DARD 2014 Postgraduate Seminar Brochure

Postgraduate Studentships
Seminar 2014
18th September 2014
Greenmount Conference Centre
Postgraduate
Studentships
CAFRE - Antrim
Seminar 2014
Postgraduate
Seminar
Postgraduate Studentships
Seminar 2014
09.00 Registration: tea/coffee
09.20 Chair’s introduction:
Louise Warde Hunter, Head of Central Policy Group, DARD
09.30 Guest speaker: Dr. David Graham, Deputy Chief Executive & Programme
Manager, Animal Health Ireland
10.10
DARD Funded PhD Student Presentations
Joanna Keenan (Year 3): Metabolomic profiling of stages of beef
production processes to develop new strategies to minimise occurrence
of meat of inferior quality.
10.25
Caroline Finlay (Year 2): Scale, production and biological diversity
on farmland: small fields and small hedges or large fields and large
hedgerows?
10.30
hilip Robinson (Year 3): An evaluation of socioeconomic factors
P
affecting the control and eradication of bovine tuberculosis (bTB) in
Northern Ireland.
10.45 Tea/coffee break - poster display of 1st year projects
11.15
Jodie Wilson (Year 2): The impact of septic tank systems as
non-agricultural pollution sources to local surface waters.
11.20
Kirsty McLaughlin (Year 3): The impact of aquatic noise pollution on fish
farming.
11.35
Elizabeth Magowan (Year 2): Badgers, bio-security and bovine
tuberculosis: risk assessment, implementation and effective knowledge
transfer.
11.40
Jonathan Lappin (Year 3): Ixodid ticks: vectors for emerging diseases.
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
11.55
Anna Gillespie: (Year 2): Development of high-value functional
dairy produce from low-value whey proteins: Mining for anti-diabetic
peptides.
12.00
Thomas Fleming (Year 3): Assessment and management of emerging
nematode pests of Northern Ireland grassland and cereals.
12.15
Victoria McCready (Year 2): Investigating the effects of aquaculture
on biodiversity and assessing the sustainability of aquaculture
systems.
12.20
Jonathan Cray (Year 3): Applied ecology of barley and potato
pathogens: development of disease-control strategies to enhance both
food safety and sustainability of crop production.
12.35
Pei Pei (Year 2): Economy-wide impacts of the Rural Development
Programme in Northern Ireland.
12.40
Arlene Robertson (Year 3): The local effects of new immigration
in Northern Ireland: Exploring experiences of social cohesion and
integration.
12.55Andrew Stevenson (Year 2): Optimisation of biomass and activity of
saprotrophic microbes in agricultural Northern Ireland soils.
13.00Chair’s closing remarks
Award of prizes for best 3rd year talk, best 2nd year talk and best 1st
year poster.
13.15
Lunch
First Year Induction
13.50Induction - information for 12 new students commencing their research
in October 2014 and their supervisors.
For further information on the DARD Postgraduate Studentships visit the DARD
website at: www.dardni.gov.uk/postgraduate-study.htm
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
Metabolomic profiling of stages of beef
production processes to develop new
strategies to minimise occurrence of meat
of inferior quality
Joanna Keenan
School of Biological Sciences, Queen’s University Belfast
Supervisors: Dr. Mark Mooney, QUB, Prof. Chris Elliott, QUB
and Dr. Bruce Moss, AFBI
Pre-slaughter processes that lead to physical and psychological stress of cattle are major
factors negatively impacting on meat quality, welfare standards and processing efficiency.
In particular, the development of dark, firm and dry (DFD) beef linked to pre-slaughter stress is
one of the most prevalent meat quality defects affecting the sustainability of the red meat sector
in Northern Ireland. However, no clear understanding of the issues surrounding pre-slaughter
stress and its link to downstream meat quality has yet evolved, and therefore is difficult to
mitigate against the detrimental consequences of pre-slaughter stress.
The aim of this current research was to apply state-of-the-art metabolomic profiling techniques
to differentiate between stressed and unstressed cattle prior to slaughter, and to identify
potential markers that can provide better information on the association between pre-slaughter
stress and meat quality.
Results from downstream meat quality measurements as assessed by carcass ultimate pH
and colour have revealed that bulls exposed to stress through mixing 24 hours pre-slaughter
produced DFD beef. In contrast however, urinary free cortisol, an accepted conventional
indicator of physiological stress, was unable to distinguish between bulls mixed prior to slaughter
and an unmixed group of bulls. This indicates that this parameter is not useful as a marker of
pre-slaughter stress in cattle. In a separate study, urinary free cortisol decreased as cattle were
held in lairage for an increased period of time with no significant correlation to meat quality
observed (Keenan et al., 2014 BSAS). Metabolomic
profiling of urine has revealed significant novel
metabolite markers that show a clear association
with the development of DFD beef. These newly
revealed markers will help combat the incidence of
DFD beef by providing an enhanced understanding
of the stress response animals’ display in relation
to pre-slaughter processes which will subsequently
allow for intervention strategies to be implemented
within the red meat sector.
Postgraduate Studentships
Seminar 2014
Year Three
Postgraduate
Seminar
Scale, production and biological
diversity on farmland: small fields and
small hedges or large fields and large
hedgerows?
Caroline Finlay
School of Biological Sciences, Queen’s University Belfast
Supervisors: Prof. Ian Montgomery, QUB, Dr. Jack Lennon, QUB,
Dr. Alison Cameron, QUB and Dr. Neil Reid, QUB
The hypothesis underpinning this research is that there would be an advantage to both
biodiversity and farmers if fields were changed from small areas with small hedges, to
large areas with large hedgerows. It will be important to understand the trade-off between
large field sizes and the size necessary in hedgerows to compensate for any loss of habitat
through removal of small hedgerows. This trade-off will have to be understood in a number
of different industries and areas, taking into consideration field patterns already existent in
Northern Ireland.
Image processing techniques have been used to digitize hedgerows in a number of
different areas of Northern Ireland using simple 3-band imagery. Using remote sensing
methods to measure a proxy of vegetation health allows the effect of hedgerows and effect
of field size on production to be quantified.
Preliminary results for grass
and silage production suggests
that fields of 2-3ha in size
have higher yields than
smaller or larger fields. Also
hedgerows that lie in an EastWest orientation have a larger
negative effect on yield than
hedges with a North-South
orientation. This is due to the
directionality of sunlight from
a southerly direction and the
effect of shading from EastWest hedgerows reducing crop
yields.
Year Two
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
An evaluation of socioeconomic factors
affecting the control and eradication of
bovine tuberculosis in Northern Ireland
Philip Robinson
Department of Geography, Durham University (DU)
Supervisors: Prof. Peter Atkins, DU, Prof. Gavin Bridge, DU
and Dr. Divya Tolia-Kelly, DU
Bovine tuberculosis (bTB) remains a significant animal health problem in N. Ireland and
eradication has not yet been achieved despite an intensive cattle testing programme which
began as a statutory programme in 1959. In this research I investigated the experiences
and opinions of the key actors in the bTB eradication programme in N. Ireland and sought
to explain why the goal of eradicating the disease has not yet been achieved. The primary
focus was upon cattle farmers and vets, but other stakeholders from the agricultural
industry were also interviewed. Using a qualitative social science approach to bTB provides
an alternative way of evaluating animal disease control and guiding future policy.
Despite early success in the programme between the late 1950s and early 1970s leading
almost to the point of eradication, the recurrent cycles of increasing and decreasing
bTB incidence since then have created atmospheres of confusion, disillusionment, and
disengagement at the frontline of control. There is therefore a need for open and frank
discussion amongst all the parties involved in bTB eradication as to why the programme is
necessary, what it aims to
achieve, and how to target
those goals within set time
frames in the future through
a partnership approach. This
research demonstrates that
animal disease control is
as much about re-building
relationships of trust and
confidence between people
as it is about animals,
disease ecology, economics,
scientific complexity, and the
technologies of detection.
Postgraduate Studentships
Seminar 2014
Year Three
Postgraduate
Seminar
The impact of septic tank systems as
non-agricultural pollution sources to local
surface waters
Jodie Wilson
School of Biological Sciences, Queen’s University Belfast
Supervisors: Dr. Lisa Connolly, QUB, Dr. Colin McRobert, AFBI
and Dr. Bob Foy, AFBI (Retired)
In Northern Ireland domestic wastewaters of the rural population are mainly treated
and dispersed by Septic Tank Systems (STS). There is a tendency for these systems
to discharge directly into waterways and drains due to the poor draining nature of the
soils which makes percolation unviable. Monitoring studies suggest STS contribute
directly to phosphorous loads, pollution and eutrophication risk. There are challenges
when attempting to assess the impact of STS on local surface waters since important
contaminants could, in principle, arise from non-domestic sources such as agriculture.
It is hoped that this project will help to build a picture as to impact of releases from septic
tanks on water quality using signature pollutants found in domestic wastewater as “tracers.”
This is potentially useful to differentiate the source of pollution when water quality issues
arise. Many of the emerging wastewater contaminants are endocrine disrupting chemicals
(EDCs) and therefore they are of heightened environmental concern. Endocrine disrupting
chemicals are compounds that at
certain concentrations can interfere
with endocrine (or hormone)
systems. They can mimic natural
hormones to either activate cellular
receptors (agonists) or block cellular
receptors (antagonists). Project
progress to date has centred on
the development and optimisation
of analytical methods (UPLC-MS/
MS), for detecting and assessing the
concentration of the “tracers” in river
water.
Year Two
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
The impact of aquatic noise
pollution on fish farming
Kirsty McLaughlin
School of Biological Sciences,
Queen’s University Belfast
Supervisors: Dr. Hansjoerg Kunc, QUB
and Prof. Bob Elwood, QUB
Much work has been done on the effects of underwater noise pollution, a rapidly growing
concern, on fish behaviour and physiology. However, we have little understanding on
how noise affects fitness enhancing behaviours such as foraging and those involved with
reproduction. Further still, our knowledge of the effects of long term noise exposure, a
situation that closely mimics that seen in the wild and in industry settings, on fish remain
limited (see Wysocki 2007). Therefore, the impact of underwater noise pollution on
essential fitness related behaviours and processes such as: reproductive success; parental
care; and foraging must be examined.
To achieve this, I investigated: (i) the impact of different noise levels on foraging, sheltering
and activity; (ii) the effect of long term noise on pair bond formation and nest site selection;
and (iii) the effect of long term noise exposure on parental care and reproductive success.
The species used in this PhD is Amatitlania nigrofasciata, a freshwater species with similar
hearing capabilities to commercially important species such as cod. Dissemination of
findings from this study to fisheries and aquaculture policy makers will enable informed
decisions to be made about fish welfare protection and the sustainability of fisheries/
aquaculture expansion.
Postgraduate Studentships
Seminar 2014
Year Three
Postgraduate
Seminar
Badgers, bio-security and bovine
tuberculosis: risk assessment,
implementation and effective knowledge
transfer
Elizabeth Magowan
School of Biological Sciences, Queen’s University Belfast
Supervisors: Dr. Mike Scantlebury, QUB, Dr. Nikki Marks, QUB,
and Dr. Robin Skuce, AFBI
Bovine tuberculosis (bTB) is regarded as one of the most challenging agricultural diseases,
inflicting financial and emotional hardship on farming communities, impacting on animal
welfare and culminating in annual costs to the government of approximately £30 million
in compensation in Northern Ireland. Despite several decades of research and efforts to
control/prevent transmission of the disease either by cattle-cattle transmission or between
livestock and wildlife reservoirs, the disease remains one of the most significant biosecurity
challenges to date. Although potential intra- and inter-specific bTB transmission routes
have been identified, the relative risk of such routes remains unclear. If these various
transmission risks were better understood, better bio-security measures could be identified
and implemented.
A range of techniques, from morphometric
analysis, GPS tracking and land surveying
to stable isotope analysis, are currently being
employed to help create a detailed picture of
bTB transmission and biosecurity in Northern
Ireland. Aspects of animal husbandry, badger
ecology and farmers’ opinions and attitudes,
that may play a role in TB transmission
between and within cattle and badger
populations, are being assessed to identify
suitable, cost-effective biosecurity solutions
to decrease bTB incidence in cattle.
Year Two
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
Ixodid ticks: vectors for emerging
diseases
Jonathan Lappin
School of Biological Sciences, Queen’s University Belfast
Supervisors: Dr. Nikki Marks, QUB
and Prof. Aaron Maule, QUB
In the past decade, Ixodid ticks have become an increasing problem within Europe and are
known to transfer a multitude of pathogens including bacteria, viruses and protozoans.
Various biotic and abiotic factors have been shown to influence tick ecology. Three of
these critical factors are micro-climate, vegetation and animal hosts, which play a key role
in the distribution and abundance of Ixodid ticks, especially the most common species,
Ixodes ricinus. Numerous tick species have been identified in N.I. including: I. ricinus; I.
canisuga; I. hexagonus; and I. trianguliceps. These species have been found on a wide
range of hosts, including: cattle; sheep; dogs; hedgehogs; mice; and badgers, which
emphasises their potential to act as disease reservoirs in transmission to/from many hosts,
including agricultural animals and humans. An example of this is the case of Babesiosis
(Red water disease), which was diagnosed and sequenced in numerous regions of
counties Fermanagh and Tyrone, and is known to be present in red deer Cervus elaphus
populations (Zintl et al. 2011).
Distribution of Ixodes spp, and
ultimately spread of disease, is
also linked with grant-funded
afforestation/reforestation and
associated deer populations
which act as perfect
reproduction final hosts
(Ruiz-Fons & Gilbert 2010). With
this in mind, it is imperative to
monitor and potentially control
the spread of ticks and the
diseases they may carry within
Northern Ireland.
Postgraduate Studentships
Seminar 2014
Year Three
Postgraduate
Seminar
Development of a high-value functional
dairy produce from low-value whey
proteins: mining for anti-diabetic peptides
Anna Gillespie
Institute for Global Food Security, School of Biological
Sciences, Queen’s University Belfast
Supervisors: Dr. Brian Green, QUB, Dr. Tassos Koidis, QUB,
and Prof. Chris Elliott, QUB
Preliminary scientific studies have demonstrated for the first time that the addition of a
small amount of whey protein isolate (WHI) to the diet curbs diet-induced obesity, glucose
intolerance and potentially delays/prevents the onset of type 2 diabetes. Wider population
studies suggest a link between dairy consumption and reduced risk of type 2 diabetes and
obesity. Therefore, it is very timely that the health-promoting mechanisms of whey protein
be elucidated and commercially exploited.
This project is investigating the mechanisms in which whey protein isolate imparts these
beneficial effects. Initially the focus was on finding small protein fragments with bioactivity
(bioactive peptides), but our research has found more potential anti-diabetic activity in
the full-length intact whey proteins. The next stage is to investigate how to deliver these
proteins to the intestine without being degraded during the digestive process so they can
elicit their effect. Animal or human trials should follow prior to discussions and formulation
of functional food products. Such products appeal to an increasingly health-conscious
population and also to escalating numbers of obese and diabetic people. Such products
will help the Northern Ireland dairy industry become more competitive and less reliant on
commodity products.
Immunofluorescence of hormone
GLP-1 in intestinal cells
Immunofluorescence of hormone
GLP-1 in intestinal cells
No treatment
Exposed to cheese whey
Year Two
Mechanisms by which whey may impart
beneficial effects
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
Assessment and management of
emerging nematode pests of Northern
Ireland grassland and cereals
Thomas Fleming
School of Biological Sciences, Queen’s University Belfast and
Pest Molecular Biology Group, Agri-Food Biosciences Institute,
Newforge
Supervisors: Prof. Aaron Maule, QUB
and Dr. Colin Fleming, AFBI
Plant parasitic nematodes (PPN) are invertebrates which cause huge losses in agricultural,
forestry and horticultural crops across the world. PPN damage in pasture and cereals is
often difficult to detect in Britain. When combined with other stresses, however, damage can
be significant, even leaving some land unusable for cereal production. There is currently
very little information on the PPN species present in Northern Ireland pasture and cereal
fields, and given the importance to local agriculture of these crops, and the expected
increases in soil temperature, the impact of these parasites is of growing concern. This
project attempted to assess the risk to NI agriculture from PPNs and to evaluate some
possible management options for growers. Specific objectives were:
1) to determine which PPNs are currently causing crop damage and identify those species
likely to emerge as more serious pests in the future;
2) to identify factors linked to soil type and local climate which may influence the distribution
and occurrence of different PPNs;
3) to examine the efficacy of natural plant resistance in crop varieties for managing PPNs; and
4) to assess the potential of naturally derived biostimulants for reducing the effects of abiotic
and biotic stress, including that caused by PPN attack.
Project results to date include a survey of NI pasture and
cereal fields which identified a diverse range of PPNs, with
several species detected at damaging levels. This also
identified environmental factors including rainfall and soil type/
quality, which may affect nematode distribution and density
in NI. Screening crop varieties on the NI recommended
lists identified plant resistance which may be effective for
managing PPNs, particularly the very destructive root knot
nematodes. Finally, experiments showed that certain natural
biostimulants appear to induce systemic plant resistance,
again offering a useful future PPN management tool for the
NI industry.
Postgraduate Studentships
Seminar 2014
Year Three
Postgraduate
Seminar
Investigating the effects of aquaculture
on biodiversity and assessing the
sustainability of aquaculture systems
Victoria McCready
School of Biological Sciences, Queen’s University Belfast
Supervisors: Dr. Nessa O’Connor, QUB, Dr. Jon Houghton,
QUB and Prof. Philippe Archambault, Université du Québec à
Rimouski, Canada
Shellfish cultivation in Northern Ireland is dominated by mussel (Mytilus edulis) and
oyster (Crassostrea gigas) production with an estimated value of £4.53 million per annum.
Reported impacts associated with intensive aquaculture include organic enrichment,
changes to benthic community structure, degradation of seagrass (Zostera sp.) habitats,
and aquaculture structures (e.g. anchors, ropes and buoys) may provide favourable
settlement conditions, for asexually reproducing jellyfish polyp life stages.
To quantify the effects of current aquaculture practices in Northern Ireland this project aims
to: (i) test the settlement capability and survivorship of jellyfish polyps on artificial substrate;
(ii) investigate the ecological interactions among jellyfish polyps and other benthic
competitors, to determine how they compete for resources on hard substrates;
(iii) investigate the impact of biodeposit production from bivalve aquaculture on seagrass
health and associated grazer communities; and (iv) quantify the physiochemical and
biological impact of kelp aquaculture on the benthos. Findings to date on jellyfish polyp
settlement and survivorship are contrary to previous settlement studies, where planulae
(jellyfish larvae) were observed selecting
horizontal under-hang habitats. Polyps survived in
abundance in vertical orientations, possibly owing
to use of a larger experimental arena and the
incorporation of a current, ensuring food, oxygen
and waste removal were sufficient. A secondary
study, investigating the ecological interactions
among jellyfish polyps and other benthic
competitors (mussels, sponges and seaweed)
associated with aquaculture platforms
will also be discussed.
Year Two
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
Applied ecology of barley and potato
pathogens: development of disease
control strategies to enhance both food
safety and sustainability of crop production
Jonathan Cray
School of Biological Sciences, Queen’s University Belfast
Supervisors: Dr. John Hallsworth, QUB and
Dr. Jonathan Houghton, QUB
Late blight and post-harvest dry-rot of potato tubers, caused by the fungus-like Phytophthora
infestans and the true fungus Fusarium spp. respectively, are major potato diseases not just
in Northern Ireland, but also in many places worldwide.
The aims of this project have been to identify and evaluate potential biological control agents
(BCAs) by: i) studying the ecology of microbial communities in the natural habitats of these
disease-causing organisms and determining key species; ii) screening for and identifying
hostile activity from these species towards the disease-causing species; iii) utilising species
interactions and manipulation of environmental parameters to both optimise any hostile
activity and to determine the failure points of the diseases; and iv) determining the efficacy of
the control under field-relevant and/ or field-trial conditions.
Results and conclusions to date include the characterisation of competitive interactions
between potential BCAs and other microbes, including disease-causing fungi (Cray et
al. 2013a; The biology of habitat dominance: can microbes behave as weeds. Microb.
Biotechnol.); identification and quantification of the mode-of-action of antimicrobial
substances produced by BCAs (Cray et al. 2013b; A
universal measure of chaotropicity and kosmotropicity.
Environ. Microbiol.); identification of the mode-of-action
of novel, natural antifungal compounds (Cray et al.
2014a; Chaotropic and hydrophobic stress mechanisms
of antifungal substances. 17th Reinhardsbrunn
Conference on Modern Fungicides Proceedings), and;
the isolation of novel microbial strains from Northern
Ireland which are inhibitory to Phytophthora infestans
and Fusarium species (Cray et al. 2014b; Inhibition
of potato pathogens by Bacillus amyloliquefaciens. In
Growth inhibition of Fusarium sambucinum by
preparation).
a bacterium, Bacillus subtilis, on nutrient agar.
Postgraduate Studentships
Seminar 2014
Year Three
Postgraduate
Seminar
Economy-wide impacts of the Rural
Development Programme in Northern
Ireland
Pei Pei
School of Biological Sciences, Queen’s University Belfast
Supervisors: Dr. Ziping Wu, AFBI, Dr. Alberto Longo, QUB
and Prof. John Davis, AFBI
The Northern Ireland Rural Development Programme (NIRDP) is a key policy for NI rural
areas. One of the main policy-focusing sectors in NI, the agri-food sector is predominantly
rural-based, and growth in this sector is important for the economy as a whole. From an
economic perspective, any policy shocks will not only have direct impact on the agri-food
sector in rural areas, but also far reaching impacts on other parts of the economy and
urban areas. This research establishes a conceptual framework to evaluate the economywide impacts of policies and market shocks to NI rural areas, and aims to provide evidence
for the strategic development of the NIRDP. The core framework is a database capable of
describing the full circular monetary and goods flows between rural and urban components
of the NI economy. The unique features of the created database include:
• using production and institution accounts to represent the structure of the NI economy;
• disaggregating agriculture, food processing and tourism related sectors to prioritise
policies, dividing institutes to capture monetary flows; and
• distinguishing rural accounts from
urban to measure the rural
contribution to the NI economy.
By linking the bespoke database,
the framework is able to capture
the complex interactions in the NI
economy. Subsequently, based on
demand analysis, the work would
simulate the NI Rural Development
Programmes and evaluate
the corresponding direct, indirect
and induced impacts on the wider
economy.
Year Two
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
The local effects of new immigration in
Northern Ireland: exploring experiences
of social cohesion and integration
Arlene Robertson
School of Sociology, Social Policy and Social Work
Queen’s University Belfast
Supervisors: Dr. Sally Shortall, QUB
and Dr. Sirin Sung, AFBI
This research focuses upon the employment experiences of migrants working within
Northern Ireland’s food processing industry, as employers respond to competitive
pressures arising from their position within a supply chain dominated by major retailers. It
is argued that access to migrant labour, along with conditions of surplus labour supply, and
the weak employment protection enjoyed by temporary agency workers (predominantly
migrants), has enabled food processing employers to transfer the pressures of a highly
competitive market onto vulnerable workers who, in turn, face insecurity within the labour
market.
Within the UK food industry, a significant transformation has taken place in terms of supply
chain relationships, most notably, a shift in power to a relatively small number of major
retailers, namely, Tesco, Asda, Sainsbury’s and Morrisons (Precision prospecting, 2005:
20, DEFRA, 2006). Competition between these major retailers around pricing is typically
intense, and, in turn, suppliers positioned upstream in the supply chain have been subject
to downward pressure on product costs, as well as increased demands related to hygiene
and quality standards (James and Lloyd, 2008; Shuttleworth, 2008). At the same time,
the introduction of just-in-time production systems by major retailers has allowed them to
transfer the challenges of demand variations onto food processing suppliers.
Against this context, food processing employers have turned to new forms of labour control
as they seek to minimise labour costs, whilst continuing to meet demands for short term
flexibility from customers. In short, the use of agency workers (predominantly foreign
nationals), has enabled employers to transfer the pressures of the product market onto
their labour force. Conditions of excess labour supply, along with the weak employment
legislation enjoyed by temporary agency workers (in particular, minimal protection against
unfair dismissal) has enabled employers to impose intensified workplace regimes,
downgraded employment conditions and demands for long, short and variable working
hours onto workers, who show minimal resistance due to employment insecurity, or, in
other words, fear of job loss.
Postgraduate Studentships
Seminar 2014
Year Three
Postgraduate
Seminar
Optimisation of biomass and activity of
saprotrophic microbes in agricultural
Northern Irish soils
Andrew Stevenson
School of Biological Sciences, Queen’s University Belfast
Supervisors: Dr. John Hallsworth, QUB
and Dr. David J. Timson, QUB
Saprotrophic microbes derive their nutrition via the decomposition of complex organic
material. Their activities are essential for soil nutrient cycles, particularly in agricultural
systems where nitrogen, potassium and phosphorus are required by crop plants (and
ultimately become incorporated into insoluble plant-cell components). In addition, soil
saprotrophs enhance soil fertility, structure, biodiversity and productivity. For instance
fungal growth and the production of humic substances can enhance the formation of soil
particles, which in turn increases both soil aeration and drainage. Humic substances also
increase soil water holding capacity as well as retention and release of ions which can be
used by crop plants (i.e. cation exchange capacity). Saprotrophic mycorrhizal fungi can also
have symbiotic interactions with crop plants which increase vitality, vigour and yield of the
latter.
Agricultural soils account for approximately
76% of the total land area in Northern Ireland,
and are primarily used for pasture land. These
soils are treated with organic cattle slurries and
manures, as well as inorganic fertilizers, but
no comprehensive study has been carried out
to determine the impact of these applications,
in combination with other environmental
parameters, on the biology and ecology of
saprotrophic microbes. This forms the focus
of the current project, with the ultimate aim
of identifying and quantifying these impacts
in order to mitigate undesirable agricultural
consequences.
Year Two
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
Improved calf performance: assessment
of new vaccine technologies to address
production losses associated with Bovine
Respiratory Disease Complex
Joanne Lemon
School of Medicine, Dentistry and Biomedical Sciences,
Queen’s University Belfast
Supervisors: Dr. Ultan Power, QUB
and Dr. Michael Welsh, AFBI
Bovine respiratory disease (BRD) is the single largest reason for morbidity and mortality
in cattle under 2 years of age and has huge economic consequences, estimated to
cost around £60 million per annum to the UK. These losses are a culmination of direct
costs, such as from mortalities and carcass removal, and indirect costs, such as from
necessary housing alterations, increased labour needed during outbreaks and vaccination
or therapeutic treatment. Growing demands lead to further intensification of farming in
Northern Ireland, resulting in an increased incidence of respiratory disease outbreaks.
BRD arises as a result of many microbiological factors, farm husbandry and management
practices and control requires a holistic approach from scientists, farmers, vets and policy
makers.
This project aims to address the indirect
financial losses associated with vaccination
against Bovine respiratory syncytial virus
(BRSV) - a major pathogen implicated in the
complex - by the creation of a novel vaccine
using proprietary nanoparticles. The bovine
immune system recognises specific peptides
of the BRS virus. These peptides will be
assessed to ensure they are recognised and
generate an immune response within cattle
before inclusion into a unique vaccine with
the nanoparticles. This new nanoparticle
technology will allow the creation of a
potentially more efficient vaccine to deal with
some of the indirect costs associated with
bovine respiratory disease.
Postgraduate Studentships
Seminar 2014
Year One
Postgraduate
Seminar
Hedgerow cutting regimes
and breeding bird success
Siobhán Porter
School of Biological Sciences, Queen’s University Belfast
Supervisors: Dr. Alison Cameron, QUB
and Dr. Richard Holland, QUB.
Hedgerows represent one of the most important semi-natural habitats for wildlife in the
agricultural landscape. In Northern Ireland, 36 species of bird are known to regularly
depend on hedgerows for food, shelter, protection from predators, and breeding purposes.
Although hedgerows have the potential to provide an important habitat for many farmland
species, their biodiversity value is greatly dependent on management.
This project aims to provide a better understanding of the effects of hedgerow cutting on
farmland birds, and the mechanisms through which these occur, with the view of providing
evidence for future hedgerow management policies.
Lines of investigation include:
i) How does the timing and frequency of
hedgerow cutting impact breeding bird
communities?
ii) How does hedgerow cutting influence
the abundance and diversity of
important invertebrate prey for breeding
birds?
iii) How does the timing and frequency
of cutting affect the functioning
of hedgerows as a resource for
overwintering birds?
Year One
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
Maximising piglet performance
pre-weaning through sow and piglet
management and nutrition during
gestation and lactation
Aimee-louise Craig
School of Biological Sciences, Queen’s University Belfast
Supervisors: Dr. Elizabeth Magowan (AFBI)
and Dr. Niamh O’Connell (QUB)
Genetic selection for prolificacy in pig production has increased litter size, which now
exceeds 12 pigs weaned per litter (Martin, 2011). However, a systematic literature search
identified that there are very few relevant papers reporting results on litter sizes of 11 or
more piglets weaned per sow. Lactation diets to maximise mammary structure and milk
yield for sows rearing large litters (13 or more piglets), therefore requires more investigation.
Limited research in this area suggests that amino acids other than lysine may become
limiting in high producing sows (Boyd et al., 2000; Kim et al., 2000; Soltwedel et al., 2006).
This project aims to collate relevant scientific material regarding improvement of birth and
wean weight and reduction within-litter variation and formulate novel gestation and lactation
diets with the aim of improving weaning weight of piglets. Also, some common nursery
management techniques for small and weak pigs will be scientifically validated.
Postgraduate Studentships
Seminar 2014
Year One
Postgraduate
Seminar
Identification of endemic avian viruses
causing poultry production problems and
their quantification by the development of
novel diagnostic tests
Ryan Devaney
School of Biological Sciences, Queen’s University Belfast
Supervisors: Dr. Victoria Smyth, AFBI
and Dr. Alan Trudgett, QUB
This project concerns the diagnosis and control of runting-stunting syndrome (RSS) in
broiler chicken flocks. RSS is an enteric disease characterised by various symptoms such
as decreased body weight in broilers, intestinal lesion development, diarrhoea and, in
severe cases, mortality. By using Roche 454 next generation pyrosequencing, this project
aims to characterise the viral microflora associated with RSS infections, including the main
causative agents and other viral pathogens which may be associated with the disease.
Once a significant viral profile has been established, a series of experimental infections will
take place in order to determine the viral community responsible for RSS infection. Novel
diagnostic tests will be considered, using real time quantitative polymerase chain reaction
(RT-PCR) techniques, along with the viral sequence in order to identify conserved sites
along the viral genome which would be appropriate for the targeting of primers to allow
future detection easier and more cost efficient.
Year One
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
The epidemiology of Hymenoscyphus
fraxineus, the cause of ash dieback,
in Northern Ireland
Emma Baxter
School of Biological Sciences, Queen’s University Belfast
Supervisors: Prof. Alistair R. McCracken, AFBI,
Dr. Louise R. Cooke, AFBI, Prof. Ian W. I. Montgomery, QUB
Ash dieback affects common ash (Fraxinus excelsior) causing dieback of leaves, shoots
and branches, and eventually tree death. It has spread across Europe since the early
1990s. This disease was first reported in Northern Ireland by DARD on 16 November
2012. The causal fungus was first identified in 2006 as Chalara fraxinea and its perfect
stage, Hymenoscyphus pseudoalbidus, in 2011. In 2014, the fungus was reclassified as
Hymenoscyphus fraxineus.
Ash is a common native tree species in Northern Ireland and is of ecological and
commercial importance. If H. fraxineus becomes established, it has the potential to change
the face of our landscape, impacting on the environment, biodiversity and economy.
Most information on H. fraxineus and its spread relates to countries with different climatic
conditions from Northern Ireland, particularly the Nordic countries where winters are colder.
This project is the first to investigate the epidemiology of the pathogen within Northern
Ireland.
Postgraduate Studentships
Seminar 2014
Year One
Postgraduate
Seminar
Investigation into the extent of pleurisy in
pigs in Northern Ireland, and the associated
management and disease risk factors
Natalie Brush
Agri-Food and Biosciences Institute and School of Medicine,
Dentistry and Biomedical Sciences, Queens University Belfast
Supervisors: Dr. John McKillen (AFBI)
and Dr. Ultan Power (QUB)
Respiratory diseases are considered to be one of the most common and expensive
diseases that affect pigs reared under confined and intensive conditions. Pleurisy in pigs
is caused by several different viral and bacterial agents, and the extent and prevalence of
the disease can also depend upon a range of different factors, including farm management
practices and environmental conditions. There is currently limited data and information on
the extent or impact of pleurisy on Northern Ireland pig herds. Pleurisy results in economic
losses due to reduced feed efficiency, poor growth, and reduced carcass quality and
vaccination costs. In Northern Ireland, pleurisy results in an approximate loss of £3.75 per
affected pig. Respiratory diseases also have an adverse effect on animal welfare.
Main research aims:
(a) Determine the prevalence of pleurisy
in Northern Ireland pig herds;
(b) Identify the microorganisms involved
and assess the farm management, and
disease-related risk factors for pleurisy;
and
(c) Determine the economic impact of
pleurisy in pigs in Northern Ireland.
Year One
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
Nutritional aspects of cow’s milk
produced in Northern Ireland
Maria Kelly
Northern Ireland Centre for Food and Health (NICHE),
University of Ulster, Coleraine
Supervisors: Dr. Alison Yeates, UUC, Dr. Maria Mulhern, UUC,
Dr. Kirsty Pourshahidi, UUC and Prof. JJ Strain, UUC, and
Dr. Ann Fearon, AFBI and Dr. Samuel Mitchell, AFBI
Iodine and selenium are essential trace elements with important roles in human health.
Iodine is essential during pregnancy and infancy for brain development while selenium
is important for immune function. Iodine is required for the production of the thyroid
hormones, triiodothyonine (T3) and thyroxine (T4). Selenium interacts with iodine in the
conversion of T4 to the biologically active T3 hormone. Previous studies have indicated
that dietary intakes of iodine and selenium are inadequate and are of current public
health concern(1, 2). Milk makes an important contribution to daily intake of iodine (33%)
but is a less important source of selenium (6%). A number of factors, including season of
production and pasteurisation, may influence content of iodine and selenium in milk. The
aim of this project is to quantify the iodine and selenium content of cows’ milk produced in
Northern Ireland and to investigate the effect of milk consumption on nutritional status of
consumers. Concentrations of iodine and selenium will be measured in cows’ milk over a
12 month period and a human intervention study will be conducted to investigate the effects
of milk consumption on the biological status of iodine and selenium.
1
ates B, Lennox A, Prentice A, et al. (2014) National
B
Diet and Nutrition Survey. Results from Years 1,
2, 3 and 4 (combined) of the rolling programme
(2008/2009 – 2011/2012). Available online:
https://www.gov.uk/government/uploads/system/
uploads/attachment_data/file/310995/NDNS_Y1_
to_4_UK_report.pdf
2
anderpump M, Lazarus J, Smyth P, et al. (2011)
V
Iodine status of UK schoolgirls: a cross-cultural
survey. Lancet 377 (9803), 2007-2012.
Postgraduate Studentships
Seminar 2014
Year One
Postgraduate
Seminar
New student research topics - due to commence
1 October 2014
• Maximising the market and non-market benefits of small, privately owned woodland through
eco-labelling: identification of willingness-to-pay - Kieran Higgins
Supervisor: Dr. Alberto Longo, QUB
• Competitiveness and resilience of Northern Ireland total beef supply chain
- Stephanie Brooks
Supervisors: Dr. Moira Dean, Institute for Global Food Security (IGFS) QUB,
Prof. Chris Elliott, (IGFS) QUB
• Genetic variation in Native Irish trees under threat from emergent fungal pathogens
- James Brown
Supervisors: Dr. Jim Provan, QUB, Prof. Ian Montgomery, QUB
• Trophic impacts of gelatinous zooplankton on commercial fisheries species
- Donal Griffin
Supervisors: Dr. Jonathan Houghton, QUB, Dr. Chris Harrod, Queen Mary University
London (QMUL)
• The role of higher protein forages and home grown protein sources within Northern Ireland
dairy production systems - David Johnston
Supervisors: Dr. Conrad Ferris, AFBI, Dr. Niamh O’Connell, QUB
• Non-anthelmintic control of nematode parasites of livestock - Zakk Massey
Supervisors: Dr. Angela Mousley, QUB, Dr. Jonathan Dalzell, QUB, Prof. Aaron Maule, QUB
• Predicting the potential threat of the interactions between climate change and invasive
species to Northern Ireland sea fisheries and aquaculture - Josie South
Supervisor: Prof. Jaimie Dick, QUB
• An evaluation of grouping and housing systems for Northern Ireland beef cattle
- Victoria Thompson
Supervisors: Dr. Francis Lively, AFBI, Dr. Denise Lowe, AFBI, Dr. Niamh O’Connell, AFBI
• Exploiting Remote Sensing Technologies to Improve farm Animal Management and
Production - Christina Mulvenna
Supervisors: Dr. Nikki Marks, QUB, Dr. Michael Scantlebury, QUB, Dr. Lewis Halsey,
Roehampton University, Prof. Aaron Maule, QUB
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
• An investigation of the regulatory efficiency of the Water Framework Directive in
Agriculture in Northern Ireland and its effect on biological water quality - Annabel Sharma
Supervisors: Dr. Brian Jack, QUB, Dr. Diane Burgess, AFBI
• An investigation into the robustness of a local beef scheme operating as part of the
NI Food Supply Chain in an international market. Is there a need for Government
intervention? - Jennifer Fegan
Supervisors: Prof. Gillian Armstrong, UU, Prof. Paul Humphreys, UU
Postgraduate Studentships
Seminar 2014
Postgraduate
Seminar
Notes
Postgraduate Studentships
Seminar 2014
DMS 14.15.093

Download Report