Current Vacancies
PhD Studentship
Linking genomic variations with the elemental composition of
the cell
School:
Environmental Sciences
Supervisor(s):
Dr Thomas Mock (Environmental Sciences); Dr Stan Kopriva (JIC)
Application Deadline:
30th January 2009
Description:
FUNDING MAY BE AVAILABLE FOR UK/EU STUDENTS. IF FUNDING IS AWARDED
FOR THIS PROJECT IT WILL COVER TUITION FEES AND STIPEND FOR UK STUDENTS. EU
STUDENTS WILL NORMALLY BE ELIGIBLE FOR TUITION FEES ONLY. INTERNATIONAL STUDENTS
WILL NOT BE ELIGIBLE FOR THIS FUNDING; THEY ARE STILL WELCOME TO APPLY FOR
THIS PROJECT BUT WOULD HAVE TO FIND ALTERNATIVE FUNDING.
The goal of this studentship is to link natural variations in genotype and phenotype of the marine diatom Thalassiosira pseudonana with its elemental composition under iron limitation. Diatoms contribute ca. 20% of the Earth total primary production and therefore influence biogeochemical cycles of elements and climate. Iron limits diatom growth in 35% of the global upper ocean and therefore is the main element influencing distribution and abundance of marine diatoms. T. pseudonana is the first diatom for which a genome sequence and microarrays are available. This species is globally distributed with many ecotypes from different marine habitats. However, no functional molecular data are available yet that can explain these natural variations. The aim of this studentship is to enable the discovery of functionally relevant variations in three different ecotypes (coastal temperate (sequenced strain), off-shore temperate and off-shore tropical ocean) and how these ecotypes respond to iron limitation. Functional variations will be identified by re-sequencing of both off-shore strains and the genome-wide response of all three ecotypes to iron limitation is going to be conducted by using microarrays. The contribution of genes and processes identified by resequencing and microarray analysis for iron homeostasis will be validated (e.g. heterologous expression, enzyme activity) in laboratory experiments. The link to the elemental composition of the cells under iron limitation will be provided by using an ICPMS for elemental abundance profiling and the VGi Isoprobe for measurements of Fe stable isotopes. This studentship will provide excellent training opportunities by the use of different cutting-edge methods and by working on a scientific question that is fundamental to global elemental cycles but hasn’t addressed yet for the marine system.
The goal of this studentship is to link natural variations in genotype and phenotype of the marine diatom Thalassiosira pseudonana with its elemental composition under iron limitation. Diatoms contribute ca. 20% of the Earth total primary production and therefore influence biogeochemical cycles of elements and climate. Iron limits diatom growth in 35% of the global upper ocean and therefore is the main element influencing distribution and abundance of marine diatoms. T. pseudonana is the first diatom for which a genome sequence and microarrays are available. This species is globally distributed with many ecotypes from different marine habitats. However, no functional molecular data are available yet that can explain these natural variations. The aim of this studentship is to enable the discovery of functionally relevant variations in three different ecotypes (coastal temperate (sequenced strain), off-shore temperate and off-shore tropical ocean) and how these ecotypes respond to iron limitation. Functional variations will be identified by re-sequencing of both off-shore strains and the genome-wide response of all three ecotypes to iron limitation is going to be conducted by using microarrays. The contribution of genes and processes identified by resequencing and microarray analysis for iron homeostasis will be validated (e.g. heterologous expression, enzyme activity) in laboratory experiments. The link to the elemental composition of the cells under iron limitation will be provided by using an ICPMS for elemental abundance profiling and the VGi Isoprobe for measurements of Fe stable isotopes. This studentship will provide excellent training opportunities by the use of different cutting-edge methods and by working on a scientific question that is fundamental to global elemental cycles but hasn’t addressed yet for the marine system.
This studentship is part of ELSA (http://www.elsa.ac.uk), a unique multi-disciplinary Alliance integrating world-class expertise in biological, earth and social sciences to tackle the challenges posed by a changing climate. Thus, this studentship offers unique opportunities in a stimulating environment.
Please contact Thomas Mock (email: t.mock@uea.ac.uk) for any questions.
References:
Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A,
Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele
K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret
F, Berges JA, Brownlee C, Cadoret J-P, Chiovitti A, Choi CJ, Coesel S, De
Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysmann
M, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kroeger N,
Kroth P, La Roche J, Lindquist E, Lommer M, Martin-Jezequel V, Lopez PJ,
Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Oudot-Le Secq M-P,
Napoli C, Obornik M, Petit J-L, Porcel BM, Poulsen N, Robison M, Rychlewski
L, Rynearson TA, Schmutz J, Schnitzler Parker M, Shapiro H, Siaut M, Stanley
M, Sussman MJ, Taylor A, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz
LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y, Grigoriev
IV (2008) The Phaeodactylum genome reveals the evolutionary history of diatom
genomes. Nature, 456: 239-244.
Parker MS, Mock T & Armbrust EV (2008) Genomic insights into marine microalgae. Annual Review of Genetics, 42: 619-645. Mock T, Samanta MP, Iverson V, Berthiaume C, Robison M, Holtermann K, Durkin C, Splinter BonDurant S, Richmond K, Rodesch M, Kallas T, Huttlin EL, Cerrina F, Sussman MR & Armbrust EV (2008) Whole genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. Proceedings of the National Academy of Sciences, USA, 105: 1579-1584.
Research Areas:
- Cells and Tissues
- Molecules and Pathways
- Organisms and the Environment
- Computational Biology
Keywords:
Analytical Chemistry; Inorganic Chemistry; Environmental Chemistry;
Ecology; Environmental Science; Geochemistry; Oceanography; Bioinformatics;
Data Analysis; Statistics
Funding Status:
Competition Funded Project (EU) ELSA: John Innes Centre and The School
of Environmental Sciences
Suitable First Degree:
Biological Sciences; Environmental Sciences
How to apply:
An application can be downloaded from our website at:
http://www1.uea.ac.uk/cm/home/services/units/mac/aao/courses/PG
Completed application forms should be submitted to the Admissions Office, Faculty of Science, University of East Anglia, Norwich, NR4 7TJ.
http://www1.uea.ac.uk/cm/home/services/units/mac/aao/courses/PG
Completed application forms should be submitted to the Admissions Office, Faculty of Science, University of East Anglia, Norwich, NR4 7TJ.