Summer Research in Dublin

Dear all,

Please circulate this notice to your colleagues who may be in contact
with potential students (3rd years), as well as to any relevent
listservs. Note the closing date for applications is March 30th 2008.

Summer Research in Dublin

Collections-Based Biology in Dublin (CoBiD)
Undergraduate Research Experience & Knowledge Award

This summer programme offers research projects and activities for
students in organismal biology using biological collections


Research Projects
extreme environments | fire ecology | DNA barcoding | freshwater
ecology | biocontrol | environmental epigenomics | terrestrial ecology
| invasive species | plant evolution and extinction | life history |
genomic imprinting


Requirements
completion of the third (junior) year of an undergraduate biosciences
degree | ability to work independently | strong interest in the
project of choice | career goals in organismal biology


Full funding for the 10-week programme will be provided for 10
successful candidates, including assistance with air transportation to
and from Dublin, accommodation in Dublin, and a small weekly
allowance, as well as project expenses. Prior experience with museum
collections is not required - one of the goals of the programme is to
expose students to new research skills. The programme is open to all
international as well as Irish and EU students.

Term dates: June 16th to August 22nd 2008

For application instructions and more information:

http://www.ucd.ie/ureka/


Applications must be received by 30 March 2008

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Project 3

Evaluation of the performance of activity traps
Mentor: Dr. Mary Kelly-Quinn

Activity traps are generally employed in standing water bodies to trap
highly mobile aquatic invertebrates. They come in various designs but
their performance has rarely been tested. This project will test the
performance of activity traps that have been designed to capture
macroinvertebrates at two levels in the water column in various pond
mesohabitats, e.g. marginal and open water. We wish to assess which
of these levels will yield the best representation of pond
biodiversity. The results from the activity traps will be compared to
data collected using sweep netting so that taxa unique to the activity
traps can be identified.
The student would be trained in a wide range of field and laboratory
techniques from use of traps to taxonomic identification techniques,
and multivariate techniques to explore inter species relationships.

References:

· Giller, P.S., O'Connor, J.P., and Kelly-Quinn, M. (1998).
Freshwater macroinvertebrates. In: Giller, P.S. (ed.) Studies in Irish
Limnology. Essays on the occasion of the XXVII Congress of Societas
Internationalis Limnologiae (SIL), Dublin, pp. 125-157.
· Riley, J., Kirby, J., Linsley, M. and Gardiner G. (2003) Review
of the UK and Scottish surveillance and monitoring schemes for the
detection of climate-induced changes in biodiversity. Report compiled
for Scottish Government. (Available online as PDF)

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Project 4

Life history of the Mayfly Baetis vernus (Ephemeroptera)
Mentor: Dr. Mary Kelly-Quinn

Mayflies are an important component of the invertebrate communities of
rivers in Ireland. Although the distribution patterns of this group
has been systematically recorded (Kelly-Quinn and Bracken, 2000),
relatively little is known about the ecology of many species,
including their life history patterns.
Baetis vernus is widespread in many peaty upland rivers in Ireland.
It shares that habitat with another baetid mayfly Baetis rhodani. The
absence of B. rhodani can be used to highlight acid impact.
Unfortunately, the life cycle of B. vernus is not well described for
these areas and is required before its indicator potential can be
assessed. This project will analyse samples collected over a one-year
periods from sites supporting B. vernus to derive the life history.
The student would be trained in a wide range of field and laboratory
techniques from taxonomy, morphometric studies, comparisons with
material in the Natural History Museum, the use of microscopes and
deploying sampling gear in different river systems.

References:

· Ashe, P., O'Connor, J.P. & Murray, D.A.. 1998, A Checklist of
Irish Aquatic Insects, Occasional Publication of the Irish
Biogeographical Society, Number 3: 1-80
· Nilsson, A, 1996, Aquatic Insects of North Europe: A Taxonomic
Handbook. Volume 1, Apollo Books
· Kelly-Quinn, M. and Bracken, J.J. (2000) The Distribution of the
Ephemeroptera in Ireland. Occasional Publication of the Irish
Biogeographical Society 5, 180pp
· Wise, E.J. 1980. Seasonal distribution and life histories of
Ephemeroptera in a Northumbrian river. Freshwater Biology 10: 101-111.

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Project 5

The biocontrol of the aquatic invasive weed Azolla filiculoides in
Ireland by the frond-feeding weevil Stenopelmus rufinasus.
Mentor: Dr. Jan-Robert Baars & Dr. Mary Kelly-Quinn

The red waterfern, Azolla filiculoides Lamarck (Azollaceae) is a small
aquatic fern which has established in Ireland as an invasive species.
It originates from South America and was probably introduced as an
ornamental fishpond plant. Although this species occupies a limited
range in Ireland, thick floating mats out compete native plants and
have serious implications for all aspects of water utilization.
Although alternative control strategies have their merit, control of
this fern elsewhere has relied on the inadvertent arrival of a small
weevil, Stenopelmus rufinasus in the United Kingdom. Recently (2007)
this small weevil, was collected on A. filiculoides in Ireland, but
its national distribution is unknown. Heavy infestations of the fern
previously recorded on the Barrow River system may have been
controlled by the arrival of this natural enemy. It is as yet unclear
when this weevil arrived in Ireland, but sporadic infestation may be
indicative of the weevil being presen
t in Ireland for a number of years. The weevil has been the cause of
one of the most successful biocontrol programmes elsewhere in the
world. It is part of a mass rearing programme in the UK in order to
supplement the natural control of this weed as part of an augmentive
biocontrol programme. This is in response to the cooler climate
resulting in weevil populations only building up to cause significant
damage late in the growing season.
The aim of this project therefore is to monitor the population levels
of the weevil on A. filiculoides at several sampling sites in Ireland.
Samples already collected will be processed in the laboratory and
field sampling will be conducted to determine the result of an
augmentive control programme initiated in Spring 2008.

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Project 6

Response of cyanobacteria to extreme environmental conditions
Mentor: Prof. Bruce Osborne

Cyanobacteria-dominated structures/mats have a long evolutionary
history and have been consistently reported from the extreme
environments that existed during early earth history. Today, these
mats are also associated with extreme habitats. Cyanobacterial mats,
for instance, are very common in polar regions where they survive
exposure to low temperatures, water deficits and exposure to high
irradiances/high UV. In Ireland, cyanobacterial mats are common in
ephemeral pools in the Burren, Co Clare, an internationally recognised
area of exposed limestone rock, where exposure and repeated cycles of
wetting and drying prevent the growth of most plant species.
As cyanobacteria can produce large volumes of O2, they are an
interesting target organism for driving potential life-support
systems, or developing artificial atmospheres. The response of these
organisms to levels of UV radiation equivalent to that seen on the
surface of Mars or other planets provides a test case for the
viability of developing artificial atmospheres from natural materials.
This project will address the ability of cyanobacterial mats to
survive under these conditions using modern ecophysiological
techniques and parallels drawn with the likely responses of
cyanobacteria to early earth environments.

References:

· Whitton, B. A. & Potts, M. (2000). The Ecology of Cyanobacteria.
Kluwer Academic Publishers. The Netherlands.
· Schopf, J. W. (1999). Cradle of Life. Princeton University Press.
· Knoll, A. H. (2003). Life on a Young Planet. Princeton University
Press

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Project 9

Earthworms in the National Botanic Gardens, Glasnevin
Mentor: Dr. Olaf Schmidt

Earthworms are overwhelmingly beneficial soil invertebrates, however
when exotic species are introduced they can potentially pose a risk to
soils, habitats and native species. For example, invasive earthworms
in North America have caused dramatic changes in nutrient and soil
organic matter dynamics, plant community composition and the abundance
of other soil organisms (Hendrix et al. 2006). All native earthworms
in Ireland belong to the family Lumbricidae, but introductions of
exotic species occur. For instance, we recorded a large population of
an octochaetid earthworm species of east-African origin in a heated
swimming pool in Cork (Rota and Schmidt 2006).
Botanic gardens and the associated transport of rooted plants are
known to facilitate the introduction of exotic soil invertebrates
including earthworms, but all records for Britain or Ireland are dated
(Blakemore 2005). This project will survey earthworms in the National
Botanic Gardens, Dublin. First, selected greenhouses will be sampled,
earthworms extracted, preserved and identified to, at least, family
level using Sims and Gerard (1999). Second, if the soil and weather
conditions during the project permit, selected outdoor plots will also
be sampled for earthworms, with a focus on warm-temperate plant plots
which may harbour earthworm species that could potentially survive
outdoors under the (changing) Irish climatic conditions. Third, new
earthworm records will be compared with the existing earthworm
collection in the Natural History Museum, Dublin. Finally, during
collection work the student will also record occurrences of exotic,
earthworm-predatory flatworms, m
ost notably Arthurdendyus triangulatus, which is wide-spread in
Northern Ireland but of uncertain status in the Republic of Ireland
(Cannon et al. 1999).

References

· Blakemore RJ (2005) Checklist of earthworms of Britain and
Ireland after Sims & Gerard (1999). In: Blakemore, R.J. (2005). A
Series of Searchable Texts on Earthworm Biodiversity, Ecology and
Systematics from Various Regions of the World. Eds.: N. Kaneko & M.T.
Ito. COE Soil Ecology Research Group, Yokohama National University,
Japan.
Online: http://bio-eco.eis.ynu.ac.jp/eng/database/earthworm/
· Cannon RJC, Baker RHA, Taylor MC, et al. (1999) A review of the
status of the New Zealand flatworm in the UK. Annals of Applied
Biology 135, 597-614.
· Hendrix PF, Baker GH, Callaham MA et al. (2006) Invasion of
exotic earthworms into ecosystems inhabited by native earthworms.
Biological Invasions 8, 1287-1300.
· Rota E and Schmidt O (2006) Dichogaster bolaui (Oligochaeta:
Octochaetidae), an unusual invader in a swimming pool in Ireland.
Journal of Natural History 40, 161-167.
· Sims RW and Gerard BM. 1999. Earthworms: Notes for the
identification of British species. Synopses of the British Fauna (New
Series) No. 31 (Revised). Field Studies Council, Shrewsbury, 169 pp.

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Project 10

Investigating the spatial variability of California Black Oak leaf
stomatal frequency in relation to altitude, latitude, climate and
ecology across California, USA.
Mentor: Dr. Matthew Haworth & Dr. Jennifer McElwain

Leaf stomatal frequency is commonly used to reconstruct the elevation
of past land surfaces and the carbon dioxide concentration of past
atmospheres. This project will investigate the variability of stomatal
frequency in relation to other biotic (i.e. ecology) and abiotic
variable (i.e. climate) in order to understand the potential
limitations of the "stomatal frequency-CO2 method", and improve its
future application.
The inverse relationship between stomata and atmospheric carbon
dioxide concentration allows plants to balance CO2 uptake against
water loss, and can allow the atmospheric carbon dioxide concentration
in which a leaf developed to be determined. This UREKA project aims
to construct stomatal frequency - carbon dioxide response curves from
relict conifers in order to gauge their responses to rising
atmospheric CO2 levels. These response curves will be used as part of
a larger project to estimate how atmospheric carbon dioxide
concentration changed across the Triassic-Jurassic boundary (200
million years ago), the fourth greatest mass extinction event in Earth
history.
Students will gain experience using stereo, epi-fluorescent and
Scanning Electron microscopy, digital image capture and image
archiving. They will also be trained in the preparation of fresh,
historical and some fossil leaf cuticle and stomatal counting
protocols.

References:

· McElwain, J.C. (2004) Climate-independent paleoaltimetry using
stomatal density in fossil leaves as a proxy for CO2 partial pressure.
Geology, 32, 1017-1020.
· Willis, KJ & McElwain, JC (2002). The Evolution of Plants. Oxford
University Press. Oxford. 352pp.
· McElwain, JC, Beerling, DJ & Woodward, FI (1999). Fossil plants
and global warming at the Triassic-Jurassic boundary. Science 285,
1386-1390.

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Project 11

Fire damage: Semi-automated quantification of charred plant organs
using image analysis
Mentor: Dr Claire M. Belcher & Dr Jennifer McElwain

The effects of fire on the terrestrial world can be devastating, not
only causing destruction of habitat but also increasing soil erosion,
however, fire can be necessary for regeneration in some vegetation
types. There is increasing need to understand fire ecology so that
future threats to today,s ecosystems can be better understood based on
current global warming predictions. Current mismanagement of forest
ecosystems using total fire suppression has lead to devastating
consequences, with stand replacing wildfires occurring more often
throughout the world. There have been relatively few attempts to study
the role of fire in pre-quaternary ecosystems even though the
conditions allowing fires to occur on earth appeared some 400 million
years ago. Throughout this long history fire has played the role of
both cause, consequence and catalyst to the development of terrestrial
life on earth. Part of the problem of studying ancient fires has been
the lack of well developed techniqu
es for identification of burned plants and plant parts.
This project will aim to develop and assess semi-automated image
analysis techniques for identifying and quantifying charred plant
remains. Semi-automated methods have been recently used to quantify
proportions of charcoal in sediment samples but have not previously
been used to identify and quantify different charred plant parts (e.g.
charred wood, cuticle and flowers) within an assemblage. Having the
ability to quickly and easily identify and quantify ancient charred
assemblages will allow ancient fire ecology to be better understood
and links between the earth,s fire and climate histories to be made.

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Kind regards,

The UREKA Team

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Collections-based Biology in Dublin
Undergraduate Research Experience & Knowledge Award
www.ucd.ie/ureka