.au/science/about/o
David James
Ageing molecular cause of a range of ur-people/academic-staff/david-james.html
diseases that limit healthy ageing in
humans. This includes cardiovascular
5disease, bone function, diabetes, liver
disease and insulin resistance.
There is an urgent need for new
antifungal therapies. We can use
drug-drug synergy to improve existing
Understanding
antifungals, however occasionally the
antifungal drug http://sydney.edu.au/science/people/dee.ca
second drug causes antagonism.This Dee Carter
synergy and rter.php
study is to probe the molecular basis
antagonism
of synergistic and antagonistic
responses using Q-PCR and probes
for oxidative stress.
In this project, you will investigate
insect hormone receptors as targets
for selective insecticides, comparing
https://www.sydney.edu.au/science/about/o
Safer, selective the receptors of pest and beneficial
Emily Remnant ur-people/academic-staff/emily-
insecticides insects such as honey bees and their
remnant.html
in-hive parasites. This project involves
working with insects, molecular
biology, genetics and biochemistry.
I am developing simulations of
experiments in 3D and VR using the
Development of Games Engine, Unity. The vision is to
Laboratory Simulations allow the user to experience the
https://www.sydney.edu.au/science/about/o
to build student consequences of their actions so that
Gareth Denyer ur-people/academic-staff/gareth-
experimental design they gain advanced trouble-shooting
denyer.html
and troubleshooting skills and are able to critically evaluate
skills. the limitations of the methods and
resulting data. Prior programming
skills not required.
A key challenge with stem cell
therapies is obtaining sufficient cell
numbers. Prolonged in vitro cell
Delaying senescence
expansion can lead to senescence, in www.sydney.edu.au/science/about/our-
in mesenchymal stem Giselle Yeo
which cells stop proliferating and lose people/academic-staff/giselle-yeo.html
cells
their phenotype. This project explores
the use of tropoelastin to extend the
functional lifespan of stem cells.
6In this project we are using new
unbiased functional genomics
Functional Genomics techniques to map out human factors
http://sydney.edu.au/science/people/greg.n
of SARS-CoV2 required for SARS-CoV2 infections. Greg Neely
eely.php
infection This project involves working both
with modified human cell lines and
human stem cell derived tissues.
We use whole genome CRISPR
genome editing to identify the
mechanisms of action for medically
Mechanisms of actions relevant drugs, environmental toxins,
http://sydney.edu.au/science/people/greg.n
for deadly toxins and and deadly venoms. This project Greg Neely
eely.php
venoms involves CRISPR genome editing and
molecular biology, human cell culture
including stem cell derived tissues,
and animal work.
We have evaluated all human genes
for a role in resistance to 27
commonly used chemotherapies and
identified new gene RDD1 (Required
http://sydney.edu.au/science/people/greg.n
A New cell death gene for Drug-induced Death 1) which we Greg Neely
eely.php
are characterizing. This project
involves CRISPR genome editing,
flow cytometry, microscopy, molecular
biology, and transgenic mice.
We can generate most human organs
(called organoids) in a dish, and use
CRISPR to change the genetic code
and learn how our genes contribute to
Human stem cell and http://sydney.edu.au/science/people/greg.n
disease. In this project you will apply Greg Neely
organoid biology eely.php
these technologies to human brain
development, human pain system,
muscular dystrophy or wasting, or
heart function.
Our goal is to develop new ways to
http://sydney.edu.au/science/people/greg.n
New pain therapies treat pain that target the underlying Greg Neely
eely.php
cause and not just to treat the
7symptoms. In this project we use new
genome editing (CRISPR) and genetic
techniques to find genes and
pathways that are necessary and
sufficient to drive pain diseases.
Humans and rodents strongly regulate
Is dietary fat intake protein intake. If our diet is protein-
biologically regulated? deficient, we eat more to reach our
Are the metabolic protein intake target, but this https://www.sydney.edu.au/science/about/o
Jibran Wali
effects of ketogenic inadvertently causes obesity. We ur-people/academic-staff/jibran-wali.html
diets dependent on study if fat intake is also biologically
their fat-protein ratio? regulated and if fat:prot in ketogenic
diets determines their health effects.
Transcription factors are critical
players in many, if not all, cancers,
and yet have not been widely
mRNA display for the
explored as therapeutic targets. We http://sydney.edu.au/science/molecular_bio
design of new cancer Joel Mackay
will harness mRNA display of massive science/mackay/selfdir2.php
therapeutics
peptide/protein libraries to design new
molecules that directly target these
transcription factors.
The remodelling of chromatin is
critical for all genome biology -
replication, transcription and repair -
How do chromatin and disease, but the mechanisms by
http://sydney.edu.au/science/molecular_bio
remodellers reshape which remodelling enzymes achieve Joel Mackay
science/mackay/selfdir2.php
the genome? this outcome is not well understood.
We will use molecular, cell and
structural biology methods to address
this mechanism.
Recently, proteins that drive
epigenetic gene regulation have been
Bromodomains as recognized as important targets for
http://sydney.edu.au/science/molecular_bio
epigenetic cancer cancer and other diseases. We will Joel Mackay
science/mackay/selfdir2.php
targets use CRISPR gene editing to explore
the mechanisms by which
bromodomain proteins regulate gene
8expression, opening up new ways to
target these proteins in disease.
Environmental conditions during early
development can affect long term risk
Effect of dietary of disease. The objective of this
carbohydrate quality project is to determine the effect of https://www.sydney.edu.au/science/about/o
on fetal development carbohydrate quality on energy Kim Bell-Anderson ur-people/academic-staff/kim-bell-
and cardiometabolic balance, maternal adiposity and anderson.html
health nutritional status, and fetal
developmental outcomes in a mouse
model.
The Promethion metabolic screening
platform at the CPC measures energy
expenditure, respiratory quotient,
Big data analysis of physical activity and food and water https://www.sydney.edu.au/science/about/o
mouse metabolic intake continuously over several days Kim Bell-Anderson ur-people/academic-staff/kim-bell-
phenotype in mice. This project seeks to create anderson.html
an automated process for the analysis
of data collected from thousands of
mice.
Plants create some of the most
striking architectures on earth and
these shapes can also play a key role
https://www.sydney.edu.au/science/about/o
Understanding cell in crop production. This project uses
Marcus Heisler ur-people/academic-staff/marcus-
polarity in plants live-imaging and molecular genetics to
heisler.html#collapseBio
understand how plant cells coordinate
their polarity, which determines
growth rates and growth directions.
Cell-type boundaries in plants play a
central role in controlling both leaf
The control of plant formation and shape, both of which https://www.sydney.edu.au/science/about/o
architecture by cell- are important to crop production.This Marcus Heisler ur-people/academic-staff/marcus-
type boundaries project utilises live-imaging and heisler.html#collapseBio
molecular genetics to understand how
these boundaries work.
Multi-Omic Data Experiments involving proteomics and
Mark Larance https://www.larancelab.com/
Analysis and metabolomics generate enormous
9Visualisation for amounts of data, that need to be
Intermittent Fasting processed, tested for statistical
significance and integrated. The
visualisation of these data is
particularly difficult and this project will
address this in the context of
intermittent fasting.
Erusiolin is a novel hormone we
discovered that we hypothesise plays
a role in appetite regulation. This
Characterisation of the project is to characterise the role of
novel hormone this hormone in mammalian Mark Larance https://www.larancelab.com/
erusiolin physiology using human clinical trial
samples, CRISPR knock-out mice,
peptide injection experiments and
bioinformatic analysis.
Intermittent fasting provides metabolic
benefits. But how the proteome in
each tissue is altered is not fully
Systems proteomics of understood. Our goal is to use state-
the intermittent fasting of-the-art proteomic analysis to Mark Larance https://www.larancelab.com/
response uncover the complex interaction
between organ systems that leads to
the beneficial effects of intermittent
fasting.
Chronic production of the cytokine
Assess the influence of
interferon-a causes an auto-
the genetic
inflammatory brain disease in mice.
background in a mouse
Our findings have identified that the
model for auto-
genetic background of mice affects Markus Hofer www.hoferlab.com
inflammatory brain
disease development and severity.
disease -
Using molecular and genetic
https://youtu.be/r_Shde
approaches, this project aims at
Dtz1M
identifying the underlying cause.
Determining the Microglia are the brain's immune cells.
molecular and genetic Our past research showed that the Markus Hofer www.hoferlab.com
basis of type I commonly used microglia cell line C8-
10interferon- B4 is resistant to type I interferons,
unresponsiveness in which are master regulators of
C8-B4 murine microglia immune responses. Using in vitro
- approaches, this project will clarify the
https://youtu.be/r_Shde molecular pathway mediating this
Dtz1M resistance.
Examine the
phagocytic capacity of
Microglia are the brain's immune cells
microglia in response
and phagocytose cell debris. IL-6 and
to the pro-inflammatory
IFN-a activate microglia in different
cytokines interleukin-6 Markus Hofer www.hoferlab.com
ways. Here, we will assess how both
(IL-6) and interferon-
cytokines regulate phagocytosis in
alpha (IFN-a) -
microglia.
https://youtu.be/r_Shde
Dtz1M
Immune activation during pregnancy
Characterise a novel
is a risk factor for neurodevelopmental
cumulative mouse
disorders in offspring. With colleagues
model for
at Westmead's Children's hospital we
neurodevelopmental Markus Hofer www.hoferlab.com
are studying a novel mouse model
diseases -
that better recapitulates human
https://youtu.be/r_Shde
immune activation than existing
Dtz1M
models.
This project will use in vitro
techniques in stem cells to study the
molecular basis of transcription during https://www.centenary.org.au/cen_program
Imaging transcription
cell fate decision. This will work take /david-richmond-laboratory-for-
in real time at single Mathias Francois
advantage of cutting edge approaches cardiovascular-development-gene-
molecule resolution
based on single molecule science, regulation-and-editing-program/
super resolution microscopy, genome
editing (crispr/cas9), and genomics.
The biological question is centred
Molecular and cellular around the molecular control of cell https://www.centenary.org.au/cen_program
biology of vascular fate during lymphatic endothelial cell /david-richmond-laboratory-for-
Mathias Francois
development during specification by a novel transcriptional cardiovascular-development-gene-
embryogenesis effector. Techniques used will cover a regulation-and-editing-program/
broad range of skills from confocal
11microscopy to gene editing
(crispr/cas9) and transcriptomics.
Iron is the most abundant transition
metal and plays the essential role in
The effect of iron on the redox reaction of electron
the photosynthetic transport. Some cyanobacteria have https://www.sydney.edu.au/science/about/o
apparatus and evolved a number of responses to Min Chen ur-people/academic-staff/min-
chlorophyll cope with the conditions of iron chen.htmlLinks to an external site.
biosynthetic pathway deficiency, including the changed
photosynthetic apparatus to propose
new energy pathways.
The project aims to study the structure
and function of photopigment-binding
Molecular adaptation of protein complexes, which can be
https://www.sydney.edu.au/science/about/o
photosynthesis controlled in desired light and nutrient
Min Chen ur-people/academic-staff/min-
powered by long- conditions. The research outcome will
chen.htmlLinks to an external site.
wavelength light provide a molecular blueprint for the
adaptation of photosynthesis with
optimized energy transfer pathway.
Synthetic biology promises to
transform every aspect of our lives,
from medicines to agriculture to
industry. This project will develop new https://www.sydney.edu.au/science/about/o
Synthetic biology tools
versatile cloning plasmids for gene Nick Coleman ur-people/academic-staff/nicholas-
for cyanobacteria
expression in cyanobacteria - these coleman.html
are especially interesting for
biotechnology since they can use
CO2 as a feedstock.
Mobile genetic elements (MGEs) like
integrons are at the heart of the
Tracking antibiotic antibiotic resistance problem. In this
resistance genes and project, we will develop novel assays https://www.sydney.edu.au/science/about/o
mobile genetic to probe the activity of integrons in Nick Coleman ur-people/academic-staff/nicholas-
elements in the different environmental coleman.html
environment compartments, to understand their
contribution to the movement of
resistance genes
12Biocatalysis aims to replace
petrochemicals with microbial
reactions on renewable feedstocks.
Green Chemistry -
We are interested in developing better https://www.sydney.edu.au/science/about/o
Biocatalysis For
expression systems for Nick Coleman ur-people/academic-staff/nicholas-
Production Of High-
monooxygenases - these enzymes coleman.html
Value Chemicals
add oxygen to organic modules,
yielding alcohols and epoxides, which
are important for many industries.
Herbicides are widely used in
agriculture to control weeds, but some
(e.g. trifluralin) have toxic side-effects
Biodegradation of and can persist for a long time in soil. https://www.sydney.edu.au/science/about/o
trifluralin - a persistent We have enriched a microbial culture Nick Coleman ur-people/academic-staff/nicholas-
herbicide that biodegrades trifluralin. The coleman.html
project will seek to identify the
microbes, enzymes and genes
responsible.
IS in the IS26 family mobilise
antibiotic resistance genes. We
recently demonstrated that they
How do insertion
undertake a novel reaction that may
sequences mobilise https://www.sydney.edu.au/science/about/o
explain their success. The project will Ruth Hall
antibiotic resistance ur-people/academic-staff/ruth-hall.html
examine whether IS in other families
genes
found associated with antibiotic
resistance genes can undertake the
same type of reaction.
Antibiotic resistance represents an
increasingly serious threat to global
public health. We propose that the
Developing new
receptor for the bacterial Signal
compounds to target https://www.sydney.edu.au/science/our-
Recognition Particle (SRP) represents
bacterial FtsY: in Sandro Ataide research/research-areas/life-and-
an ideal target for the development of
search of new environmental-sciences/ataide-lab.html
novel antibiotics. In this project we will
antibiotics
perform screening of developed
compounds using biophysical
methods and in vivo assays.
13Quantitative cross-
This project will develop quantitative
linking mass https://www.sydney.edu.au/science/about/o
strategies for exploring the protein
spectrometry in Stuart Cordwell ur-people/academic-staff/stuart-
interactome in different models of
bacterial or cordwell.html
disease
cardiovascular disease
Exploring the
This project will explore how
nutritional https://www.sydney.edu.au/science/about/o
nutritional cues from human gut
requirements of Stuart Cordwell ur-people/academic-staff/stuart-
infection modify the Campylobacter
Campylobacter jejuni cordwell.html
jejuni proteome and metabolome
infections
Novel virulence factors
This project will explore the effects of
of Pseudomonas https://www.sydney.edu.au/science/about/o
novel virulence factor gene deletions
aeruginosa required for Stuart Cordwell ur-people/academic-staff/stuart-
on Pseudomonas aeruginosa
cystic fibrosis lung cordwell.html
phenotypes and omics profiles
infection
Exploring the role of N-This project will explore the role of N- https://www.sydney.edu.au/science/about/o
glycosylation in glycosylation in protection against Stuart Cordwell ur-people/academic-staff/stuart-
Campylobacter jejuni Campylobacter jejuni proteases cordwell.html
This project will investigate the
Investigating potential
protective capabilities of https://www.sydney.edu.au/science/about/o
vaccine antigens of
Pseudomonas aeruginosa antigens in Stuart Cordwell ur-people/academic-staff/stuart-
Pseudomonas
mouse models of cystic fibrosis lung cordwell.html
aeruginosa
disease
This project will characterise the
structure and function of resistance-
conferring eIF4E variants and
Understanding eIF4E- establish the physicochemical rules
https://www.sydney.edu.au/science/about/o
mediated potyvirus that underlie eIF4E-based recessive Tara Christie
ur-people/academic-staff/tara-christie.html
resistance resistance. This study will pave the
way for the identification and design of
new and robust forms of recessive
resistance.
Most serpins act as potent,
Physiological functions
irreversible ‘suicide-substrate’ https://www.sydney.edu.au/science/about/o
of spring-loaded
inhibitors of proteases (i.e. enzymes Thomas Roberts ur-people/academic-staff/thomas-
‘suicidal’ proteins
that cleave proteins or peptides). roberts.html
(serpins) in plants
However, the physiological functions
14of most plant serpins remain
unknown. This project aims to
elucidate the roles of key serpins in
model plant species through a
combination of bioinformatics and
biochemical experiments.
Indian mustard is an important crop
for oil production and soil
The next Manuka?
rehabilitation. The aim of this project
Identifying bioactive
is to identify valuable bioactive https://www.sydney.edu.au/science/about/o
compounds in honey
compounds in honey from bees Thomas Roberts ur-people/academic-staff/thomas-
from bees feeding on
feeding on fields of Indian mustard. roberts.html
fields of Indian
This would involve sophisticated
mustard
chemical analysis including HPLC and
mass spectrometry.
SARS-CoV-2 is able to cause severe
lung injury through the process of
fibrotic injury. This project will
https://www.sydney.edu.au/science/about/o
Induction of of fibrosis examine the mechanisms by
Tim Newsome ur-people/academic-staff/timothy-
by SARS-CoV-2 signalling by the TGF-b pathway may
newsome.html
contribute to this phenomenon and
evaluate this pathway as a drug
target.
15Biology Honours Projects 2021
Title Description Name Surname Contact
This project will use a selection of molecular
Investigating the biology techniques (eg PCR), biochemistry
mechanism of (eg protein expression, characterization,
https://www.sydney.edu.au/science/about/our-
transgenerational crystallisation) and genetic manipulations (eg Alyson Ashe
people/academic-staff/alyson-ashe.html
epigenetic CRISPR) to characterize genes involved in
inheritance transgenerational epigenetic inheritance
using the model organism C. elegans.
C. elegans are a valuable model organism
that are found globally. But, their biodiversity,
Discovery of new range and associated viruses in Aus. are
C. elegans unknown. This project will perform sampling https://www.sydney.edu.au/science/about/our-
Alyson Ashe
species and their around the Sydney region, followed by people/academic-staff/alyson-ashe.html
viral pathogens molecular biology techniques and deep
sequencing to define known and novel
species.
Oysters are the kidneys of coastal
environments, but most of this important
The capacity of
oyster habitats have been lost due to
oyster reefs to https://www.sydney.edu.au/science/about/our-
harvesting and contamination. This project Ana Bugnot
improve water people/academic-staff/ana-bugnot.html
aims to gather and combine published data
quality
in a meta-analysis on the role of oysters in
regulating water quality.
Characterizing Sediment burrowing animals (bioturbators)
bioturbation play key roles in the healthy functioning of
activity in marine sediments. This study will https://www.sydney.edu.au/science/about/our-
Ana Bugnot
sediments characterise the species living close to oyster people/academic-staff/ana-bugnot.html
surrounding reefs and assess their role in promoting
oyster reefs nutrient cycling of oyster deposits.
Our gut microbiome impacts health through
Diet x https://www.sydney.edu.au/science/about/our-
its contribution to digestion and interaction Andrew Holmes
microbiome people/academic-staff/andrew-holmes.html
with the enteric endocrine, lymphoid and
16interactions in nervous systems. Projects can be focussed
animal health on mechanisms through which diet can
manipulate microbe outcomes or animal
outcomes (immunometabolic functions).
Water drives productivity for many Australian
Characterising
plants yet the physiological and biophysical
biophysical
properties that govern water use is poorly https://www.sydney.edu.au/science/about/our-
patterns of water
characterised. Working with the Mt Annan Andrew Merchant people/academic-staff/andrew-
use among
botanic gardens and a range of techniques merchant.htmlLinks to an external site.
Australian tree
this project will investigate properties among
species
contrasting Eucalyptus taxonomy.
Under predicted climatic changes, net carbon
Comparative
exchange between the biosphere and the
measures of
atmosphere will be impacted. Leaf chemical https://www.sydney.edu.au/science/about/our-
carbon capture
and physiological properties governing net Andrew Merchant people/academic-staff/andrew-
among
carbon capture will be characterised among merchant.htmlLinks to an external site.
Australian native
Australian plant taxa to support modelling of
vegetation
future vegetation carbon exchange.
Collective animal behaviour is a widespread
and crucially important phenomenon,
occurring in organisms from bacteria to
humans. Recent developments in technology https://www.sydney.edu.au/science/our-
Understanding
have allowed us the opportunity to research/research-areas/life-and-
animal Ashley Ward
understand the mysteries of collective environmental-sciences/animal-behaviour-
aggregations
systems. Your project will involve lab and lab.html
fieldwork as well as the opportunity to
engage with advanced analytical techniques
to break new group in this field
Krill are fundamental to the success of the
Antarctic ecosystem, yet as our climate
https://www.sydney.edu.au/science/our-
changes, the future is uncertain. This project
Predicting the research/research-areas/life-and-
will investigate how krill will cope under
future of environmental-sciences/animal-behaviour-
conditions of elevated temperatures and Ashley Ward
Antarctic krill in a lab.html
decreasing pH in the Southern Ocean. The
changing ocean
project will combine lab work at the
Australian Antarctic Division with analysis
based in Sydney
17CRISPR genome editing is now being used
to develop novel plant products worldwide.
Australia recently passed regulations that
Gene editing to https://www.sydney.edu.au/science/about/our-
enable the commercialisation of products
improve the people/academic-staff/brian-jones.html
produced with CRISPR SDN-1 induced Brian Jones
flavour of food
mutations. The Honours projects in our lab
crops
centre on metabolic engineering with
CRISPR/Cas9 to produce novel market-
oriented plant products.
You will work on a lizard with an unusual
reproductive strategy: both live-bearing and
Biology of egg- egg-laying. The projects will answer
laying and live questions such as: Do oviparous and Camilla Whittington www.camillawhittington.com
birth in skinks viviparous lizards interbreed? Has oviparity
‘re-evolved'? Suitable for students wishing to
build their molecular biology skills.
Several projects are possible, including those
addressing:
- Do seahorse dads transport amino acids to
The biology of
developing babies?
male pregnancy Camilla Whittington www.camillawhittington.com
- How do seahorse dads protect the babies
in seahorses
from infection?
These projects would suit students interested
in fundamental biology/physiology.
This project will determine whether
environmental conditions can modify the
Is reproductive reproductive phenotype of egg-laying and
mode affected by live-bearing lizards. It will help determine Camilla Whittington www.camillawhittington.com
environment? whether phenotypic plasticity has played a
role in the evolution of viviparity. It would suit
a student interested in physiology/lab work
We currently have little more than a “black
Does size matter box” view of what limits the production of https://www.sydney.edu.au/science/our-
for plant uptake plant-available nutrients. This study will move research/research-areas/life-and-
Charles Warren
and soil cycling beyond the black box view of nutrient environmental-sciences/plant-ecophysiology-
of organic N? availability and tease apart the limiting steps and-ecosystem-processes.html
in release of plant-available nutrients.
18Soil respiration is one of the largest
components of the global C cycle, and also
Uncovering the one of the hardest to model. A key aspect of
https://www.sydney.edu.au/science/our-
source of CO2 this difficulty is that we do not have a good
research/research-areas/life-and-
that’s respired mechanistic understanding of how drying Charles Warren
environmental-sciences/plant-ecophysiology-
when dry soil is followed by rewetting affect soil
and-ecosystem-processes.html
rewet processes. This project will uncover the
source of the carbon that is respired when a
dry soil is rewet.
Phosphorus availability is a large challenge
How do soil for soil microbes because their “food” (plant
microbes fine- litter or organic matter) rarely meets their
https://www.sydney.edu.au/science/our-
tune their cellular physiological requirements. Organisms can
research/research-areas/life-and-
composition to minimise nutrient limitations by altering their Charles Warren
environmental-sciences/plant-ecophysiology-
cope with physiological requirements. This project will
and-ecosystem-processes.html
nutrient determine how soil microbial modulate their
imbalances? cellular composition to cope with nutrient
imbalances.
Canopy height data for a remnant forest at
the USyd Llara farm will be compared to
Can native tree
measurements of species and trunk diameter
habitat variation https://www.sydney.edu.au/science/about/our-
at ground level. Use of lidar for agricultural David Gallacher
be estimated people/academic-staff/d-gallacher.html
purposes has increased in recent years and
from lidar?
may contain information of on- and near-farm
wildlife habitats
In this project, you will investigate insect
hormone receptors as targets for selective
insecticides, comparing the receptors of pest
Safer, selective https://www.sydney.edu.au/science/about/our-
and beneficial insects such as honey bees Emily Remnant
insecticides people/academic-staff/emily-remnant.html
and their in-hive parasites. This project
involves working with insects, molecular
biology, genetics and biochemistry.
In this project you will investigate the origins
Pandemic in the
of a novel incursion of parasitic mites in
pacific: https://www.sydney.edu.au/science/about/our-
honeybees in Fiji, and characterise the viral Emily Remnant
Honeybee virus people/academic-staff/emily-remnant.html
diversity transmitted from mites to bees over
dynamics during
time as the invasion spreads. This project
19an early Varroa involves molecular biology, genomics and
invasion. bioinformatics.
How can animals compensate behaviourally
Physiological
or physiologically for potentially negative
and behavioural
effects of environmental variability? This is
responses of https://www.sydney.edu.au/science/about/our-
not a distinct project but a research area Frank Seebacher
animals to people/academic-staff/frank-seebacher.html
within which a project can be designed.
environmental
Check out recent publications on Scopus or
variability
Google Scholar for more details.
Is dietary fat
intake
Humans and rodents strongly regulate
biologically
protein intake. If our diet is protein-deficient,
regulated? Are
we eat more to reach our protein intake https://www.sydney.edu.au/science/about/our-
the metabolic
target, but this inadvertently causes obesity. Jibran Wali people/academic-staff/jibran-wali.htmlLinks to
effects of
We study if fat intake is also biologically an external site.
ketogenic diets
regulated and if fat:prot in ketogenic diets
dependent on
determines their health effects.
their fat-protein
ratio?
Studies have examined the flammability of
individual fuels rather than mixtures that
naturally occur. In this project, the
Do all fuels burn https://www.sydney.edu.au/science/about/our-
flammability of mixed fuels will be compared Malcolm Possell
the same? people/academic-staff/malcolm-possell.html
to individual fuels through burning
experiments, coupled with physical and
chemical characterisations of the fuels.
Two possible projects: (1) Examine the
Near infrared relationships between near-infra red (NIR)
spectroscopy as spectroscopy and the burning conditions of
a fire severity mixed/composite fuels; (2) examine whether https://www.sydney.edu.au/science/about/our-
Malcolm Possell
metric – relationships identified among burning people/academic-staff/malcolm-possell.html
application to the conditions and laboratory grade NIR scans
real world hold true when using substantially cheaper,
portable handheld devices?
Understanding Plants create some of the most striking https://www.sydney.edu.au/science/about/our-
cell polarity in architectures on earth and these shapes can Marcus Heisler people/academic-staff/marcus-
plants also play a key role in crop production. This heisler.html#collapseBio
20project uses live-imaging and molecular
genetics to understand how plant cells
coordinate their polarity, which determines
growth rates and growth directions.
Cell-type boundaries in plants play a central
The control of role in controlling both leaf formation and
https://www.sydney.edu.au/science/about/our-
plant architecture shape, both of which are important to crop
Marcus Heisler people/academic-staff/marcus-
by cell-type production.This project utilises live-imaging
heisler.html#collapseBio
boundaries and molecular genetics to understand how
these boundaries work.
This project will investigate how an important
group of transcription factors, homeodomain
Genetic
proteins, control plant development. You will https://www.sydney.edu.au/science/about/our-
regulation of leaf Mary Byrne
have the opportunity to use and build skills in people/academic-staff/mary-byrne.html
shape
genetics, molecular biology and
developmental biology.
This project will use gene editing to study
gene function testing the potential to
Using gene
generate multiple mutations and to tag genes
editing to study https://www.sydney.edu.au/science/about/our-
with a reporter to follow gene expression. Mary Byrne
gene function in people/academic-staff/mary-byrne.html
You will have the opportunity to use and
plants
build skills in genetics, molecular biology and
developmental biology.
Wheat is one of the world’s most important
Investigating sources of food. A major goal in agriculture is
flower making superior hybrid wheat. This project
https://www.sydney.edu.au/science/about/our-
development to will study development of male reproductive Mary Byrne
people/academic-staff/mary-byrne.html
aid production of organs in varieties important for making
hybrid wheat hybrids. The project will build skills in
developmental biology and genetics.
Ongoing work in the City of Sydney Council
region indicates that Brown Rat populations
The impacts of
may have gone down in the city, due to a
COVID-19 on https://www.sydney.edu.au/science/about/our-
reduction of resources (fewer people eating Mathew Crowther
Sydney’s rat people/academic-staff/mathew-crowther.html
in the city etc). This project will involve
population
trapping rats, and looking at other sources of
data, to see if rats have increased in the city
21and is it resource driven. The project will
compare commercial to residential areas to
see if human movement changes have
affected rat densities.
Lab rats show fear responses to cat fur, and
there is evidence that wild rats do as well.
Do extracts from We have a number of extracts from cat fur
cat fur affect and we are interested if they are the active https://www.sydney.edu.au/science/about/our-
Mathew Crowther
rodent component for this fear response. Work will people/academic-staff/mathew-crowther.html
behaviour? be done either at the University of Sydney
using lab rats or at Macquarie University
fauna park using wild rats.
Many small mammal species look similar, but
this would be expected if their main sense in
communication is smell. Differences in
pheromone profiles may be important in the
Do Antechinus speciation process and mate selection. We
https://www.sydney.edu.au/science/about/our-
species smell are interested in testing these differences in Mathew Crowther
people/academic-staff/mathew-crowther.html
different? pheromone profiles using the marsupial
genus, Antechinus. This will involve getting
samples from different species of
Antechinus, and examining there differences
in the laboratory.
Populations of koalas are declining in the
Spatial and well-known koala hotspot of the Liverpool
population Plains, NW NSW. This project will look at
https://www.sydney.edu.au/science/about/our-
modelling of building a a spatially explicit population Mathew Crowther
people/academic-staff/mathew-crowther.html
koalas in the model, incorporating landscape and diease,
Liverpool Plains to address the best way of addressing koala
decline.
Koalas are declining in many parts of
Australia, and road fatalities are a major
Studying koala
contributor. Fences can be effective in
movements to https://www.sydney.edu.au/science/about/our-
reducing koala mortality, but are very Mathew Crowther
reduce road people/academic-staff/mathew-crowther.html
expensive and have their own issues in
fatalities
fragmenting populations. We aim to study the
movement of koalas with accelerometers, as
22well as road and traffic conditions, to better
manage landscape for koalas
Lantana control:
A group of landholders in the Tarbuck Bay
Does the
area, NSW have united to tackle lantana
identification of a https://www.sydney.edu.au/science/our-
infestations on their properties. A community-
beneficial use research/research-areas/life-and-
based approach to lantana management will Michael Walsh
improve environmental-sciences/precision-weed-
be evaluated. The influence of identified local
community- control-group.html
beneficial uses of this weed on group
based
motivation will be assessed.
management
Oyster mushrooms can be grown on many
different substrates, including straw, spent
Investigating the
coffee grounds and paper waste. Bacteria
role of bacteria in https://www.sydney.edu.au/science/about/our-
colonize the substrate together with the Michael Kertesz
growing oyster people/academic-staff/michael-kertesz.html
mushroom mycelium. The project will study
mushrooms
the succession of bacterial diversity during
mushroom growth on different substrates.
Button mushrooms are grown in a selective
compost, using chicken manure and soy-
Optimizing
based supplements to provide the nitrogen
Nitrogen content
(N) needed for mushroom growth. The https://www.sydney.edu.au/science/about/our-
in cultivated Michael Kertesz
project will investigate alternative N sources, people/academic-staff/michael-kertesz.html
button
studying their effect on the microbes in the
mushrooms
compost, and on mushroom yield and N
content.
Iron is the most abundant transition metal
The effect of iron
and plays the essential role in the redox
on the
reaction of electron transport. Some
photosynthetic https://www.sydney.edu.au/science/about/our-
cyanobacteria have evolved a number of
apparatus and Min Chen people/academic-staff/min-chen.htmlLinks to
responses to cope with the conditions of iron
chlorophyll an external site.
deficiency, including the changed
biosynthetic
photosynthetic apparatus to propose new
pathway
energy pathways.
The project aims to study the structure and
Molecular https://www.sydney.edu.au/science/about/our-
function of photopigment-binding protein
adaptation of Min Chen people/academic-staff/min-chen.htmlLinks to
complexes, which can be controlled in
photosynthesis an external site.
desired light and nutrient conditions. The
23powered by long- research outcome will provide a molecular
wavelength light blueprint for the adaptation of photosynthesis
with optimized energy transfer pathway.
The unseeing Many non-coding RNA (ncRNA) were
regulatory expressed without defined functions. It is
network of clear now that they have a very important
https://www.sydney.edu.au/science/about/our-
Acaryochloris regulatory roles.In A. marina many ncRNAs
Min Chen people/academic-staff/min-chen.htmlLinks to
marina, a were actively expressed under certain
an external site.
chlorophyll d- conditions. Using bioinformatics tools, we will
containing predict targeting genes and regulatory
cyanobacteria networks.
The marine isopod Cirolana harfordi displays
Physiology and live birth, can venture, out onto land and, into
behaviour of the hyposaline water. It is also a social animal
https://www.sydney.edu.au/science/about/our-
marine and displays fearlessness in relation to Murray Thomson
people/academic-staff/murray-thomson.html
crustacean predators. Various projects on the physiology
Cirolana harfordi and behaviour of this amazing animal are
available.
This project will explore the potential for
Using chemical olfactory camouflage to reduce the house
camouflage to mouse's ability to find newly sown wheat
protect wheat grains as a non-toxic alternative to control Peter Banks https://conservation-behaviour.sydney.edu.au
seeds from mouse damage on wheat yields. It will be
mouse damage field based, working in collaboration with
CSIRO
Messing with This field project will explore how information
their minds: can be used to manipulate decision-making
using by animals in order to better detect wildlife. It
information to will explore how strategic use of information Peter Banks https://conservation-behaviour.sydney.edu.au
improve wildlife can increase rates of wildlife detections by
monitoring harnessing animal motivations to visit
devices monitoring devices
Measuring the
The paradox: humans need plants to survive
environmental
but many humans have "plant blindness". https://www.sydney.edu.au/science/about/our-
value of our Rosanne Quinnell
This project aims to critique methods for people/academic-staff/rosanne-quinnell.html
University
valuing trees (e.g. economic, environmental,
campus
24ecological, psychological) focusing on the
flora of our USYD campuses.
To rear their larvae, honeybees need to
Effects of hive regulate the temperature inside the hive
insulation on bee around an optimum of 34.5°C. This project
Tanya Latty www.tanyalatty.com
colony will test the effect of hive design and
thermoregulation insulation on colony temperature regulation
under heat stress.
In this project, you will design and test
Designing artificial flowers for use with wild, free-flying
artificial flowers pollinators. This project would suit a student
for studying the with an interest in design/craft. This project Tanya Latty www.tanyalatty.com
behaviour of wild can be extended to investigate flower
pollinators preferences of insects using artificial
flowers.
For optimal health, honeybees need to
Understanding regulate the temperature inside the hive to
temperature about 34.5°C. This project will use
variation within sensors throughout the hive to investigate Tanya Latty www.tanyalatty.com
honeybee how colonies respond to temperature
colonies fluctuations.The data we collect will help us
protect beehives in a rapidly warming world.
Blue banded bees are important and
abundant pollinators. In this project, you will
How do blue
investigate flower preferences in blue
banded bees
banded bees with the goal of understanding Tanya Latty www.tanyalatty.com
choose which
which floral traits are preferred by foraging
flowers to visit?
blue banded bees. This project will require
data collection during the summer months.
Rewarding flowers can either benefit nearby
How does
flower species by attracting additional
pollinator choice
pollinators to the area (facilitation), or they
behaviour
can compete with nearby flowers by stealing Tanya Latty www.tanyalatty.com
influence
pollinators (competition). This project will
interactions
investigate the floral attributes that influence
between flowers?
competition and facilitation.
25The project will involve monitoring vertebrate
and insect scavengers on animal carcasses
Alpine along an altitudinal gradient in Kosciuszko
scavenging National Park. The results will inform how Thomas Newsome https://thomasnewsome.com/
dynamics decomposition processes shift with altitude
and provide insights into the impacts of
climate change on food web dynamics.
This work will use beach-dwelling flies to
examine how organisms gather and
Communication,
exchange visual information in order to solve
courtship, and
life's daily challenges. The questions are Thomas White https://tomwhite.io
adaptation in the
many, but will entail fieldwork on Australia's
wild
beautiful beaches and lab-based analyses of
behaviour, colour, and visual perception.
Underwater This project explores the multiple benefits of
cows: marine restoring marine underwater forests via the
herbivores and removal of herbivores and their potential use https://www.sydney.edu.au/science/about/our-
Ziggy Marzinelli
restoration of as a food resource. It involves field and people/academic-staff/e-marzinelli.html
underwater aquarium experiments at the Sydney Institute
forests of Marine Science.
26Cell and Developmental Biology Honours Projects 2021
Title Description Name Surname Contact
This project will use a selection of molecular
Investigating the biology techniques (eg PCR), biochemistry
mechanism of (eg protein expression, characterization,
https://www.sydney.edu.au/science/about/our
transgenerational crystallisation) and genetic manipulations Alyson Ashe
-people/academic-staff/alyson-ashe.html
epigenetic (eg CRISPR) to characterize genes involved
inheritance in transgenerational epigenetic inheritance
using the model organism C. elegans.
Our gut microbiome impacts health through
its contribution to digestion and interaction
Diet x
with the enteric endocrine, lymphoid and
microbiome https://www.sydney.edu.au/science/about/our
nervous systems. Projects can be focussed Andrew Holmes
interactions in -people/academic-staff/andrew-holmes.html
on mechanisms through which diet can
animal health
manipulate microbe outcomes or animal
outcomes (immunometabolic functions).
CRISPR genome editing is now being used
to develop novel plant products worldwide.
CRISPR/Cas9 Australia recently passed regulations that
genome editing enable the commercialisation of products
https://www.sydney.edu.au/science/about/our
for market- produced with CRISPR SDN-1 induced Brian Jones
-people/academic-staff/brian-jones.html
oriented novelty mutations. The Honours projects in our lab
in plants centre on metabolic engineering with
CRISPR/Cas9 to produce novel market-
oriented plant products.
Micro-cells occur in Cryptococcus during
Micro-cell
human infection stress. In this project we
variants in the
will determine 1) what triggers microcell
yeast pathogen http://sydney.edu.au/science/people/dee.cart
production; 2) whether the number of micro- Dee Carter
Cryptococcus er.php
cells changes over time during the growth
and their role in
phase of cultures; 3) whether micro-cells
infection
are are capable of reverting to normal cells.
27Growth in the mammalian host can be
The production of stressful for fungal pathogens.
morphologically Cryptococcus can respond by developing
altered unusual cellular morphologies that may http://sydney.edu.au/science/people/dee.cart
Dee Carter
Cryptococcus allow dormant survival. We will examine er.php
cells in response these in detail using microscopy,
to stress microbiological growth dynamics, cellular
probes and molecular methods.
There is an urgent need for new antifungal
therapies. We can use drug-drug synergy to
Understanding improve existing antifungals, however
antifungal drug occasionally the second drug causes http://sydney.edu.au/science/people/dee.cart
Dee Carter
synergy and antagonism.This study is to probe the er.php
antagonism molecular basis of synergistic and
antagonistic responses using Q-PCR and
probes for oxidative stress.
A key challenge with stem cell therapies is
obtaining sufficient cell numbers. Prolonged
Delaying
in vitro cell expansion can lead to
senescence in www.sydney.edu.au/science/about/our-
senescence, in which cells stop proliferating Giselle Yeo
mesenchymal people/academic-staff/giselle-yeo.html
and lose their phenotype. This project
stem cells
explores the use of tropoelastin to extend
the functional lifespan of stem cells.
In this project we are using new unbiased
Functional functional genomics techniques to map out
Genomics of human factors required for SARS-CoV2 http://sydney.edu.au/science/people/greg.nee
Greg Neely
SARS-CoV2 infections. This project involves working ly.php
infection both with modified human cell lines and
human stem cell derived tissues.
We use whole genome CRISPR genome
editing to identify the mechanisms of action
Mechanisms of for medically relevant drugs, environmental
actions for deadly toxins, and deadly venoms. This project http://sydney.edu.au/science/people/greg.nee
Greg Neely
toxins and involves CRISPR genome editing and ly.php
venoms molecular biology, human cell culture
including stem cell derived tissues, and
animal work.
28We have evaluated all human genes for a
role in resistance to 27 commonly used
chemotherapies and identified new gene
A New cell death RDD1 (Required for Drug-induced Death 1) http://sydney.edu.au/science/people/greg.nee
Greg Neely
gene which we are characterizing. This project ly.php
involves CRISPR genome editing, flow
cytometry, microscopy, molecular biology,
and transgenic mice.
We can generate most human organs
(called organoids) in a dish, and use
CRISPR to change the genetic code and
Human stem cell
learn how our genes contribute to disease. http://sydney.edu.au/science/people/greg.nee
and organoid Greg Neely
In this project you will apply these ly.php
biology
technologies to human brain development,
human pain system, muscular dystrophy or
wasting, or heart function.
Our goal is to develop new ways to treat
pain that target the underlying cause and
not just to treat the symptoms. In this project
New pain http://sydney.edu.au/science/people/greg.nee
we use new genome editing (CRISPR) and Greg Neely
therapies ly.php
genetic techniques to find genes and
pathways that are necessary and sufficient
to drive pain diseases.
Plants create some of the most striking
architectures on earth and these shapes
can also play a key role in crop production.
Understanding https://www.sydney.edu.au/science/about/our
This project uses live-imaging and
cell polarity in Marcus Heisler -people/academic-staff/marcus-
molecular genetics to understand how plant
plants heisler.html#collapseBio
cells coordinate their polarity, which
determines growth rates and growth
directions.
Cell-type boundaries in plants play a central
The control of role in controlling both leaf formation and https://www.sydney.edu.au/science/about/our
plant architecture shape, both of which are important to crop -people/academic-staff/marcus-
Marcus Heisler
by cell-type production.This project utilises live-imaging heisler.html#collapseBioLinks to an external
boundaries and molecular genetics to understand how site.
these boundaries work.
29Experiments involving proteomics and
Multi-Omic Data metabolomics generate enormous amounts
Analysis and of data, that need to be processed, tested
Visualisation for for statistical significance and integrated. Mark Larance https://www.larancelab.com/
Intermittent The visualisation of these data is particularly
Fasting difficult and this project will address this in
the context of intermittent fasting.
Erusiolin is a novel hormone we discovered
that we hypothesise plays a role in appetite
Characterisation regulation. This project is to characterise the
of the novel role of this hormone in mammalian
Mark Larance https://www.larancelab.com/
hormone physiology using human clinical trial
erusiolin samples, CRISPR knock-out mice, peptide
injection experiments and bioinformatic
analysis.
Intermittent fasting provides metabolic
benefits. But how the proteome in each
Systems
tissue is altered is not fully understood. Our
proteomics of the
goal is to use state-of-the-art proteomic Mark Larance https://www.larancelab.com/
intermittent
analysis to uncover the complex interaction
fasting response
between organ systems that leads to the
beneficial effects of intermittent fasting.
This project will investigate how an
important group of transcription factors,
Genetic
homeodomain proteins, control plant https://www.sydney.edu.au/science/about/our
regulation of leaf Mary Byrne
development. You will have the opportunity -people/academic-staff/mary-byrne.html
shape
to use and build skills in genetics, molecular
biology and developmental biology.
This project will use gene editing to study
gene function testing the potential to
Using gene
generate multiple mutations and to tag
editing to study https://www.sydney.edu.au/science/about/our
genes with a reporter to follow gene Mary Byrne
gene function in -people/academic-staff/mary-byrne.html
expression. You will have the opportunity to
plants
use and build skills in genetics, molecular
biology and developmental biology.
Investigating Wheat is one of the world’s most important https://www.sydney.edu.au/science/about/our
Mary Byrne
flower sources of food. A major goal in agriculture -people/academic-staff/mary-byrne.html
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