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Health and environmental impacts of urbanized surface waters: a comparative transcriptomics and network biology approach

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Principal Supervisor: Dr Luisa Orsini, School of Biosciences, UoB
Co-supervisor: Dr Shan He, School of Computer Science, UoB
Collaborator: Dr James Bentley Brown, University of California Berkeley

Urbanization and land use introduce metals, pesticides and herbicides into surface waters altering their status and inducing severe consequences on environmental health and human disorders 1-3. Government proposals for increased housing in rural areas will spread the effects of urbanization into currently unaffected areas. Understanding the long-term consequences of urbanization on environmental and animal health is critical to design effective mitigation strategies to urbanization. However, the effects of urban pollution on animal life is currently circumstantial because such effects occur over decades and experimental evidence is lacking.
We will measure transcriptomic changes and associated ecologically endpoints (growth and reproduction) in waterfleas 4, crustaceans used to assess water quality in inland water systems, after exposure to lead (Pb), the herbicide Glyphosate (Roundup™), and the insecticide Chlorpyrifos, (Dursban™) (aim 1 below). These chemicals of common use in urbanized areas have a demonstrated toxic effect on the fitness of this species 5-9. Most importantly they enter the food chain affecting several non-target species including humans. Daphnia are filter feeders, taking in microscopic and colloidal food that is unavailable to most organisms. Then they transfer these substance to other macroinvertebrates and vertebrates being major food sources for these species. Being the first target of water pollution, Daphnia are ideal to understand the effect of urbanization and pollution on inland water ecosystems.

Because Daphnia is basal in the food chain of these ecosystems, we can study the effect of urban pollutants on other taxa, including invertebrates and vertebrates (aim 2 below). This aim will be achieved using computational tools and available information on public databases. We will search for conserved orthologue genes in biochemical pathways identified in aim 1 across distant taxa. Computational techniques in network biology will be applied to analyse the data. In particular, we will investigate robust methods for constructing co-expression networks from transcriptomic data, and then adapt and apply the ensemble module identification algorithms developed in Dr He’s group to search for differentially expressed co-expression modules and evolutionary conserved modules.

1) To identify changes in biochemical pathways and associated ecological endpoints (growth and reproduction) induced by long-term exposure to common pesticides, herbicides and heavy metals in a sentinel species for water quality.
2) To use a comparative transcriptomic analysis and network biology approaches to determine which of the pathways identified in aim 1 are conserved in other taxa, including humans. This will help identifying the underlying environmental causes of neurodegenerative and reproductive disorders.

The project has two main outcomes
1) The identification of pathways that respond to the tested chemicals and their associate fitness costs on growth and reproduction of Daphnia. These compounds can be flagged as posing a risk to environmental health.
2) The identification of pathways that respond to the tested chemicals and are conserved across taxa, including humans, potentially involving the same toxicological modes of action 10. The pathways identified with this second outcome will help identify compounds that affect non-target species in urban water, relevant to environmental health and to understand bioaccumulation. In addition, the comparative approach used will be of relevance for medical researchers studying the underlying environmental causes of diseases such as neurodegenerative and reproductive disorders. Identifying conserved pathways between humans and other taxa that are linked to urban toxicants will guide clinicians to specific biochemical pathways, allowing research to move from circumstantial evidence to knowledge of the pathways involved.

Please find additional funding text below. For further funding details, please see the ‘Funding’ section.
The School of Biosciences offers a number of UK Research Council (e.g. BBSRC, NERC) PhD studentships each year. Fully funded research council studentships are normally only available to UK nationals (or EU nationals resident in the UK) but part-funded studentships may be available to EU applicants resident outside of the UK. The deadline for applications for research council studentships is 31 January each year.

Each year we also have a number of fully funded Darwin Trust Scholarships. These are provided by the Darwin Trust of Edinburgh and are for non-UK students wishing to undertake a PhD in the general area of Molecular Microbiology. The deadline for this scheme is also 31 January each year.

Funding Notes

All applicants should indicate in their applications how they intend to fund their studies. We have a thriving community of international PhD students and encourage applications at any time from students able to find their own funding or who wish to apply for their own funding (e.g. Commonwealth Scholarship, Islamic Development Bank).

The postgraduate funding database provides further information on funding opportunities available View Website and further information is also available on the School of Biosciences website View Website


1 Gasnier, C. et al. Glyphosate-based herbicides are toxic and endocrine disruptors in human cell lines. Toxicology 262, 184-191 (2009).
2 Senut, M. C. et al. Lead exposure disrupts global DNA methylation in human embryonic stem cells and alters their neuronal differentiation. Toxicol Sci 139, 142-161 (2014).
3 van Wijngaarden, E. & Dosemeci, M. Brain cancer mortality and potential occupational exposure to lead: findings from the National Longitudinal Mortality Study, 1979-1989. Int J Cancer 119, 1136-1144 (2006).
4 Miner, B. E., De Meester, L., Pfrender, M. E., Lampert, W. & Hairston, N. G. Linking genes to communities and ecosystems: Daphnia as an ecogenomic model. Proceedings of the Royal Society B-Biological Sciences 279, 1873-1882 (2012).
5 Cuhra, M., Traavik, T. & Bohn, T. Clone- and age-dependent toxicity of a glyphosate commercial formulation and its active ingredient in Daphnia magna. Ecotoxicology 22, 251–262 (2013).
6 Dill, G. M. et al. in Glyphosate resistance in crops and weeds: history,vdevelopment, and management. (ed V.K. Nandula) 1–33 (Wiley, 2010).
7 Palma, P. & Barbosa, I. R. Embryo-toxic effects of atrazine environmental concentrations on the crustacean Daphnia magna. Global Journal of Environmental Sicnece and Technology 1, 12 (2011).
8 Theegala, C. S., Suleiman, A. A. & Carriere, P. A. Toxicity and biouptake of lead and arsenic by Daphnia pulex. J Environ Sci Heal A 42, 27-31 (2007).
9 Zhang, L., Gibble, R. & Baer, K. N. The effects of 4-nonyphenolandethanol on acute toxicity,embryo development, and reproduction in Dapnhia magna. Ecotoxicol.Environ.Saf 55, 330-337 (2003).
10 Gerstein, M. B. et al. Comparative analysis of the transcriptome across distant species. Nature 512, 445-448 (2014).

How good is research at University of Birmingham in Biological Sciences?

FTE Category A staff submitted: 42.80

Research output data provided by the Research Excellence Framework (REF)

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