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BEES Postgraduate Booklet 2017-2018

Postgraduate Information Book

2017-2018

http://www.ucc.ie/en/bees/

February 2018

This handbook was prepared by the School Graduate Studies Committee and should be used as a reference manual, and not as a definitive document.



Table of Contents

Head of School Foreword 41 The School of Biological, Earth and Environmental Sciences 4

1.1 School Staff Members 81.2 Research Interests 101.3 School and associated Research Centres 18

1.3.1 The Aquaculture & Fisheries Development Centre (AFDC) 181.3.2 The Aquatic Services Unit (ASU) 20

2 Postgraduate Study in the School of BEES 222.1 Graduate Studies Committee 222.2 Postgraduate Representatives/Staff Meetings/School Assemblies 232.3 Registration 232.4 Fees 232.5 Demonstrating and other teaching 242.6 Postgraduate training modules 252.7 Invigilation/supervision of exams 252.8 Possible sources of additional funding 252.9 Annual progress review 262.10 Submission of Theses 27

2.10.1 PhD Theses 272.10.2 MSc Theses 27

2.11 Publications 272.12 Communication 272.13. School of BEES Postgraduate Travel Fund 282.14 The Delap Postgraduate Research Prize 29

3 Facilities & Equipment 313.1 Working Space 31

3.1.1 Desk space 313.1.2 Laboratory usage 313.1.3 Plant Growth rooms (Butler Building) and glasshouses 313.1.4 Maintenance and provision of culture collections and tissue culture stock material (Butler Building) 33

3.2 Fridges, freezers, cold rooms and constant temperature rooms 333.3 Photography and audiovisual (AV) Equipment 333.4 Chemicals and other consumables and equipment 343.5 Microscopes, balances and SEM 343.6 Field equipment 343.7 Computing facilities and printing 353.8 Computer purchase and network connection 35

3.8.1 Purchase of a standard Windows machine 353.8.2 Purchase of a customised Windows machine 363.8.3 Purchase of a standard Apple product 363.8.4 Purchase of customised Apple products 363.8.5 Portable devices/laptops 373.8.6 UCC Network Policy 373.8.7 On-campus computer support 373.8.8 Internet 373.8.9 Computer training and courses 39

3.9 Vehicle 393.10 Requisitions and expenses 39


3.11 School workshop 393.12 Waste management 39

4 Insurance and security 394.1 Accident & Travel Insurance 394.2 Security 404.3 Safety 404.4 Disability facilities 40

5 Other Services 415.1 Library facilities 415.2 Languages 415.3 Careers information 415.4 Accommodation 425.5 Student Health and Dental Service 425.6 Student financial support 435.7 Students’ Union 435.8 Crèche 435.9 Student Advisor & Ombudsman 445.10 Term dates for 2015/2016 44

Appendix I Copying and plagiarism 45Appendix II Health and Safety information 48Appendix III Demonstrating hours log sheet 49


FOREWORD

Welcome to the School of Biological, Earth and Environmental Sciences (BEES). On behalf of the School I would like to take this opportunity to formally welcome you and wish you all the best in your pursuit of your MSc/PhD degree. Your contribution to research and teaching in BEES is critical and we look forward to your participation. This booklet is a guideline to facilitate your time in the School, which we hope will be a fruitful and stimulating one.

Wishing you satisfaction and success in your postgraduate work,

Professor Sarah CullotyHead of School

1. The School of Biological, Earth and Environmental Sciences (BEES)

The School’s mission is to “advance and apply our understanding of the natural world through excellence in research, teaching and innovation”.

The School includes the disciplines of Ecology, Environmental Science, Geology, Plant Science and Zoology. The School of BEES is one of the primary academic units in the College of Science, Engineering and Food Science (SEFS). The School of BEES serves the needs of the community by meeting the growing demand for well-trained graduates and postgraduates, including specialists in many of the applied fields such as Earth Sciences, Ecology, Environmental, Freshwater and Marine Biology, Geology, Pathobiology, Fisheries and Aquaculture and Plant Biotechnology. Courses offered through the School include:

A) The following single honours undergraduate degree programmes: BSc Applied Plant Biology BSc Earth Science BSc Ecology and Environmental Biology BSc Environmental Science BSc Geography BSc Geology BSc International Field Geosciences BSc Zoology BSc Science Education (Biology)

B) The following taught postgraduate programmes:

MSc Applied Environmental Geology MSc Marine Biology PGCert Marine Biology

The following Diploma courses are run through the Centre for Adult & Continuing Education (CACE) in association with the School of BEES:

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Diploma in Field Ecology (final year 2017-2018) Diploma in Geology

The School also hosts a number of visiting students who spend either a full year or part of the year studying in the School.

The School of BEES, University College Cork, is located in three buildings on the North Mall (Distillery Fields) campus, approximately 15 minutes from the main campus: the Enterprise Centre, the Butler Building and the Cooperage. The School is engaged in teaching, research, training and consultancy. Much of its environmental research is carried out in association with the Environmental Research Institute (ERI), a multidisciplinary institute with over 300 researchers across UCC. Professor Sarah Culloty, Head of BEES, is also Director of this institute. The ERI is located in two dedicated Buildings: one on the Lee Road and at the Beaufort Building in Ringaskiddy, County Cork. Additional activities of the institute take place in associate schools. The ERI contains a number of dedicated centres including the Aquaculture and Fisheries Development Centre, located within the School in the Cooperage, and the MaREI centre focusing on marine and energy research based in the Beaufort Building). A number of BEES postgraduates and postdoctoral researchers are based at the ERI, in both the Lee Road and Beaufort Building facilities.

Enterprise Centre (EC)The School is administered from the EC. The Head of School’s office is on the first floor. The offices of the School Manager, Alison O’Connell, and Senior Executive Assistants (SEAs) Ms Elaine Kelly and Ms Mary McSweeney are located on the first floor opposite the central stairway in the School Administrative hub. The offices of academic staff in the Zoology and Ecology fields are also located on the first floor. Professor Marcel Jansen and Professor Astrid Wingler (both Plant Biology) also have their offices in the Enterprise Centre, at the west end of the first floor, while Dr Valerie Cummins (Zoology) is currently based in the Butler Building. Dr Debbie Chapman, Head of the Environmental Science Discipline, is currently based in the ERI, where she is leading a major UN-funded project on water quality, GEMS.

In addition, there are offices for researchers and a Seminar/Meeting Room that can be booked through the School office. The Geology Museum is incorporated into the Ted Nevill laboratory on this floor at the west end of the building (Room CEC1.04).

There is also a café on the ground floor which is open from 8.30 – 4.00 during term time.

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Cooperage BuildingThis building contains three teaching laboratories; several research laboratories; a number of workshops; an open access MSc hub room (wifi-enabled) for BEES postgraduates; and the offices of some of the technical staff (Dr Elizabeth Cotter, Mr Luke Harman, Dr Alison Harrison, Dr Ronan Hennessy, Ms Mary Lehane, Mr Allen Whitaker). A number of BEES emeritus professors also have offices here, along with Professor John Benzie and Dr Philip McGinnity. There are also several Postdoctoral/Senior Researcher offices and postgraduate offices.

Specialist LaboratoriesAquaculture Hatchery (G.41)Aquaculture Laboratory (G.07)Aquaculture Tank Room (G.42)Ecology/Marine Laboratory (G.28)Ecotoxicology & Water Chemistry Laboratory (G.28)Microscope Room (G.22)Molecular Genetics and Immunology Laboratory (G.25)Palynology Room (G.07B) Post-mortem Laboratory (G.05)Rock-cutting Laboratory (G.32A)Thin Section Room (G31)Wet Laboratory (G.06)

Ecology/Marine LaboratoryThe Ecology/Marine laboratory can accommodate up to 13 researchers in the fields of terrestrial, aquatic and marine ecology. The majority of the researchers use the lab to carry out microscope work. The laboratory contains work stations (available on a hot-desk basis), storage facilities, sinks, balances, two ovens and a muffle furnace. A constant temperature room is located adjacent to the laboratory for cold storage of samples, and there are also several sheds for long-term sample and equipment storage. The laboratory is in constant use and so it is imperative that all users maintain the lab in a clean and tidy state. Additionally, health and safety regulations must be adhered to at all times. All samples and equipment must be clearly labelled, especially when stored in the communal areas. A copy of the laboratory rules can be found in the laboratory or can be obtained from the Laboratory Manager.

Other FacilitiesFirst Aid Room (G.33) Canteen (G.36)Museum (G.14) Photocopier/Hub Room (G.37)Controlled Temperature Rooms (n=4) Toilet/Shower (male and female)Chemical Store (G.09)

The Aquaculture and Fisheries Development Centre (AFDC) is located in this building. This centre is embedded within BEES but is also part of the ERI. Its Director is Professor Sarah Culloty.

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Butler BuildingThe First Year Teaching Laboratory is situated in this building on the ground floor. A number of staff with a plant science interest have their offices on the first floor (Dr Barbara Doyle-Prestwich, Dr Eoin Lettice) while those in the field of Geology are located on the top floor (Dr Ed Jarvis, Dr Maria McNamara, Dr Pat Meere, Dr John Reavy, Dr John Weatherill and Professor Andy Wheeler). The Jackson Laboratory (BB2.20) and the Sweetman Laboratory (BB2.21) are also located on this floor. In addition, the following Technical Staff are located on the ground floor: Ms Eileen Daly, Dr Eileen Dillane, Mr Don Kelleher (Chief Technical Officer) and Ms Mairéad Kiely. The office of the Senior Demonstrator (Dr Simona Paolacci) is located on the ground floor next to the technicians’ office, along with a number of postdoctoral researchers. Several postgraduates and Postdoctoral/Senior Researchers have offices on the ground and second floors of the Butler Building.

Specialist Laboratories:Plant Physiology Lab (1.21) Pathology/Microbiology Lab (1.5)Molecular Biology (1.3)

Other facilitiesPlant Growth Rooms (G.18, 1.18) Chemical Store (1.22)Solvent Store (1.23) Cold Room (1.20)Common Room (G.22) Toilet/Shower (1.24)Preparation Room (G.23) First Aid/Nursing Mothers Room (2.17)Chlorophyll Fluorescence and Imaging (1.13)

Environmental Research Institute (http://www.ucc.ie/en/ERI/)The ERI Buildings are located on the Lee Road about 3km from the North Mall Campus on the Lee Road towards Blarney, and in the Beaufort Building in Ringaskiddy about 16km away. Professor Sarah Culloty is its Director, and it is managed by Dr Paul Bolger. The Beaufort Building has an Operations Manager, Mr Jeremy Gault, and the Manager of MaREI centre is Dr Gillian Bruton. Ms Helen McMahon provides administrative support in the Lee Road building and Ms Cora Edwards and Gráinne Lynch in the Beaufort Building.

The Aquatic Services Unit (Manager, Ger Morgan) is located in the Lee Road Facility.

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1.1 School of BEES Staff Members

Academic StaffProfessor John BenzieDr Fidelma ButlerDr Deborah Chapman (Head of Discipline Environmental Science)Professor Sarah Culloty (Head of School)Dr Valerie CumminsDr Javier del Barco-TrilloDr Tom Doyle (from April 2018)Dr Barbara Doyle-PrestwichDr Simon HarrisonDr Rossana Henriques Professor Marcel Jansen Dr Ed Jarvis Dr Mark Jessopp Dr Kate Kiseeva (from April 2018)Dr Eoin LetticeDr Rob McAllen Dr Maria McNamaraDr Patrick Meere Dr Jean O’DwyerProfessor John O’Halloran (Chair of Zoology, UCC Registrar and Senior Vice President)Professor John Quinn (Head of Discipline Zoology, Ecology)Dr Tom Quirke Dr Ruth Ramsay (sabbatical 2017)Dr John Reavy Dr Tom ReedProfessor Emer RoganProfessor Mathijs Schouten (Visiting Professor)Dr Timothy SullivanDr John WeatherillProfessor Andy Wheeler (Head of Discipline Geology)Professor Astrid Wingler (Head of Discipline Plant Science)

Emeritus/a ProfessorsProfessor Gavin Burnell Professor Alan CassellsProfessor Tom Cross Professor John DavenportProfessor John GambleProfessor Paul Giller (Chair of Ecology)Professor Ken Higgs Professor Peter JonesProfessor Máire MulcahyProfessor Alan Myers

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Adjunct ProfessorsProfessor Kathryn BrunerMr Garth Earls Professor David Reid (Marine Institute, Galway)Professor Richard Smosna

Research Staff Butler BuildingDr Aaron LimMs Karen CoganDr Grace CottDr James JepsonDr Sean JohnstonDr Luke McDonaldMs Naomi O’ReillyDr Simona PaolacciDr Enrico PirottaMr Christopher RogersDr Richard Unitt

Enterprise CentreDr Paddy Sleeman

Cooperage/AFDCDr Sam BayleyDr Jamie CoughlanDr Jodie CraneDr Gabrielle DavidsonDr Steve HuttonDr Adam KaneDr Ipek KulahciDr Sharon LynchDr Philip McGinnityDr Maria O'Mahoney Dr Michael ReichertMs Kathryn Simmons

CMRC Staff who teach and/or supervise BEES studentsDr Michelle Cronin

Technical Support Dr Elizabeth CotterMs Eileen DalyDr Eileen DillaneMr Luke HarmanDr Alison HarrisonDr Ronan HennessyMr Don Kelleher (Chief Technical Officer)Ms Mairéad Kiely

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Ms Mary LehaneDr Giliane OdinMr Allen Whitaker

Administrative SupportMs Siobhán BoyleMs Alison O’Connell (School Manager)Ms Elaine KellyMs Mary McSweeney

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1.2 Research Interests of Staff

Research in the School reflects the interests of the staff, but School staff members are always willing to discuss any aspect of ecological, environmental, geological, zoological and plant science research with prospective postgraduate students. Some of the main research areas are outlined below.

1.2.1 Geology research interestsThe principal research strengths are:

Palaeozoic and Mesozoic palynology: Palynology is the study of organic-walled microfossils (such as pollen, spores, and dinoflagellate cysts) while palynofacies analysis is the study of all particulate organic remains preserved in sediments. Current research in this area comprises stratigraphic and systematic palynological studies of Lower Palaeozoic, Devonian, Carboniferous and Cretaceous rocks in Ireland and selected sections in Europe and North America. Emphasis is placed on the taxonomy, biostratigraphy and evolution of the microfloras (Dr Ed Jarvis, Professor Ken Higgs).

Evolution of terrestrial ecosystems in the Devonian rocks of Ireland: With particular reference to the biodiversity of the fauna and flora, and their palaeoecology and palaeoenvironmental setting. Specific areas of research include: the Lower Devonian Dingle Group in Co. Kerry; the Middle Devonian Caherbla Group on the Dingle Peninsula; the late Middle Devonian Valentia Slate formation on Valentia Island (Tetrapod trackway sites); the Upper Devonian Kiltorcan Formation in Co Kilkenny; and Harrylock Formation at Hook Head, Co. Wexford (Dr Ed Jarvis, Professor Ken Higgs).

Caledonian and Variscan structural studies of the British Isles and adjacent areas: Current studies include an investigation of the role and nature of upper crustal fluids in the development and Variscan inversion of the Munster/South Munster Basins. Work is also underway looking at developing and testing new strain analysis techniques in low grade sedimentary rocks and applying them to regional studies in the Variscan of south west Ireland and northern Spain and to Laramide deformation in Western Montana. Analogue models are being developed to investigate the role of basement architecture in basin inversion (Dr Pat Meere, Dr John Reavy).

Petrogenetic and structural studies of Caledonian magmatism: This involves combined petrological and structural studies into the nature of Caledonian magmatism in Ireland and Britain (Dr John Reavy).

Marine Geology: Current research concerns geological studies in both deep marine and near-shore/shelf environments using expertise and in-house facilities for seabed mapping (side-scan sonar, multibeam echosounder, video imagery and GIS), shallow seismics interpretation and sediment core analysis. A key research strength is on deep-water, temperate carbonates and the geology cold-water coral ecosystems. Other focuses include sediment transport and benthic boundary layer processes. Quaternary palaeoenvironmental marine archives and applied marine studies (Professor Andy Wheeler,).

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Fossil Preservation: Current work on fossil preservation – ‘taphonomy’ focuses on the preservation of non-biomineralised ‘soft’ tissues (e.g. integument, muscle, internal organs) in fossils, and applying them to studies of the anatomy, physiology, ecology and behaviour of ancient animals. A current major focus is the preservation of pigmentary and structural colours in various animal groups, in particular, insects and feathered taxa, throughout the Phanerozoic, in order to better understand the evolutionary history of coloration patterns in extant animals and aspects of the fossilisation process. Current research involves both fossil-based and experimental approaches to investigate the processes of soft tissue degradation and preservation. By understanding the various biological, sedimentological and diagenetic factors that control soft tissue preservation, we can begin to tease apart patterns (biases) in the fossil record (Dr Maria McNamara).

Ore Geology and Mineralogical Research: Current research involves the development of genetic models for ‘Irish-Type’ ore deposits based upon a multidisciplinary approach including mineralogy, fluid chemistry and geochronology (Dr Pat Meere, Dr Richard Unit, Dr Sean Johnston).

1.2.2 Plant Science, Zoology, Ecology and Environmental Science research interests

There are a wide variety of opportunities available for research in these areas, with a number of specialist research laboratories fitted with modern equipment and instruments. The School has an Aquaculture and Fisheries Development Centre, including a fish/shellfish holding facility; while the related Aquatic Services Unit provide a wide range of environmental consultancy services. There are three research field laboratories at the Marine Nature Reserve at Lough Hyne (http://www.ucc.ie/en/bees/research/loughhyne/); and there is a strong collaboration with and utilisation of research facilities at Fota Wildlife Park (http://www.fotawildlife.ie/) and the TEAGASC centre at Moorepark (http://www.agresearch.teagasc.ie/moorepark/). Access is also available to scanning and transmission electron microscopes, photomicrographs (fluorescent and normal illumination) and a full range of computing facilities. Fieldwork equipment includes field vehicles, boats, SCUBA, cameras (still and video, film and digital), environmental monitoring units, electro-fishing units and sampling and analytical equipment for marine, freshwater and terrestrial ecology.

Marine Biology and Ecology: Ecology of marine shores. Biology and conservation of marine mammals. Fisheries. Biology of inter-tidal and sub-littoral animals with particular reference to Lough Hyne. Marine fouling and antifouling. Biology and conservation of sea turtles. The impact of climate change and introduced species in the marine habitat. Seagrass ecosystems. Ecophysiology of plant and animal communities in salt marshes and brackish lagoons in relation to environmental influences.

Freshwater Biology, Ecology and Management: Invertebrate community ecology. Agricultural and urban influences on freshwater ecology. Wetland ecology and biodiversity. Riparian ecology. Lake littoral ecology. The ecology

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of mammals (e.g. otter), birds (e.g. mute swan and dipper ecology). The distribution of breeding birds and of fish in relation to water quality. The ecology, biology and genetics of salmonid fishes. Water quality monitoring and assessment. Biology and ecology of plankton and coarse fish communities (especially in relation to water quality). Water resources management, especially lakes and reservoirs.

Terrestrial Biology and Ecology: Mammals (e.g. badgers, bats, deer, hares, goats, hedgehogs, squirrels), birds (e.g. gulls), reptile and insect (e.g. dung beetles) ecology. Forest biodiversity assessment and management. The use of birds and invertebrate populations in native and plantation forests as indicators of biodiversity in our forests with a view to informing management decisions.

Animal Behaviour: Behaviour of birds, exotic animals such as cheetahs, macaques, oryx and lemurs in captivity and environmental enrichment (in collaboration with Fota Wildlife Park). Animal personality and cognition. Domestic animals, e.g. dairy cattle; and marine and freshwater animals.

Pest Control: Effects of agricultural practice on cereal pests. Parasitic pests carrying diseases. Birds as hazards to aircraft and human health.

Health and Pathobiology: Understanding the health, diseases and immune systems of animals. A wide range of fish and shellfish are studied. The relationship of disease to environment. Water quality and human health, including the impacts of agriculture on human health through the contamination of water resources.

Pollution and Environmental Disturbance: The biology, ecology and management of waste treatment lagoons. Effects of flooding on river animals. Effects of afforestation on river water quality and ecology. Effects of pollutants and pesticides on marine, freshwater animals and birds.

Ornithology: The ecology and population dynamics of terrestrial and aquatic birds. Applied aspects include bird surveys for ecological assessment, birds at airports and dumps and pollution monitoring.

Aquaculture and Fisheries: Biology and aquaculture potential of commercial shellfish and finfish and the potential of other new species for aquaculture development. Fish biology. Fisheries management and conservation. Deep water fisheries. Research into the genetics, diseases and nutrition of farmed species. Restoration of fisheries, aquaculture/environment interactions.

Molecular Ecology: Fisheries (population definition/stock discrimination in Atlantic salmon, migratory brown trout, whiting, Atlantic cod, European hake, blue whiting, poor cod, turbot, Atlantic halibut, haddock, herring, orange roughy, Crassostrea gigas, genus Mytilus, Ruditapes phillipinarum, Haliotis discus hannei, Nephrops norwegicus and the ommastrepid squid, Illex condetii and Todaropsis eblanae). Aquaculture (investigation of reared strains of Atlantic salmon, rainbow trout, Atlantic cod, haddock, turbot and Atlantic halibut, to compare genetic composition with wild progenitors, to assign progeny to parents, and to guide stocking, ranching and farming). Interactions between natural populations and inadvertently (farmed escapes) and deliberately (stocked and

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ranched) released reared strains of Atlantic salmon, using field experiments and microsatellite DNA “tags”; and the effect of diseases introduced by reared salmon on MHC composition of wild salmon and brown trout. Molecular systematics (Nearctic and Palearctic crow species; echinoderms of the genus Asterina; gadoid fish of the genus Trisopterus). Conservation genetics (endangered riparian brush rabbit from the San Joaquin valley CA, USA; golden eagles (in relation to re-introduction to Ireland); common, bottlenose, striped and Atlantic white-sided dolphins; endemic Bermudan skink; cubozoan jellyfish Chironex fleckeri). Agriculture (milk protein genetics in dairy cattle (with Teagasc); the European badger Meles meles, in relation to inbreeding and bovine tuberculosis). Forensics (predators of sheep ticks Ixodes ricinus; corvid, columbid and larid birds, involved in collisions with aircraft). DNA markers currently used are microsatellites, transcribed sequences (e.g. MHC, growth hormone, transferring, pantophysin (synaptophysin) and rhodopsin), SNPs and sections of the mitochondrial genome. Currently, there is involvement with the Beaufort Fish Genetics programme, EU Salsea Merge, Eircod and an SFI project on bottlenose dolphins.

Conservation and protected areas: Management of protected areas (e.g. national parks and nature reserves) and conservation of rare/endangered species. Impacts of alien species on native flora and fauna and the development of control measures for these species. Promotion of increased sustainability by use of native flora in landscaping.

Sustainable agriculture: Based on tissue culture, plant genetic manipulation, biological control and precision or site-specific agriculture and horticulture.

Mutation breeding and selection in vitro to develop fungal resistant lines: The use of autotrophic cultures for the establishment and evaluation of biological inoculants for use in microplant establishment and in the field. Holistic biological control strategies involving combined applications of arbuscular mycorrhizal fungi, plant growth promoting rhizobacteria and elicitors of host plant resistance.

Plant communication systems: Spectral emissions and volatile stress signals. Given the deterioration of water quality in crop production, we are also investigating the association between human pathogenic bacteria in plants using green fluorescent protein (GFP)-labelled bacteria.

Functional genomics: Physiology, genetics, biochemistry of abiotic stress tolerance and biotic stress resistance (pathogen and pest); chemical signaling in plant-pest and plant-pathogen interactions; and the development of novel crops as sources of bioactive chemicals. The integration of fundamental and applied aspects.

Stress response: Our principal strategy has been to analyse induced mutants (primarily, isolated in wheat) altered with respect to broad-spectrum stress response. The second strategy has been to isolate or synthesise chemicals that elicit improved response to biotic or abiotic stresses.

Chemical signaling: The principal model system studied has been the potato cyst nematode (PCN)-potato interaction. Hatching factors (HFs) in the potato root leachate stimulate hatch of the specialist pest, PCN. Other systems studied

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include the wheat-Ustilago tritici (loose smut fungus) interaction and the tritrophic badger-blowfly-stinkhorn fungus interaction.

Novel crops: Using a combination of conventional genetics, natural product chemistry and agronomy, we are involved with commercial partners in two projects involving the domestication of wild plants as novel commercial sources of industrially significant carotenoids.

Genetic Engineering: Plant biotechnology for plant improvement using Agrobacteria and other bacterial genera. Use of biolistics and in planta transformation systems. Environmental safety of transgenics. Biotic stresses in plants and the use of stress markers to improve transformation efficiencies. Tissue culture of medicinal plants and the use of medicinal plants to treat human disease. Molecular detection of plant pathogens.

Molecular-physiological mechanisms underlying the adaptation and/or acclimation of plants to hostile environments, i.e. stress: This has involved work on herbicides and herbicide-resistance, heavy metals, drought, excess PAR, bacterial toxins and synthetic auxins.

1.2.3 Research Interests of Staff

Academic Staff and Emeritus Professors: please see individual staff pages at http://www.ucc.ie/en/bees/staff/

1.2.4 Research Staff (and associated academic staff member where applicable)

Dr Jamie CoughlanCurrently employed as a senior postdoctoral researcher investigating the stock composition of inshore Atlantic salmon fisheries operating off the coast of Ireland, using microsatellite DNA techniques. Other research activities include isolation and characterization of molecular markers and population genetic studies in a multitude of marine, freshwater and terrestrial species (e.g. haddock, cod, orange roughy, trout, golden eagles, badgers), as well as investigations of genetic variability of cultured fish and shellfish species. Also involved in a pilot project with the Marine Institute assessing the utility of single nucleotide polymorphisms (SNPs) as a tool to identify and manage mixed stock fisheries. (Professor Tom Cross)

Dr Michelle Cronin (based in MaREI, ERI)

Seal ecology including population assessment and distribution, foraging ecology and habitat use. Biological and physical interactions of top predators, including seals and seabirds, with fisheries. Currently working as a research fellow on the Beaufort-funded ‘Ecosystems approach to fisheries management’. Main focus is top predator habitat use and overlap with fisheries using telemetry technologies.

Dr Sharon Lynch

Currently employed as a research fellow in the shellfish health and disease research group and histology laboratory manager. Research interests include

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shellfish health (oysters, scallops, abalone, mussels, clams), immunology and life cycle studies of shellfish parasites and disease-causing pathogens. Diagnostic techniques, including cytology, histology, polymerase chain reaction (PCR) and in situ hybridisation (ISH), are routinely used to screen for parasites and pathogens. Currently involved in several EU-funded projects investigating the influence of climate change on shellfish productivity in the Irish Sea, shellfish restoration and the validation of diagnostic techniques routinely used to screen for shellfish pathogens and disease. Further information at http://research.ucc.ie/profiles/D026/slynch/Home. (Professor Sarah Culloty)

Dr Paddy Sleeman

Mammal ecology, in particular carnivores (badgers, foxes and lion) and bats, especially bats that forage on rivers; diseases, mainly tuberculosis and rabies, parasites and behaviour. Ecological reconstruction of islands off Africa and Madagascar. Organiser of the first, second and third Post-glacial Colonisation Conferences: www.fotawildlife.ie/mind-the-gap. (Professor Emeritus John Davenport)

Dr. Richard Unitt

My current work involves petrological and physical characteristics of high and very-high polished stone value (hPSV & vhPSV) stone aggregates. I will be comparing standard physical property testing against modern petrographic digital microscopy and metrology on a mixed volcano-sedimentary sequence. This will help to create exploration and calibration tools to an industry standard to identify and characterise future resources. Additional research includes mineralogy, fluid dynamics and paragenetic sequencing of copper-bearing ore deposits in Ireland. I also investigate industrial uses of the geophysical technique of electrical resistivity including outlining buried lithium pegmatites and quantification of quarry resources.

Dr. Sean Johnston

Sean’s PhD focused on metal enrichment in sediment and how this relates to wider geodynamic and geochemical variations in seawater chemistry. He worked on iron sulphides in black shales in order to unravel the nature of the depositional environment, metal enrichment process and what effect metamorphism has on trace element partitioning. Sean is currently working with the Cu Research Group in UCC looking at geochemical controls on the distribution of Cu deposits across southern Ireland.

Dr Jodie Crane

My primary research interests are in bioacoustics and seabird ecology. During my PhD I worked on the structure and function of call repertoires in birds, and how vocal communication mediates social behaviour within groups. I am particularly interested in whether social complexity drives vocal complexity, and in relationships between the different calls comprising a species’ repertoire. More recently, I have developed interests in the relationship between communication and

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cognition which I hope to explore using wild great tits as a model system, during my work with Professor John Quinn. My interests in seabird ecology have led to me becoming involved in a number of tracking projects around the UK and Ireland, and I currently lecture on seabird conservation in the postgraduate ‘Marine Megafauna’ module at UCC.

Dr Gabrielle Davidson

Gabrielle is a comparative psychologist and a behavioural ecologist with a keen interest in the development, function and evolution of cognition. Her doctoral work investigated how rooks, jackdaws and carrion crows respond to where others are looking (i.e. gaze sensitivity), and how this influences decision-making when foraging, finding nesting locations, guarding chicks and escaping predators. Her current research with Professor John Quinn focuses on developing rigorous cognitive tasks to investigate the evolution of intelligence in wild populations, using wild great tits as a model system. These methods will help us answer key questions regarding heritability of and selection on cognitive traits.

Dr Ivan de la Hera Fernandez

Using birds as main model organisms, I have tackled a wide range of fundamental ecological and evolutionary research questions, sometimes also with conservation implications. Most of my research is intended to better understand the natural variation in avian life-histories. In this regard, I am deeply interested in avian adaptations to migration, and particularly attracted by the way in which different costly life-history stages (i.e. moulting, breeding and migration) trade off against each other within the annual cycle of birds. In this new professional stage at UCC and within the EVOECOCOG project led by Prof. John Quinn, I expect to learn much about cognition and thus broaden my knowledge of life-history evolution.

Dr Michael Reichert

I am interested in the evolution of animal behaviours. Most of my previous research examined the evolution of acoustic communication behaviour in frogs and insects. I am particularly interested in the effects of the physical and social environment on behavioural plasticity in relation to aggression, signalling competition and female preferences. At UCC, I am working as a Senior Postdoc under a project led by Prof. John Quinn examining the evolutionary ecology of cognition in wild great tits http://ornithology.ucc.ie/current-projects/evolutionary-ecology-of-cognition/. For this project, I am particularly interested in how variation in cognition relates to variation in sexual signalling.

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1.3 School and associated Research Centres

1.3.1 The Aquaculture & Fisheries Development Centre (AFDC) (School of BEES, also part of ERI)

The AFDC (http://afdc.ucc.ie), which is located in the Cooperage, was established in 1987 to provide a focus for the collective aquaculture and fisheries expertise of UCC in a single entity in research and development; essentially, a centre of excellence. Physically, the AFDC consists of a purpose-built suite of laboratories and offices and recirculation units. Since its establishment, the AFDC has built up a significant public profile and, more importantly, has made a valid and valuable contribution to the development of aquaculture and fisheries, both nationally and internationally, through successful participation in research programmes, regional development and training initiatives. In 2014 the centre consisted of 32 personnel: 5 Principle Investigators, 2 Research Associates, 5 Postdoctoral Researchers, 5 Research Assistants, 12 PhD students and 3 MSc students. With 16 projects valued at ~ €9m running under the AFDC umbrella, the centre produces approximately 18 peer-reviewed publications per year. In these activities, the AFDC has co-operated with and maintains active links with universities, research institutions and companies worldwide. Professor Sarah Culloty is the current Director of the AFDC and Dr Maria O’Mahoney is the Manager.

Thematic Areas: The work activities of the AFDC can be grouped into themes on the basis of existing expertise and past projects.

Aquaculture Research (PI Professor Gavin Burnell)

Existing Culture Species: Optimisation of the production of existing cultured finfish and shellfish species. Development of new production strategies. Improvement of management and husbandry practices. Minimisation of environmental impact. Product and market development. Development of artificial diets.

New Species: Evaluation of the potential for the culture of new native species; finfish, shellfish and algae. Species and site selection. Growth evaluation and enhancement. Development of feeding formulations. Larval rearing technologies.

Novel Technologies: Development of novel production technologies. Design and commercial application of recirculation systems. Artificial reef design and enhancing productivity.

Shellfish Health Research (PI Professor Sarah Culloty)

Health and Disease: Health protocols and disease control in shellfish culture and fisheries. Undertaking health monitoring and disease testing. Epidemiology, pathology, pathogen life cycles, host response (i.e. physiology/immunology) and mechanisms to reduce the impact of disease including the development of resistant stock and diagnostics. Development of mechanisms to ameliorate the impact of disease.

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http://afdc.ucc.ie/


Marine Mammals and Fisheries Research (PI Professor Emer Rogan)

Fisheries Management: Fisheries biology and management of demersal and deep water fish species, such as hake and orange roughy. Impact of discarding on fish stocks and fish stock assessment. Modelling and distribution of fishing effort. Ecosystem approach to fisheries management.

Marine Mammal Ecology and Biology: Marine mammal fisheries interactions and the functioning of marine ecosytems, relating dietary analysis to bioaccumulation, migratory patterns and oceanographic and bathymetric parameters. Acoustics and genetics.

Molecular Genetics of Aquatic Animals Research (PIs Professor Tom Cross, Dr Phil McGinnity)

Molecular Genetics: Stock discrimination and enhancement. Broodstock development. Genetic Stock Identification of exploited fish species, conservation genetics of endangered species, population studies.

What facilities are available to you as a postgrad?

The AFDC facilities include recirculating fish and shellfish systems, laboratories (Wet and Dry) and offices. Seawater (Grade A) is delivered on-site and stored. The AFDC has facilities for seawater filtration and UV treatment, if required.

In the AFDC, there are three Tropical Marine Centre (TMC) 5000-litre Reservoir-Based Filtration Units. There are also a number of smaller scale recirculation systems which can be operated as marine or freshwater. These units, ranging between 500 and 5000 litres, can be used as holding facilities or for experiments/trials. There are also two temperature-controlled rooms, with photoperiod control available, in which a wide variety of research can be conducted. A range of tanks, pumps and auxiliary equipment is also available to allow the production of research specific systems/units to suit almost any form of aquatic research.

The freshwater and marine fish rearing areas are complete with the Oxyguard computerised water monitoring and analysis system. Video monitoring is also available. The indoor recirculation units consist of mechanical and biological water filtration, water treatment systems involving UV sterilisation and ozonation, and temperature control conditioning units to enable full control of environmental parameters/variables. Light intensity and photoperiod are available in some areas and may be locally controlled on a number of discrete systems. The range of tank designs and sizes available allows fish and shellfish to be held at each life cycle stage, and also for experimental replicates to be conducted. Algal culture and live feed production areas are available to support the culture of many species through their larval stages. A recirculating shellfish nursery system, broodstock holding/conditioning unit, thermally controlled hatchery and live feed production units are custom designed to provide a series of systems suitable to the needs of a number of shellfish species. The two tank rooms of the AFDC are fully backed-up with a 50KVa Generator fitted with an Automatic Transfer Switch (ATS) and Digi-dialler.

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The dedicated AFDC Laboratory houses water quality analysis equipment, a Beckman Z2 coulter counter (particle size analyser) and drying oven as well as the standard laboratory equipment. On-site laboratories provide dedicated research facilities and technical support essential to research at the AFDC.

Additional laboratory facilities available at the AFDC include:

Molecular genetics laboratory Water quality testing Wet lab/post mortem room Tissue culture laboratory Histology and Immunology laboratory

Whom should I contact about use of facilities?

Director, Professor Sarah Culloty Location: First Floor, Enterprise Centre. Tel: 021 490 4646. Email: [email protected]

Manager, Dr Maria O’MahoneyLocation: Room G.02 Cooperage Building. Tel: 021 4904541. Email: [email protected]

1.3.2 The Aquatic Services Unit (ASU) The Aquatic Services Unit (www.ucc.ie/asu) is a constituent unit within the Environmental Research Institute. The ASU undertakes environmental consultancy and research. Originally set up over 25 years ago as part of the Department of Zoology, it maintains strong links with the School of BEES. It has a proven track record in laboratory analysis, environmental monitoring and environmental impact assessment. The unit engages in collaborative research within UCC and with institutes in Ireland and abroad.

The ASU specialises in projects dealing with the aquatic environment, in freshwater, marine and transitional waters. In recent years it has greatly increased its survey capability for fish and aquatic invertebrates in inland and transitional water including surveys of freshwater pearl mussel, white-clawed crayfish and freshwater and estuarine fish using a broad range of methods.

Water quality impact studies and analysis in freshwater and marine waters are core specialisations of the ASU and they also undertake toxicity testing for Local Authorities and IPPC licence holding industries. The unit has developed a well-resourced, experienced and flexible field sampling capability, enabling prompt deployment anywhere in Ireland to collect water, sediment, soil, biological and other environmental samples.

Its analytical laboratory operates under a system of Good Laboratory Practice and has participated in an international Laboratory Proficiency Scheme (Aquacheck) since 1995 and more recently the Environmental Protection Agency’s laboratory proficiency. The unit has also developed close working links with a number of Irish and overseas approved laboratories for specialist analyses. Currently the ASU is an EPA-approved lab for 26 water quality parameters.

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http://www.ucc.ie/asu

mailto:[email protected]



Please contact Mr Ger Morgan ([email protected]) to discuss collaborations and costings for analysis

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2. Postgraduate Study in UCC and the School of BEES

The University Calendar is at http://www.ucc.ie/calendar/postgraduate/.

Information on admission to postgraduate studies for EU and non-EU applicants is at http://www.ucc.ie/calendar/postgraduate/General/info014.html

Information for first year postgraduate students: http://www.ucc.ie/en/graduatestudies/incoming/.

PhD degree regulations: http://www.ucc.ie/calendar/postgraduate/Doctor/index.html

MSc degree by research regulations and MSc degree by coursework and minor thesis regulations: http://www.ucc.ie/calendar/postgraduate/Masters/index.html

For all matter relating to submission of all theses (including forms for three months’ advance notice of submission) and results please see http://www.ucc.ie/en/graduatestudies/thesis/.

UCC Dean of Graduate Studies

The current Dean of Graduate Studies is Doctor Máire Leane.

Tel: +353 21 490 2810E-mail: [email protected]

Graduate School of the College of SEFS

The Head of the Graduate School of the College of SEFS is appointed for a three-year period. The current Head is Professor Justin McCarthy (Department of Biochemistry). He can be contacted at [email protected]. One of the roles of the Graduate School is to organise training workshops specifically for SEFS postgraduates, e.g. on careers management, induction for new SEFS research postgraduates and the Graduate School would welcome suggestions for new workshops or modules.

2.1 BEES Graduate Studies Committee

The function of the Graduate Studies Committee is to facilitate and review the progress of postgraduate research students in the School. The current Chair of the GSC is Dr Pat Meere ([email protected]). The committee works to implement the recommendations of the Academic Council Graduate Studies Committee on procedures for all matters relating to postgraduate degrees.

Ms Elaine Kelly looks after issues related to postgraduates and submits information regarding payment to new postgraduate students to Payroll, Fees Office and the Revenue Commissioners. This ensures the student is paid the stipend element of their studentship.

Please see the University document regarding the Code of Practice for Supervision 22




http://www.ucc.ie/en/graduatestudies/thesis/

http://www.ucc.ie/calendar/postgraduate/Masters/index.html

http://www.ucc.ie/calendar/postgraduate/Doctor/index.html

http://www.ucc.ie/en/graduatestudies/incoming/

http://www.ucc.ie/calendar/postgraduate/General/info014.html

http://www.ucc.ie/calendar/postgraduate/


of Research Students, which includes sections on the responsibilities of the student, responsibilities of the supervisor/supervisory team and responsibilities of the academic unit: http://www.ucc.ie/research/rio/ethics.html.

The Irish Universities Quality Board has produced guidelines for Good Practice in the Organisation of PhD Programmes in Irish Higher Education:http://www.iuqb.ie/news/latest_news13e1.html?article=8f6458a4-a515-4aa1-9110-a351c7eab1ab

2.2 Postgraduate Representatives/Staff Meetings

Postgraduate representatives/Staff meetings are held at regular intervals during the year, or on request to discuss particular issues. Any queries may be addressed to the chair of the Graduate Studies Committee, Dr Pat Meere.

Postgraduate representatives are elected each year by the postgraduate body in the School. The current representatives are Ms Maria Gkaragkouni and Ms Valentina Rossi.

We welcome approaches from postgraduates about any matter whatsoever. Matters may also be raised with the current postgraduate representatives. It is the Postgraduate Representatives’ responsibility to organise postgraduate meetings, which at present occur typically once a term, all postgraduates are welcome to attend. Postgraduate notice boards are located in the main postgraduate laboratories. E-mail: [email protected]

2.3 Registration

Please see websites given above about registration in your first and subsequent years.

Stipends will not be paid until after registration has been completed. If this causes financial problems for you, please consult the Head of School. Where fees are being paid through a grant, other than a college studentship, a letter is usually required at the time of registration, clarifying the source of funding. All PhD students carrying out research must be registered in all years until they submit. Candidates for Masters Degrees must be registered students in the academic session in which their thesis is presented.

2.4 Fees

Fees are payable for higher degrees. Responsibility for payment rests with the postgraduate student. A number of supporting mechanisms have been put in place to help pay for fees. Further information can be found on the Finance Office website at http://www.ucc.ie/en/financeoffice/fees/.

Funding for a PhD degree is divided into three categories:

Self-funding (sometimes augmented local authority grants); Research grants;

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http://www.ucc.ie/en/financeoffice/fees/


http://www.iuqb.ie/news/latest_news13e1.html?article=8f6458a4-a515-4aa1-9110-a351c7eab1ab

http://www.iuqb.ie/news/latest_news13e1.html?article=8f6458a4-a515-4aa1-9110-a351c7eab1ab

http://www.ucc.ie/research/rio/ethics.html


Research assistantships.

Fees for Non-EU Students: All students whose home residences are outside the European Union pay the Economic Fee. However, non-EU nationals may apply for a fee waiver: please contact the Fees Office for further details.

All enquiries regarding fees should be addressed to:Fees Office,University College Cork,Cork.http://www.ucc.ie/en/financeoffice/fees/ Tel: 021 490 2678

2.5 Undergraduate demonstrating and other teaching

All registered postgraduate research students in receipt of funding are required to demonstrate for 50 hours. Postgrads who are required to demonstrate over the 50-hour threshold will be paid for the additional hours worked. It is the individual postgraduate's responsibility to consult the person running the class and to prepare properly in order to demonstrate effectively. However, each lecturer usually holds a pre-practical talk prior to each laboratory practical to inform demonstrators of the layout of the practical and the topics involved. In the case of dissections, postgraduates should liaise with the relevant lecturer and technical officers if they require a specimen for practice prior to the practical. First year postgraduates will be given an introductory talk on the responsibilities and requirements of demonstrating. If for some reason a demonstrator is unavailable to fulfil their demonstrating responsibilities, it is up to the postgraduate to arrange a suitable replacement and to inform the lecturer/office of the situation, in advance. White coats should be worn during biology practicals (compulsory for first year practicals and during dissections).

Demonstrating responsibilities are allocated as much as possible based on the postgraduate’s own field of study. Elaine Kelly draws up the demonstrating schedule for Biology and Environmental Science postgraduates, while Pat Meere allocates Geology hours. From 2016-2017 onwards, all demonstrators are required to keep track of their hours: see Appendix for a copy of the tally form.

A BEES postgraduate module on Teaching and Learning for Graduate Studies (five credits) for postgraduate demonstrators and tutors, is available: http://www.ucc.ie/modules/descriptions/PG.html#PG6017

As part of demonstrating, you will be involved in the continuous assessment of undergraduate students. This is a serious responsibility, as these marks contribute to the students' yearly assessment and ultimately degree results. Lecturers can provide demonstrators with a breakdown of marks for each practical. Postgraduates will be told the deadlines for submission of marks to the lecturer.

Occasionally, postgraduate students may be asked to give lectures and this should be welcomed, since both demonstrating and lecturing provide invaluable teaching experience and should be noted on your curriculum vitae.

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http://www.ucc.ie/modules/descriptions/PG.html#PG6017

http://www.ucc.ie/en/financeoffice/fees/


2.6 Postgraduate training modules

From 2014-15 all new PhD students are registered on a structured PhD and are required to take a minimum of 15 credits of taught modules during their registration. The BEES module PG6017 may form five of these credits. If, following a Training Needs Analysis (TNA) with a student’s supervisor(s), it is decided that the student will not take any taught modules, applications for exemptions for the credit-weighted component is applied for at submission stage. A number of generic training modules are also available for UCC postgraduate students, particularly in their first year. Please consult the Dean of Graduate Studies for further information: [email protected]. Further details of the modules are available on-line at http://www.ucc.ie/calendar/postgraduate/Doctor/page008.html

Undergraduate modulesIn some cases, postgraduates may wish/need to sit in on lectures given to BEES undergraduates or taught postgraduates (e.g. GIS modules). Information about all modules can be found at: http://www.ucc.ie/modules/ while details of the timetables for each of them can be obtained from http://timetable.ucc.ie/ or from the course co-ordinator for the MSc Marine Biology.

2.7 Invigilating/Supervision of Exams

Students may apply to be considered for invigilating exams for which they will be paid. Further details can be found at http://www.ucc.ie/en/exams/invigilators/. Please contact the Exams Office for further information: [email protected].

2.8 Possible Sources of Additional Funding

Some external bodies may provide funding (on a competitive or application basis) for specific elements of postgraduate study.

Conference Travel: Science Foundation of Ireland Marine Institute British Council Research Grants American Association of Petroleum Geology

Research: Science Foundation of Ireland Irish Research Council Royal Irish Academy Marine Institute Heritage Council Department of Education European Union EU Cost Actions American Association of Petroleum Geology

For mobility via ERASMUS and SOCRATES, see http://www.ucc.ie/international. 25

http://www.ucc.ie/international

http://www.aapg.org/

http://www.cost.eu/

https://europa.eu/european-union/index_en

http://www.education.ie/en/

http://www.heritagecouncil.ie/home/

http://www.marine.ie/Home/

https://www.ria.ie/

http://www.ircset.ie/

http://www.sfi.ie/

http://www.aapg.org/

https://www.britishcouncil.org/education/science/researcher-links

http://www.marine.ie/Home/

http://www.sfi.ie/


http://www.ucc.ie/en/exams/invigilators/

http://timetable.ucc.ie/

http://www.ucc.ie/modules/

http://www.ucc.ie/calendar/postgraduate/Doctor/page008.html


http://www.ucc.ie/modules/descriptions/PG.html


2.9 Annual Progress Review for Research MSc/PhD Students in the School of Biological, Earth and Environmental Science

The progress review document for research students in the College of SEFS is available at http://www.ucc.ie/en/media/studyatucc/postgrads/formsandregulations/ProgressReviewPolicyforResearchStudents/pdf.

PROGRESSION SEMINAR: After 12 months the student will be required to submit a comprehensive report (1,500–2,000 words) and deliver a 20-minute presentation to a combined Thesis Committee. After the seminar the student will be questioned about the report and seminar. The purpose is to allow the Thesis Committee (one member of which sits on the GSC) to determine if the candidate should be allowed to continue with the Research MSc/PhD. The report should summarise the work to date and provide a detailed plan of Year 2 and an outline of Year 3 and Year 4 if applicable. A template will be provided for the report. In the event that progress to date is deemed unsatisfactory the student may (a) be advised to submit a revised report within 1 month or (b) be recommended to submit for a MSc or (c) have their candidature terminated.

Students, after 24 months of their PhD studies, will be required to submit annual progress report (1,500–2,000 words) to the GSC. A template will be provided for the report.

REVIEW SEMINAR: After 36 months, students engaged in a four-year PhD programme will be required to submit a comprehensive progress report (1,500–2,000 words) and deliver a 20-minute presentation to a combined GSC and thesis committee. After the seminar the student will be questioned about the report and seminar. The purpose of this seminar is for the GSC and Thesis Committees to review progress in the research programme and determine if there are any logistical impediments to completion of the PhD programme within four Years. The report should summarise the work to date and provide a detailed plan of Year 4. A template will be provided for the report. Students engaged in a three-year PhD programme who fail to submit a completed thesis after 38 months will also be required to have a Review Seminar.

THESIS SUBMISSION: Prior to the viva voce examination, the student will be required to give a Seminar (30 minutes) on the research results of the PhD. The purpose of this is to disseminate their research data and share their postgraduate experience. This seminar will be open to anyone to attend. Students have to be registered in order to submit their thesis. Details on the process of thesis submission are available at http://www.ucc.ie/en/graduatestudies/thesis/.

2.10 Submission of Theses

The time required for the analysis of data and writing up should not be underestimated! Writing-up sections as papers as you go along is preferable and is usually encouraged by the supervisor. In this way you will be able to see the thesis

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http://www.ucc.ie/en/media/studyatucc/postgrads/formsandregulations/ProgressReviewPolicyforResearchStudents/pdf

http://www.ucc.ie/en/media/studyatucc/postgrads/formsandregulations/ProgressReviewPolicyforResearchStudents/pdf


taking shape and you may be able to publish some of the work prior to submitting your thesis. One of the criteria for the degree of a PhD is that the work is worthy of publication, as a whole or part (see University Calendar for regulations).

For full details of submission of theses, please see http://www.ucc.ie/en/graduatestudies/dissertation/.

Please be fully aware of the School of BEES policy on copying and plagiarism (details in Appendix I).

Details on thesis binding are available from http://www.ucc.ie/en/exams/thesis/binding/

2.10.1 PhD theses

Please refer to the following websites with respect to submission of theses:


http://www.ucc.ie/calendar/postgraduate/Doctor/ABDoctoralExaminationProcedures.pdf

UCC permits PhD theses to be presented in the form of a Publication-based Thesis. The research described in a Publication-based Thesis will be presented in the form of a set of manuscripts or other scholarly outputs from the work undertaken during the PhD student’s period of registration, typically with each manuscript forming one chapter of the thesis. Postgraduate students in the School of BEES are strongly encouraged to present their doctoral thesis in this format.

If the Examiners recommend that the PhD degree be awarded, the candidate must re-submit one hard-bound copy of the PhD Thesis, embodying any changes prescribed by the Examiners, for UCC and a further bound copy (or copies) for the supervisor(s). Please note that your supervisor is no longer an internal examiner of the submitted thesis.

2.10.2 MSc theses

Please refer to the following websites with respect to submission of theses:


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http://www.ucc.ie/en/exams/thesis/binding/

http://www.ucc.ie/en/graduatestudies/dissertation/


2.11 Publications

It is normal procedure in Ireland that all publications resulting from a PhD project be published jointly, with the postgraduate as senior author and the supervisor(s) as junior author(s). Any other arrangement is a matter of agreement between the postgraduate and the supervisor(s).

2.12 Communication

PhD and MSc by research students are expected to give a seminar shortly after they commence their research and at least one other during their studies. Students on taught MSc courses present their Master’s projects at a seminar at the end of their studies. Regular consultation with your supervisor(s) is vital. Furthermore, postgraduates are encouraged to attend all discipline seminars.

Postgraduates are encouraged to attend one or more major meetings/conferences during their graduate studies and if possible to contribute a paper or poster. Some limited funding for BEES students may available from within the School (see BEES Postgraduate Travel Fund).

You will be expected also to produce one or more posters of your work for display in the School. In addition, postgraduate students are expected to attend lectures and seminars given by visiting academics and members of staff.

2.13 School of BEES Postgraduate Travel Fund

All registered BEES research postgraduates, whether in receipt of funding or not, are eligible to apply to the Postgraduate Travel Fund. Each application for funding will be considered on its own merit. The BEES Travel Fund will only usually be available to support one travel grant for a postgraduate student during his/her course of study with BEES.

The student needs to write a personal statement explaining the importance of attending a particular conference, meeting, workshop or, if a training course, the relevance to their research. If it is a conference, symposium or other similar meeting, the student must be presenting either a poster or paper: funding will not be provided simply for attendance. The abstract of this should be given to the GSC at the time of application for funding.

In the letter to the GSC, the student should show that s/he has attempted to secure funding from other available sources and that the activity cannot be funded through current grants (relevant documentation must be attached to the application).

Up to 75% of the unfunded amount may be granted for overseas conferences. With respect to local conferences, the GSC will consider funding the whole amount.

Students can be funded up to one year after the end of their scholarship, as long as the student does not have any funding from an alternative source (e.g. employment).

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Students should apply through the GSC Chair in writing three months in advance of a conference. The grant can cover the cost of economy class travel, reasonable accommodation, the registration fee and receipted meals. As the aim is to support as many students as possible, value for money must be demonstrated. Conditions for applying for funding will be reviewed each academic year.

Elaine Kelly looks after issues related to the administration of this fund.

2.14 The Delap Postgraduate Research Prize

The Delap Prize for postgraduate published research was inaugurated in 2017, and is named after Maude Delap, an Irish marine biologist who was the first person to observe and describe the full life cycle of jellyfish.

The prize is awarded to the best peer-reviewed academic paper (including review papers, book chapters) accepted for publication in a given academic year (1st

September – 31st August) by a registered or recently graduated postgraduate student. Applicants must clearly be the first/principal author of the publication and have the School of BEES as their primary affiliated institution. The prize is awarded at three levels: Gold (€900), Silver (€700) and Bronze (€500). The recipients of all three prizes in 2017 were recent graduates of the School. Each applicant is required to submit a digital (ideally PDF) copy of their research paper and a short statement (max. 200 words) outlining the potential impact sand novelty of the published research. They are also required to present evidence confirming that their work has been accepted for publication in an additional short statement (max. 100 words) outlining their specific contribution to the paper. Applications are sent using e-mail to the Chair of the GSC, copied to Elaine Kelly, and must be received before 17.00hrs on the 15th of September 2018. Judging for the awards will be carried out by a panel of five BEES staff members drawn from all disciplines within the School, and will include the HOS and the Chair of the GSC. The Chair of the GSC will chair the judging panel and will select School staff appropriate for the topic range of research papers submitted. Panel membership selection will be very sensitive to any potential conflict of interest between panel members and applicants. The judging criteria for the award will include the following four criteria: Journal Ranking (50%) : We will ask each Delap Prize applicant to select a single Science Citation Index (SCI) subject category as part of their application process and from which the applicant’s journal will be ranked. Nature and Science will be the default top 2 journals for all subject lists. Some journals may well appear on several subject category lists so it will be the responsibility of the applicant that they select a subject category that ranks their particular journal the highest.

Impact (15%): Our approach is to recognize both scientific and societal impacts. One approach to help us measure more broader societal impact is to use altmetrics which

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https://en.wikipedia.org/wiki/Maude_Delap



are non-traditional metrics used as an alternative to more traditional citation impact metrics, such as impact factor and h -index .

Novelty (15%): This will be primarily judged on the statement submitted by the applicant.

Applicant Contribution (20%): This will be primarily judged on the statement submitted by the applicant.

Prize winners will be required to give a short (10 minutes) presentation to the School at a dedicated Delap Prize Seminar event at the end of Semester 1 in the year of the award.

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https://en.wikipedia.org/wiki/H-index

https://en.wikipedia.org/wiki/Impact_factor

https://en.wikipedia.org/wiki/Citation_impact


3. Facilities and Equipment

Please note that use of specialised (common) equipment must be agreed with supervisors and technical staff.

3.1 Working Space

3.1.1 Desk space

Postgraduate students will be allocated desk/working space in one of the postgraduate offices. It is in the interest of all users to keep desk space clean and tidy. Offices are not to be used as laboratory space. PhD students who have not completed their studies by the end of their fourth year may be required to relinquish their bench space unless otherwise agreed with the Head of School. On completion of your postgraduate studies you should vacate your space ensuring you remove all personal belongings and specimens and return all School equipment. If you are to work in some other capacity and/or require space, you should consult with Professor Sarah Culloty

3.1.2 Laboratory Usage

Practical laboratories may have a laboratory manager, often one of the resident postgraduate researchers, with whom you are required to co-operate. Before undertaking any work in any laboratory you should find out who is the appointed manager. With respect to practical work, specialist activities must be carried out in the designated laboratories. Only those engaged in research in these designated laboratories (i.e. Freshwater and Marine, Histology (Dr Sharon Lynch), Ecotoxicology, Tissue Culture, Molecular laboratories) should work there and access is only by permission of laboratory manager or supervisor.

No access is permitted to the Radioisotope Laboratory in the Butler Building without prior permission from Professor Marcel Jansen. Intending users must undergo induction/training as directed by the College Radiation Officer.

Only those carrying out relevant research may gain access to the recirculation unit. The recirculation unit should not be used as a thoroughfare or for access to other laboratories and no sea-water should be removed from the tanks without prior permission from Luke Harman (ext. 4668), whom you should contact if you need to use any of the tanks.

3.1.3. Plant Growth rooms (Butler Building) and glasshouses

Internal growth rooms Ground Floor G18, First Floor 1.12Conditions: 16-hour photoperiod 08:00 – 24:00 hours

Temperature 22°C +/- 1–2°CThermostat Control set point 25°C

You must contact the Technical Officer(s) in charge of the Plant Growth room(s) prior to depositing any cultured plant material. The Technical Officer in Charge,

31


Eileen Daly, will allocate space and an ID monitoring badge. This monitoring badge will identify the user and the date the cultures were set up.

Users should ensure cultures are properly sealed: this applies particularly to explants set up on petri dishes. Users should also be vigilant in checking cultures for mite infestation. Should this arise it would pose a serious threat not only to an individual researcher’s material, but also to stock material in general. Users of the Plant Growth room(s) should also monitor cultures regularly. Contaminated cultures should be placed in autoclave bag(s) and disposed of following autoclaving. Any noticeable changes in Plant Growth room conditions should be immediately reported to the Butler Building Technical Officers.

External growth roomThis growth room is located within the shed adjacent/parallel to Glasshouse B. It has limited shelving with some fluorescent lighting. There is also a limited number of high pressure sodium lamps used for experiments in progress, as well as a UV Light box to aid sporulation of cultures. The Room operates on a 16-hour cycle with a temperature high of 19°C and low of 12°C.

Three growth cabinets and a drying oven are also located in the shed. Mairéad Kiely has responsibility for managing the external growth room and growth cabinets. For the present status of the room and cabinets please consult Professor Marcel Jansen.

GlasshousesThere are two glasshouses located to the west of the Butler Building. These are presently referred to as Glasshouse A (field crops) and Glasshouse B (horticultural glasshouse). Technical supervision the glasshouses is provided by Butler Building technical staff: please contact Don Kelleher for details. A set of guidelines is in place for good working practice: if you intend to use the glasshouses you must familiarize yourself with these guidelines and sign the relevant glasshouse logbook to that effect. During the course of the academic year there is likely to be pressure for space in each glasshouse as dictated by project experimental work.

Introducing soil or compost to (teaching) laboratories in the Butler Building should only be done under strict guidelines and with the prior approval of supervisory and technical staff. Restrictions are in place particularly regarding the Tissue Culture and Pathology laboratory and the Plant Growth rooms. Sterilisation of soil-based material in the autoclave room also requires the prior consent of technical staff. There are two autoclaves in the room adjoining the Tissue Culture laboratory. Requests can be directed to Eileen Daly and guidelines on safe and proper use will be provided.

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3.1.4 Maintenance and provision of culture collections and tissue culture stock material (Butler Building)

The repository of bacterial and fungal cultures is managed and maintained by Eileen Daly. Requests for cultures should be directed to Eileen as should applications for new items to be added to the current listing.

3.2 Fridges, freezers, cold rooms and constant temperature rooms

Samples stored in fridges and freezers should be well-packed and clearly labelled (with name and date), otherwise it is likely that they may be discarded during periodic clear-outs. Permission to store samples should be sought from the technician in charge. You should also try to store your samples for the minimum length of time necessary, as space is at a premium. Please note that only samples for molecular genetic studies may be stored in the -70°C and designated -20°C freezers in the Cooperage (please contact Professor Tom Cross if you need to use these freezers).

Similarly, the constant temperature rooms are mainly for experimental work and are not store-rooms. In the Cooperage the 4°C constant temperature room can be used to hold samples prior to their sorting, but the benches should be kept clear for experiments. Allen Whitaker is the Technical Officer in charge of this room.

In the Butler Building, you should check with the Technical Officer in charge of the Cold Room before using or depositing any materials therein. S/he will issue guidelines to authorized users on best practice associated with use of the cold room in addition to assigning designated and labeled storage space. An outline of allocated space is posted outside the cold room.

3.3 Photography and Audio-visual (AV) Equipment

Colour photographs (or colour printing) for your thesis have to be paid for by you and not the School.

The School of BEES has the following cameras available:

Samsung 4MP digital camera for field/lab Nikon 4MP digital camera for use only in lab Sony digital camcorder for use in field-limited use Microscope/camera set-up – permission only

All cameras must be booked before use, particularly field cameras and may be unavailable at certain times of the year.

Audiovisual equipment may be used in the building, by prior arrangement with the Technical Officers. A flatbed scanner and a slide/negative scanner are located in the MSc Lab. (G13a): contact the Technical Officers for the password to use this.

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3.4 Chemicals and other consumables and equipment

Having sufficient chemicals for your project is your responsibility. Orders for both chemicals and equipment must be made through the UCC online ordering system, Agresso (http://www.ucc.ie/en/agresso/; see also Section 3.9.5 below). Many chemicals and consumables are supplied under contract by specific suppliers and must be purchased from these companies. Technical Officers can advise on companies under contract to UCC, or you can consult the Procurement Office webpage at http://www.ucc.ie/en/procurement/ucconly/. Once ordered, chemicals may take up to six weeks to arrive. If you notice that a particular chemical is running low, please inform your supervisor or technical staff. If you need to use alcohol/ethanol for your project, please contact Allen Whitaker/Don Kelleher.

The opening hours of the Chemical & Solvent stores in the Butler Building are: Monday to Friday: 09:30–10:30 and 14:30–15:30. Requests for chemicals from the stores should be left in the post tray attached to the Cold Room where they will be collected and processed by Don Kelleher. It is imperative that superfluous chemical stock is not allowed build up as disposal costs are prohibitive. Additionally, safety considerations are of paramount importance, since some chemicals may be hazardous and therefore need to be kept in small quantities. Where possible/appropriate in such cases, alternative products may need to be identified.

Agrichemicals: This category is now strictly controlled. Pesticide cabinets are located in the Chemical Store. If you need access to agrichemicals for your research, please liaise with Don Kelleher.

3.5 Microscopes, Balances and Scanning Electron Microscope (SEM)

Under no circumstances are you to move any of the microscopes or balances from one laboratory to another without prior approval from the appropriate lab manager or consulting the Technical Officers beforehand. Unsupervised moving of specialised equipment may cause it to be damaged or result in the equipment requiring re-calibration. There are facilities for taking photomicrographs using a compound microscope: this equipment may be used only with permission from a supervisor and only after instruction. If you need to use the SEM, please contact the Technical Officers in the Cooperage.

3.6 Field Equipment

The technical staff should be consulted about available equipment in the department. Each postgraduate is responsible for checking in advance that a particular item is in working order, cleaning up after use and reporting any problems to the relevant technician. Field meters must be booked in advance with either Alison Harrison or Liz Cotter (Technical Officers, the Cooperage), both of whom can also provide instructions on their use and maintenance. Information concerning diving equipment can be obtained from the School's Diving Officer, Dr Rob McAllen. Only those qualified, insured and approved by the School's Diving Officer may use Departmental SCUBA equipment.

Those wishing to use the laboratories or field equipment at Lough Hyne should, after 34

http://www.ucc.ie/en/procurement/ucconly/

http://www.ucc.ie/en/agresso/


discussion with their supervisor, consult with Rob McAllen about usage and maintenance, as well as noting that a permit from the Wildlife Service is required for field work at the Lough under the 1976 Wildlife Act protecting flora and fauna.

3.7 Computing Facilities and Printing

There is an open-access computer laboratory on the first floor of the Enterprise Centre, which is available for all students, undergraduate and postgraduate, in Distillery Fields. The lab may sometimes be block-booked for classes: there is a three-week timetable on the wall outside both doors. Bookings are managed by administration staff in the School of BEES. UCC’s Computer Centre is responsible for the upkeep of all computing equipment in this lab, as well as for maintaining printing supplies. Any problems with the computers or printer, or requests for paper or toner, should be directed to [email protected], or (021) 490 1818.

The School has recently purchased printers to ensure that there is at least one printer in all postgraduate rooms. An annual fee of €50 will be deducted from student research grants to cover the running costs of these printers.

The Image Analysis Laboratory in the Butler Building has two computers for postgraduate use, as well as a flatbed scanner. Image analysis equipment is also available but may only be used with permission from the lab manager/Technical Officers.

No software should be introduced onto School computers except that which is licenced to the School/University. Virus-detecting software is installed on all School machines but may not detect all viruses. Therefore, every effort should be made to avoid possible contaminated sources.

3.8 Computer Purchase and Network Connection

The School of BEES has in place the following Standard Operating Procedure (SOP) for the purchase of computers by staff and research postgraduates. It also summarises the UCC network connection policy. The SOP covers the purchase of UCC-owned computers, whether standard or customised, from either a School or research cost code. Computers can be either portable or desktop, and supplied by Dell or Apple.

It is the responsibility of the purchaser to ensure this procedure is followed and the minimum machine specifications are obtained. It is the responsibility of UCC IT Services to ensure the machine is configured for use on the UCC network.

3.8.1 Purchase of a standard Windows machine

Decide whether a laptop or desktop is required, and contact [email protected], who will seek a quotation from Dell, which will be forwarded on receipt. The computer is ordered direct from Dell (not through IT Services) via Agresso’s Punchout system, using the relevant cost code. The machine will be delivered to IT Services for imaging and configuration. You will be notified when the machine is ready for collection; you should then organise delivery to your desk by contacting General Services: [email protected].

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3.8.2 Purchase of a customised Windows machine

Choose the desired computer specifications from the Dell website (http://www.dell.com/ie/business/p). Mandatory specifications which ensure compatibility with UCC’s hardware purchase policy are:

o Five-year warrantyo Professional or Ultimate operating systemo Latitude model for portable, or OptiPlex for desktop

Contact Karen Doyle at [email protected] for a quotation. Use the Agresso Punchout system to order the computer, using the relevant cost code. The computer will be delivered to your desk. Contact the IT Helpdesk (tel. 2120) to confirm they are able to receive the computer for imaging and configuration; this may take up to one week to complete. The IT Helpdesk will have been informed of the purchase by Dell and will be expecting contact. Contact General Services ([email protected]) to arrange for delivery of the computer to IT Services, and for its return once you have been notified that it is ready for collection.

Detailed information on hardware purchase can be found at: http://www.ucc.ie/en/is/itservicecatalogue/hardwarepurchase/

3.8.3 Purchase of a standard Apple product

The official vendor of Apple products for UCC is CompuB on Opera Lane: www.compub.com. When ordering your machine, ensure you purchase the five-year warranty available from CompuB. There are a number of adapters and cables which need to be purchased to ensure compatibility with UCC hardware and network. Details are listed at Reference 2 below.

3.8.4 Purchase of customised Apple products

If purchasing an Apple machine and you require non-standard specifications (increased RAM or internal drive size), you are then choosing what is known as a BTO (built to order). This can delay the arrival of the device by up to ten working days.

Installing Windows on a Mac using software such as Bootcamp or Parallels is not supported by IT Services. If Windows-specific software is required, purchase of a Windows computer (Dell) is necessary.

Detailed information on buying Apple products can be found at: http://www.ucc.ie/en/is/itservicecatalogue/appleimacipadiphone/

3.8.5 Portable devices/laptops

Encryption of portable devices is mandatory to ensure compliance with UCC’s data protection policy. If choosing a laptop as your primary machine, for good ergonomics, consider buying a docking station including a monitor and keyboard).

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http://www.compub.com/

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http://www.dell.com/ie/business/p


3.8.6 UCC Network Policy

UCC’s network policy can be found at http://www.ucc.ie/en/media/support/itpolicies/procedures/AccessToITServices.pdfIn summary, core staff are automatically provided with full UCC network access upon generation of a staff number by Human resources. For research postgraduates, notification from Head of School to Head of Operations is required requesting the postgraduate be provided with a central domain account. A central domain account allows access to the Local Area Network (LAN), Agresso, Apollo, Eduroam and Network Attached Storage folders (NAS or shared folders).

Only UCC-owned machines can physically connect to the network. Personally-owned computers can connect to the wireless (wifi) network only.

3.8.7 On-campus computer support

Queries regarding software and hardware problems can be made to the Computer Help Desk (tel. 2120).

3.8.8 Internet

Postgraduates should read the policies on computer/IT use on the UCC homepage before accessing external websites (http://www.ucc.ie/en/it-policies/policies/). Any illicit use of computers will result in removal of computer privileges.

3.8.9 Computer training and courses

Training courses in computing (Excel, Word, Access, PowerPoint etc.) are conducted periodically or, given sufficient demand, can be organised on request by the Computer Training Centre (tel. 2724). Further details can be found below in Section 5.10 Computer Centre.

3.9 Vehicle

A vehicle is available for registered postgraduates’ use. It is under the management of Allen Whitaker (ext. 4669, [email protected], mobile: 087 224 8739) and any problems or queries should be addressed to him.

Postgraduates must have a CLEAN current full driving licence to use the BEES vehicle. A copy of the licence prior to usage must be given to Allen Whitaker.

A person without a full driving licence must use a qualified driver to chauffeur him/her (registered student/staff etc.) and is responsible for the condition of the vehicle (see item below). All other conditions are the responsibility of the driver.

BEES policy is that all postgraduates who need to undertake field work as part of their studies should hold a full driving licence. Postgraduates without a licence should endeavour to obtain a full driving licence as soon as possible. Lack of such a licence may seriously impede your career prospects.

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The vehicle should be used for all official College business. Any usage other than legitimate department business is not permitted and is not covered by insurance. Accidents, if they occur, should be reported immediately to Allen Whitaker who in turn will contact the insurance brokers, garage etc. A report should also be made to your supervisor and to Dr Barbara Doyle-Prestwich, the School’s Health and Safety Officer.

The vehicle is the responsibility of those using it. It should be checked before use for cleanliness, tyre pressures, oil and water levels and should be left in a clean state after the journey. If drivers receive a vehicle in less than good order, this should be reported to Allen Whitaker immediately, as they automatically take over responsibility when they drive away.

Strictly only a maximum of five persons in the car. Each passenger by law must have a seat belt provided and they must be tied at all times. It is the responsibility of the driver at all times to make sure this is adhered to. If this is violated, the insurance is null and void, and in the event of an accident the driver is then liable for full cost, including third party claims.

All fines, speeding, parking etc., are the responsibility of the driver.

The vehicle must be driven and treated with respect. No off-road usage is allowed.

The vehicles should be booked well in advance with Allen Whitaker. A monthly usage sheet, showing the availability of the vehicle, is displayed on the General Noticeboard in the Cooperage building.

Mileage should be recorded at the beginning and end of each journey and logged in the book provided. Postgraduates on funded projects should provide Allen Whitaker with their grant number in advance.

Private vehicles may only be used when this has been sanctioned by supervisors and Professor Sarah Culloty. Travel expenses to cover fuel cost only are reimbursed on presentation of fuel receipt. All expenditure should be preapproved by the supervisor(s) and subsequently signed off by the supervisor and/or the Head of School.

Extreme care should be taken when driving through water, since in all diesel cars the air intake is located in a low position and will suck up water causing the engine to seize up.

Overloading is not allowed.

Use by non-college personnel is not allowed (thus picking up of hitch hikers is not allowed).

Driving licences are checked annually. Under the insurance policy you must notify Allen Whitaker in advance of any penalty points you have on your licence or as you acquire them.

3.9 Requisitions and Expenses

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All requisitions for consumables and equipment must be made through UCC’s online purchasing system, Agresso (http://www.ucc.ie/en/agresso/). Your supervisor should contact Agresso Support ([email protected]) to request login credentials for you. Guidelines on how to place orders and claim expenses on Agresso are provided at http://www.ucc.ie/en/agresso/howto/.

All requisitions for chemicals should be made to the Technical Officers, who will either provide what you need from the chemical stores, or order them on your behalf from the appropriate supplier.

If you are in receipt of a research grant, you will be allocated a research code, which must be used when placing orders or claiming expenses on Agresso. We do not recommend that you spend your own money on requisitions for your research, but if you have to, please keep all receipts to ensure that you are fully reimbursed when you submit your expense claim. Petty cash is not available to postgraduates on research grants.

3.10 School Workshop

A School workshop is available for the construction of specific field apparatus, etc. It is located in the Cooperage, and access can be arranged with the Technical Officers, with the approval of your supervisor.

3.11 Waste Management

Bins are provided outside the Butler Building and Cooperage for waste and recycling disposal: please ensure that you use the correct bin. Laminated magazines should be put in the rubbish bin and not recycled. Recycling bins are also available in laboratories and the staff tea room.

4. Insurance and security

4.1 Accident and travel insurance

All registered students are covered by the University's Personal Accident Insurance Policy. The accident section of the Policy covers students within College premises, travelling to or from, or participating in, or supporting, sports or other activities or functions organised by the College. It also applies when students are travelling on field trips or educational tours or on other College-related business. The travel section of the same Policy provides cover for loss of baggage, personal effects, cancellation and curtailment, medical expenses, hijacking, etc., however there is a minimum excess charge.

4.2 Security

All postgraduates should take every precaution to safeguard their own, as well as university property by keeping all valuables locked away. This applies particularly to laptop computers, money of any kind, cash, cheques, petty cash, handbags, briefcases, jewellery, etc. The university carries no insurance for theft of personal goods and does not hold itself responsible for the safety of any personal articles or

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valuables left on university premises. Doors, office drawers, filing cabinets etc. should be kept locked whenever possible.

It is the responsibility of everybody in the School to check on all strangers. After 6.00pm on weekdays and at the weekends/Bank Holidays access to the Cooperage and Butler Building is by swipe card only, and all users of the Enterprise Centre must enter via the main door and sign the logbook. Suspicious conduct should be reported immediately to the security desk (contact details below). Please contact Elaine Kelly to get your student ID activated for swipe access.

Distillery Fields Security Desk: 4567Tyndall/Lee Maltings security hut: 4100Bill Cashman, Security Supervisor: 4145Security desk, UCC main campus: 2266Duty Security Supervisor, UCC main campus: 2271General Services: 2264/2265

4.3 Safety

At the outset of your research project, both you and your supervisor should undertake a risk assessment of both your laboratory and field work. Your supervisor should be able to provide you with the relevant documentation; alternatively, you may contact the School Health and Safety Officer, Dr Barbara Doyle-Prestwich. Each postgraduate is expected to heed relevant safety warnings and to abide by good laboratory and field work practice. You are also expected to make yourself aware of the various emergency assembly points for your building.

4.4 Disability Facilities

There are two wheelchair-accessible entries to the Enterprise Centre ground floor. The Butler Building is also accessible by wheelchair, and a lift is available to provide access to the upper floors of both buildings. Wheelchair-accessible toilets are provided on both floors of the Enterprise Centre and the ground floor of the Butler Building. The Cooperage is a single-storey building.

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5. Other Services

5.1 Library Facilities

http://www.ucc.ie/library. Tel: 021 490 2794; Fax: 021 427 3428

The main college library (Boole Library) is situated on campus and includes a dedicated postgraduate library. Dr Maria McNamara is the current BEES Library Representative and should be consulted regarding library matters. The library catalogue (http://booleweb.ucc.ie/) can be searched via the internet system.

Journals and books not held in the library can be requested via Inter-library Loan (ILL). Details of how to submit ILL requests are on the library’s website, along with information on getting access to other university libraries.

Electronic information is becoming more and more accessible through the library ERL service (Electronic Reference Library). Please contact the library for the latest information regarding electronic databases available online.

Library chargesCheck the following link for charges related to inter-library loans etc. http://booleweb.ucc.ie/index.php?pageID=511

5.2 Languages

Postgraduates are reminded of the importance of foreign language ability. There is a self-access facility (in the O’Rahilly Building on Main Campus) where you can learn a language in your own time, at your own pace and at a very reasonable cost.

Further information can be obtained from the Language Centre (http://www.ucc.ie/en/esol/, 021 490 2043). The Centre also runs evening language courses during the academic year, as well as fortnight-long intensive courses in the summer.

5.3 Careers Information

UCC Careers Office is at 3-4 Brighton Villas, Western Road (http://www.ucc.ie/en/careers/, Tel: 021 490 2349).

Notices about grants and jobs are also displayed on a number of notice boards in the School and via email. The Graduate School of the College of SEFS, with UCC Careers Service, runs day-long Professional Development Courses, which you will be informed about via your UCC email account.

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5.4 Accommodation

http://www.ucc.ie/en/accom/

The services provided by the Office of Residence and Student Activities include the following:

accommodation (residential); administration and financial support services to clubs and societies; Campus Watch

Students requiring assistance with advice on procuring accommodation in Cork should contact the office. (http://www.ucc.ie/en/asa/ Tel: 021 490 2353).

5.5 Student Health and Dental Service

http://www.ucc.ie/services/health/welcome.htm

Postgraduate students are entitled to free doctors’ visits with the UCC Student Health Services (‘Ardpatrick’, College Road, opposite the O’Rahilly Building). Postgraduates should consult the website as certain services/procedures incur a small charge e.g. vaccinations, eye tests etc. Holders of medical cards are entitled to medical consultation at the Student Health Service but will be required to pay for prescriptions. EU students are entitled to free medical consultation and prescriptions in Ireland with the E111, E109, and E128 health cards but are required to pay for prescriptions obtained at the Student Health Service. If you are travelling abroad within Europe, you should ensure that you have a current valid European Health Insurance Card (EHIC). All non-EU students who have no medical card entitlements are advised to have adequate medical insurance; however, they are entitled to free medical visits at the Student Health Service.

The Student Health Service also provides advice and care for the particular psychological and physical problems of students. This service is not designed to provide full general practice cover and students should register with a General Practitioner. However, for students living away from home, an emergency service is provided. There is also a student counselling service to assist students who may have personal problems or difficulties with study.

Dental Health

UCC runs the Cork Dental School and Hospital, which is at the back of the Cork University Hospital campus in Wilton. The Dental Hospital operates a walk-in clinic from Tuesday to Friday from 09:00-10:00 and 14:00-15:00. However, in an emergency, patients will be seen outside these hours. All visits and treatments incur a charge, but the hospital strives to keep costs at a competitive level. Patients are advised to arrive early as the clinic will close when the maximum patient capacity is filled.

Tel: 021 454 5100 Email: [email protected]

5.6 Student Financial Support 42


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http://www.ucc.ie/en/financeoffice/assistance/

The Student Assistance Fund provides financial assistance for full-time higher education students who are experiencing financial difficulties whilst attending college. For full details on eligibility and how to apply, please visit www.ucc.ie/en/studentbudget/saf/.

In order to be eligible to apply for student assistance, you must be registered on a full-time undergraduate or postgraduate course of not less than one year’s duration in a participating college. Unlike the maintenance grant schemes, you cannot be considered for Student Assistance prior to registering in a participating college.

Contact details

Student Assistance Fund Office1st Floor1-2 Brighton VillasUniversity College Cork,Western Road, Cork

Tel: 021 490 3562

Email: [email protected]

5.7 Students’ Union

The Students’ Union consists of all registered students of the College, and its primary function is the promotion of the interests of its members. The Students’ Union represents postgraduates at all levels within the University as well as at a local and national level (USI – The Union of Students in Ireland). The Union is headed by a President and an Executive Committee elected from among the student body. For further information on the Student’s Union see http://collegeroad.ie/ .

5.8 Crèche

http://www.ucc.ie/en/creche/

Crèche Cois Laoi, on the Brookfield Campus on College Road, is available for children of College staff and students. It caters primarily for children aged 4 months to 12 years and can accommodate up to 80 children. Facilities include a Nursery room, Toddler rooms, Montessori and Naíonra, a specifically-designed Sensory Room, after-school care and an Outdoor Play Area. Opening hours are Monday to Friday 08:00-18:00hrs. The Crèche is managed by the Students’ Union, which also operates a financial support scheme towards Crèche costs for certain students.

5.9 Student Advisor and Ombudsman

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http://www.ucc.ie/en/studentbudget/saf/

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http://www.ucc.ie/en/studentombudsman/

Students from time to time will need help and advice during their time in the College. In general, they are advised by fellow students or members of staff. However, in some instances the students may not know where to seek help and advice. In such cases, the Student Advisor and Ombudsman is available to give general advice, help deal with serious cases of grievance, and perhaps refer the student to someone more appropriate if this is the student’s wish.

The Ombudsman’s office exists to enable any student who has any grievance with the College, its staff or fellow students, to have that grievance evaluated and action taken if appropriate. All contact with the Ombudsman is guaranteed to be absolutely confidential and remain so unless it is the wish of the student that it is otherwise.

The Ombudsman will sympathetically and impartially examine any grievances that a student may have in order to ascertain the facts and validity of the case. S/he has access to all relevant persons in the College and has freedom to investigate. S/he is independent from any institutional influence and reports directly to the President of the College. In general, s/he serves as a mediator to resolve disputes informally rather than an arbitrator.

5.10 Term dates for 2016/2017

https://www.ucc.ie/en/media/support/recordsandexaminations/SemesterDates2016-17.pdf.

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https://www.ucc.ie/en/media/support/recordsandexaminations/SemesterDates2016-17.pdf

http://www.ucc.ie/en/studentombudsman/


Appendix I

COPYING AND PLAGIARISM – a School of Biological, Earth andEnvironmental Sciences handout to all staff and students.

COPYINGCopying is a simple matter to understand. If, in a piece of work submitted for assessment, a student copies the work of another student, then that is unacceptable practice. As it may be difficult to determine who copied whom, it is assumed that the practice of allowing someone to copy your work is equally unacceptable.

Many pieces of written work stem from joint practical work – groups of two or more students may collect data and work out results. Where this is the case, it is reasonable that results sections of written reports are near-identical. However, it is NOT acceptable that introductory sections, discussions and descriptions of methods are identical – written assessments must be the work of the individual student.

Penalties for CopyingBEES academic staff would be well within their rights to give a zero mark to participants in copying. It is also the case that copying is an offence under UCC regulations and can be reported to the Registrar’s Office. At the very least, staff who identify copying will simply divide the mark given by the number of participants. In other words, if two students submit identical or near-identical work and this work is graded at 60%, each student will be given 30%; if three students are involved the mark will be 20%, and so on. This will not be a matter for debate and staff will not be expected to contact students to discuss the matter. If students copy, then they will automatically suffer consequences.

PLAGIARISMPlagiarism was originally defined as the presentation of someone else’s written work as your own. In the present electronic age, and in a scientific context, plagiarism extends to drawings, figures, computer software, audio-visual material etc. Essentially plagiarism is theft – a plagiarist steals the intellectual property of others.

If you write or produce software/audio-visual material professionally, plagiarism can be an actionable matter and there are cases of substantial damages being awarded against plagiarists.

In the university context, plagiarism becomes a potential problem for both students and academic staff, particularly in the assessment of either examination scripts or other written work (essays, dissertations, theses etc.). It is becoming apparent that the ease of downloading web-based material makes plagiarism technically easier than hitherto. It is also evident that plagiarism can often be inadvertent or the result of ignorance. This handout is designed to explain clearly what plagiarism is, and what it is not. The handout will be given to all BEES staff and students, so that no-one can claim ignorance as a defence against accusations of plagiarism.

What plagiarism is:If you memorize a piece of text that someone else wrote and write it down in an examination as if it was your own writing, and without putting the material in quotation marks, or without identifying the person who wrote it, this is plagiarism – even if some words differ from the original.

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If you copy a piece of text, a figure or a photograph from published or unpublished work into a dissertation/thesis/essay without identifying the source (and putting text inside quotation marks), thereby giving the impression that you have produced it yourself, then this is plagiarism.

It is still plagiarism if you preface a direct quotation with something like ‘Smith says that’, but do not put the subsequent quotation inside quotation marks – because you are still giving the impression that the text is your own.

Plagiarism does not require wording to be absolutely identical with the original. If you plagiarise text and then modify it, this is still plagiarism. Basically, if you summarize someone else’s ideas or judgements, you must refer to that person in your text and refer to his/her work in your bibliography. In this context it is fair to write ‘Smith says that’, provided that the subsequent text is your own, not Smith’s (and provided you give a proper reference to Smith’s work).

Plagiarism applies to a series of short quotations from different sources as much as it applies to a long quotation from a single source.

Plagiarism applies to anyone else’s work, not just to published material. Copying material from another’s thesis without attribution is plagiarism, even if it is simply a mechanical piece of an appendix, describing a straightforward technique. When in doubt, always cite the source.

What plagiarism is not:If you write a passage that has a high incidence of direct, properly referenced quotations, that is not plagiarism, but such a piece of material will not demonstrate interaction with what is being quoted, nor will it show whether you really understand the material being quoted – an examiner is entitled to give no great value to such material.

If you memorize your lecture notes for an examination and regurgitate them whole or in part for a written examination answer this is not plagiarism – and you do not have to acknowledge or cite the lecturer.

Notes:Do not confuse plagiarism and copyright! If you see an image on the web, or a figure/picture in a book, it may be copyrighted and illegal for you to use without permission from (and possible payment to) the owner/author. Quite a lot of web material is usable for educational or scientific purposes under certain conditions. For undergraduate work (e.g. honours dissertations, project reports) it is normally fair to use such material in presentations, but you should always cite the source, and not use the material in any other way.

For scientific work, particularly when writing reviews or books, you may wish to use published figures. Sometimes you will have to seek permission to do so: in other cases where this may be technically difficult you can redraw the figure (substantially) and use the figure with a suitable citation (e.g. redrawn from Smith & Jones, 1884).

Best PracticeUCC plagiarism policy states that “in almost any academic pursuit, one learns from the ideas and work of others. Therefore, in preparing any work presented as part of one’s course or for research or scholarship, one must rely on other people’s work to develop one’s own. It is imperative, however, that this work is fully acknowledged, following the standard referencing practice with the particular discipline.” http://www.ucc.ie/en/exams/procedures-regulations/plagiarism/ .

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http://www.ucc.ie/en/exams/procedures-regulations/plagiarism/


When referring to another person’s work, one should ideally paraphrase (put into your own words) the work and reference the source after your paraphrased text. e.g. BEES is an exciting place to study (O’Connor, 2008; O’Connor & Biggs, 2009; O’Connor et al., 2010).

At the end of the document, you should have a reference list detailing the full reference, e.g. O’Connor, T. (2008). Reflections on a life at UCC. Cork University Press, Cork, pp.280. O’Connor, T. & Biggs, J. (2009). Integrated learning approaches in the environmental sciences. Journal of Teaching & Learning, 28, 10-25. O’Connor, T., Biggs, J. & Smalls, A. (2010). The way we were. In: (ed. by J. Jay & D. Light) University College Cork, the world and everything else. Cork University Press, Cork,534pp.

If you feel that the statement made by the original author cannot be improved, then you can quote. You must enclose the exact words in quotation marks and cite the source, e.g. “the lectures were great but the field courses were the high point of the year” (p. 53, O’Connor, 2008).

Turnitin plagiarism detection softwareTurnitin plagiarism detection software is currently used for all 3rd and 4th year project for BSc Environmental Plant Biotechnology and 4th year BSc Ecology and BSc Zoology. Students are required to submit a Turnitin “originality report” with their projects. Turnitin may be used in other modules and by the module coordinator for “suspect” work.

Penalties for plagiarismUniversities and faculties vary in their reactions to plagiarism. NUI Cork Marks & Standards, 2000 (page J1, items 13 & 14) specifically mentions plagiarism in the context of formal examinations. It states that “A significant amount of unacknowledged copying shall be deemed to constitute prima facie evidence of deliberation. Any candidate found violating these regulations shall be requested to leave the Examination Hall, by the Senior Invigilator and have their case reported to the Registrar and Vice President for Academic Affairs”. By extension, a significant amount of plagiarism in essays, dissertations or theses should also be reported to the Registrar and Vice President for Academic Affairs for adjudication. In the event of a member BEES suspecting plagiarism s/he will report it to the head of School and the matter will be fully investigated as set out in the University Guide to Examinations. Postgraduate penalties are rather more complex, because of the greater extent of external moderation. An External Examiner is morally entitled to refuse to pass a thesis that demonstrates plagiarism. Plagiarism that found its way into the peer review arena, or even the scientific literature itself, could have profound negative effects on the career of the plagiarist.

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Appendix II – Health & Safety Briefing

Staff and PhD students:1. Complete all risk assessments (RAs), whether for lab or field:

http://www.ucc.ie/en/occupationalhealthandsafety/faqs/)

2. A copy should be emailed to [email protected] for storage on the BEES shared folders

3. A hard copy should be kept available in the lab where the work is being performed with the most recent Material Safety Data Sheet attached (this is available from company that supplied the material). Contact the relevant Technical Officer with any queries: Don Kelleher, Butler building, Luke Harman/Mary Lehane, Cooperage.

PIs/Supervisors/Technical Officers:4. Ensure compliance of research team including students

5. In the case of fourth year undergraduates and MSc, ensure they have read, signed and have been given a copy of the appropriate RAs. They also need access to MSDS sheets.

6. Any ‘high risk’ work should, where possible, be carried out during normal working hours.

7. Only fourth years who have obtained written permission from Head of School are allowed to work beyond normal working hours (5.30pm). Out of hours there should always be a nominated staff member or a PhD student working in the building at the same time (who has been introduced to the student).

Staff:8. Risk assessments also apply to individual modules (e.g. fieldtrips, laboratory classes,

industrial visits etc.). Completed RAs should be emailed to [email protected]

Useful links: http://www.ucc.ie/en/media/academic/schoolofbees/documents/HealthandSafetyBriefingSept2015.pdf https://www.ucc.ie/en/occupationalhealthandsafety/ http://www.sigmaaldrich.com/ireland.html

Safety information, along with the fieldwork manual and associated appendices are available at: http://www.ucc.ie/en/bees/ under the ‘Current Students’ tabUCC’s code of conduct and safety instructions for students on fieldwork can be found at http://ocla.ucc.ie/Insurance/

Specific risk assessment:Your supervisor is the first person to speak to. Hard copies of risk assessments are available in labs.

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http://ocla.ucc.ie/Insurance/


http://www.sigmaaldrich.com/ireland.html

https://www.ucc.ie/en/occupationalhealthandsafety/

http://www.ucc.ie/en/media/academic/schoolofbees/documents/HealthandSafetyBriefingSept2015.pdf

http://www.ucc.ie/en/media/academic/schoolofbees/documents/HealthandSafetyBriefingSept2015.pdf



http://www.ucc.ie/en/occupationalhealthandsafety/faqs/

Appendix III Demonstrating Hours Log Sheet

POSTGRADUATE DEMONSTRATING HOURS

Postgraduates are responsible for keeping track of their demonstrating hours, and for getting these totals signed off by the module co-ordinator

Student Name Module Code Total LAB hours

Total FIELD hours

TOTAL HOURS Signed by Module Co-ordinator

bees postgraduate booklet€¦ · web viewsamsung 4mp digital camera for field/lab. nikon 4mp...

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