- How to design a protein factory? Proteins shaping the plant endoplasmic reticulum (deadline: 11 December 2020)
- Integration of shape and function: identifying the genetic and neural circuitry underlying rapid male genital evolution (deadline: 11 December 2020)
- Bile acid metabolism in metabolic associated fatty liver disease (MAFLD) and hepatocellular carcinoma (HCC) (deadline: 11 December 2020)
- Mixed signals: How different signalling modes are established in neurons (deadline: 11 December 2020)
- Molecular mechanisms of flagellum length control in protozoan parasites (deadline: 11 December 2020)
Department of Biological and Medical Sciences
3 Year, full-time PhD studentship
Project title: How to design a protein factory? Proteins shaping the plant endoplasmic reticulum
Eligibility: Home UK/EU and International students.
Closing date: 11 December 2020
Start date: September 2021
Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2020/21 bursary rate is £15,285)
University fees and bench fees at the UK rate will be met by the University for the 3 years of the studentship.
Main Supervisor: Dr. Verena Kriechbaumer
Fees: Tuition fees up to UK level will be paid by the University. Any EU and international student awarded the studentship would need to cover the difference between international, EU and UK fees. Please note, fees increase by 4% annually.
Project:
Background: A great proportion of the planet’s food supply is produced, processed and transported through the plant secretory pathway. Here the endoplasmic reticulum (ER) forms the first compartment and is a major factory for protein/lipid synthesis and quality control. The ER structure is highly dynamic and composed of two morphologically distinct domains: cisternae and tubules, which are joined at 3-way junctions to create a polygonal network.
A number of proteins have been identified that are involved in the organization of the cortical ER network in plants. These include reticulon proteins (creating/maintaining tubules) and Lunapark proteins (cisternae regulation).
Though both cisternae and tubules are present in all eukaryotic cells, the proportion of each structure varies between cells and species which has been suggested to influence underlying cellular processes and protein secretion. E.g. secretory cells, such as pancreatic and salivary glands, display a higher proportion of cisternae, whereas cells with a lower requirement for protein secretion, e.g. cortex cells, tend to have a higher proportion of tubular ER. But a convincing link between structure and function of the ER has not been established.
Workplan: High-resolution confocal microscopy as well as electron microscopy will be used to capture both ER structure and dynamics in presence and absence of known ER shaping proteins as well as recently identified novel proteins. Changes to structure and dynamics will be quantified using our specialist software AnalyzER.
To link structure and dynamics with ER function a variety of protein production and secretion assays as well as membrane lipid analysis will be applied.
We will expand this work to tomato as a crop and have identified and expressed the corresponding ER-shaping proteins and found a link to pathogen response.
For informal inquiries please contact Dr Verena Kriechbaumer: vkriechbaumer@brookes.ac.uk
Requirements:
Applicants should have a first or upper second class honours degree from a Higher Education Institution in the UK or acceptable equivalent qualification in Biological Sciences or related disciplines. EU Applicants must have a valid IELTS Academic test certificate (or equivalent) with an overall minimum score of 7.0 and no score below 6.0 issued in the last 2 years by an approved test centre.
How to apply:
Applications should be sent to hlsapplications@brookes.ac.uk and should include the following application form:
/documents/research-opportunities/phd-studentship-application-jan-14/
Department of Biomedical and Medical Sciences
3 Year, full-time PhD studentship
Project title: Integration of shape and function: identifying the genetic and neural circuitry underlying rapid malegenital evolution
Eligibility: Home UK/EU and International students
Closing date: 11 December 2020
Start date: September 2021
Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2020/21 bursary rate is £15, 285)
University fees and bench fees at the UK will be met by the University for the 3 years of the Studentship.
Supervisors: Dr. Daniela Nunes (Oxford Brookes University), Carolina Rezaval (University of Birmingham), Casper Breuker (Oxford Brookes University) and Saad Arif (Oxford Brookes University)
Fees: Tuition fees up to UK level will be paid by the University. Any EU and international student awarded the studentship would need to cover the difference between international, EU and UK fees. Please note, fees increase by 4% annually.
Project Description:
Background
The size and shape of male genitalia are remarkably diverse in animals with internal fertilization and this phenomenon is long thought to be driven by sexual selection. Changes in genital morphology could impact reproductive success by directly changing the function of the evolved organ and/or through behavioural modification of either or both sexes, for example through effects on female choice. However, causal links between morphological and behavioural changes have been difficult to establish because these components have often been addressed separately from a genetic, developmental and neural perspective.
Aims
This project aims to determine how genes known to contribute to the divergence in male genitalia between two closely related species, Drosophila simulans and Drosophila mauritiana, affect genital coupling, mating behaviour and reproductive success in these species. To obtain a better understanding of the mechanisms driving behavioural changes we will also conduct genetic screens to identify CNS neurons that are able to modulate the mating choices of both males and females as a response to the changes in the morphology of the male genitalia.
The results of this project will provide unprecedented insights into the mechanisms through which morphological changes affect behavioural phenotypes and the evolution of reproductive isolation between species and speciation more generally.
Training
Training will be provided in genomic engineering using CRISPR/Cas9, Molecular biology, Drosophila genetics, Behavioural assays, Bioimaging, Optogenetics, Thermogenetics, Neurogenetics and neural circuit bashing using the state-of-the-art facilities available Oxford Brookes University and at the University of Birmingham.
For informal inquiries about the project please contact Dr Daniela Nunes: msantos-nunes@brookes.ac.uk
Requirements:
Applicants should have a first or upper second class honours degree from a Higher Education Institution in the UK or acceptable equivalent qualification in biological science or related discipline. EU Applicants must have a valid IELTS Academic test certificate (or equivalent) with an overall minimum score of 7.0 and no score below 6.0 issued in the last 2 years by an approved test centre.
How to apply:
Applications should be sent to hlsapplications@brookes.ac.uk and should include the following application form:
/documents/research-opportunities/phd-studentship-application-jan-14/
Department of Biomedical and Medical Sciences
3 Year, full-time PhD studentship
Project title: Bile acid metabolism in metabolic associated fatty liver disease (MAFLD) and hepatocellular carcinoma (HCC)
Eligibility: Home UK/EU and International students
Closing date: 11 December 2020
Start date: September 2021
Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2020/21 bursary rate is £15, 285)
University fees and bench fees at the UK rate will be met by the University for the 3 years of the Studentship.
Supervisors: Dr. Laura Gathercole, Prof. Jeremy Tomlinson (University of Oxford), Prof. Sue Vaughan, Prof. Dave Carter
Fees: Tuition fees up to UK level will be paid by the University. Any EU and international student awarded the studentship would need to cover the difference between international, EU and UK fees. Please note, fees increase by 4% annually.
Background
Patients with metabolic associated fatty liver disease (MAFLD) are at a greatly increased risk of hepatocellular carcinoma (HCC). Bile acids are steroid compounds that are synthesised in the liver and, acting through the bile acid receptor FXR, can activate hepatoprotective signalling pathways. However, the physical properties of bile acids mean that certain species are cytotoxic and cause oxidative stress.
It is known that bile acid homeostasis is altered in patients with MAFLD. We hypothesise that hepatic bile acid synthesis and metabolism are dysregulated and that this results in both an increase in the cytotoxicity of the bile acid pool and a loss of cytoprotective bile acid signalling, so promoting MAFLD progression and increasing the risk of developing HCC. Furthermore, that sex specific differences in the regulation, or dysregulation, of bile acid synthesis and metabolism contributes to the increased prevalence of MAFLD and HCC in males.
Workplan
The student will use invivo and liver spheroid models, combined with molecular and state of the art bioimaging techniques, to investigate the impact that manipulating bile acid synthesis and metabolism has on oxidative stress, hepatoprotective signalling and carcinogenesis, as well as the mechanisms that underpin sex specific differences.
For informal inquiries about the project please contact Dr Laura Gathercole: lgathercole@brookes.ac.uk
Requirements:
Applicants should have a first or upper second class honours degree from a Higher Education Institution in the UK or acceptable equivalent qualification in biological science or related discipline. EU Applicants must have a valid IELTS Academic test certificate (or equivalent) with an overall minimum score of 7.0 and no score below 6.0 issued in the last 2 years by an approved test centre.
How to apply:
Applications should be sent to hlsapplications@brookes.ac.ukand should include the following application form:
/documents/research-opportunities/phd-studentship-application-jan-14/
Department of Biomedical and Medical Sciences
3 Year, full-time PhD studentship
Project title: Mixed signals: How different signalling modes are established in neurons
Eligibility: UK/EU and International students
Closing date: 11 December 2020
Start date: September 2021
Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2020/21 bursary rate is £15, 285)
University fees and bench fees at the UK rate will be met by the University for the 3 years of the Studentship.
Supervisors: Dr Maike Kittelmann, Prof. Isabel Bermudez, Dr Ryan Pink, Prof Janet Richmond (external)
Fees: Tuition fees up to UK level will be paid by the University. Any EU and international student awarded the studentship would need to cover the difference between international, EU and UK fees. Please note, fees increase by 4% annually
Project:
Signal transduction from neurons happens on multiple levels: Neurotransmitters are released from synaptic vesicles at the active zone of synaptic connections and are highly specific to their target cells. Neuropeptides on the other hand are released from dense core vesicles and can modulate synaptic activity or act as long range signalling molecules to play a modulatory role in most behaviours. A third and even less understood mode of signalling is achieved through the release of exosomes from the plasma membrane of the neuronal cell body, axon or dendrite. However, how the components of these different signalling modes are correctly localised, their release sites established and maintained during development and how they interact with each other is still not well understood. While a variety of synaptic proteins have been suggested to be transported in precursor vesicles to the synaptic bouton, there is very little data on what distinguishes a precursor vesicle morphologically, what their cargo content is and how they are transformed locally into distinct synaptic and dense core vesicles. Additionally, multivesicular bodies have been suggested to be involved in protein sorting, recycling and transport in neurons as well as stabilization and modulation of neuromuscular signalling through the release of exosomes. We will use the powerful model organisms C. elegans with its vast range of genetic tools, fluorescent and electron microscopy as well as behavioural assays to better understand how synaptic components are transported to their correct release site, how extracellular cues from exosomes influence and modulate the formation of such sites as well as the effect on neuronal wiring and behaviour when these processes are disrupted.
For informal inquiries about the project please contact Dr Maike Kittelmann: maike.kittelmann@brookes.ac.uk
Requirements:
Applicants should have a first or upper second class honours degree from a Higher Education Institution in the UK or acceptable equivalent qualification in biological science or related discipline. EU Applicants must have a valid IELTS Academic test certificate (or equivalent) with an overall minimum score of 7.0 and no score below 6.0 issued in the last 2 years by an approved test centre.
How to apply:
Applications should be sent to hlsapplications@brookes.ac.uk and should include the following application form:
/documents/research-opportunities/phd-studentship-application-jan-14/
Department of Biomedical and Medical Sciences
3Year, full-time PhD studentship
Project title: Molecular mechanisms of flagellum length control in protozoan parasites.
Eligibility: Home UK/EU and International students
Closing date: 11 December 2020
Start date: September 2021
Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2020/21 bursary rate is £15, 285)
University fees and bench fees at the UK rate will be met by the University for the 3 years of the Studentship.
Supervisors: Prof Sue Vaughan, Dr Jack Sunter, Dr Philippe Bastin (Pasteur Institute)
Fees: Tuition fees up to UK level will be paid by the University. Any EU and international student awarded the studentship would need to cover the difference between international, EU and UK fees. Please note, fees increase by 4% annually.
Project:
The flagellum is a whip-like organelle, with both motility and sensory functions that protrudes from the cell body of almost all eukaryotic cells. It is a microtubule based structure that extends from a basal body, which is docked to the cell membrane at the base of the flagellum. Despite the ubiquitous nature of the flagellum in eukaryotic cells, its length can vary dramatically between organisms and even between tissues in the same organism. Therefore understanding flagellum length control is critical to dissecting the different flagellum functions.
We use the divergent eukaryotes Leishmania and Trypanosomato study flagellum length control. During the Trypanosoma cell cycle a new flagellum is assembled alongside the old flagellum and at a certain point the assembly of this new flagellum is ‘locked’ and can no longer extend or shorten. We have recently shown this lock is due to the presence of the protein CEP164C at the base of the flagellum. DespiteLeishmania being closely related to Trypanosoma its flagellum is able to undergo dramatic changes in length not seen in Trypanosoma.
Aim
To dissect the molecular mechanisms of flagellum length control mechanisms of Leishmania and Trypanosoma.
Workplan
The student will generate deletion mutants and cells expressing fluorescently tagged proteins and use a broad range of molecular cell biology techniques coupled with advanced light and electron microscopy to analyse the resulting phenotypes.
For informal inquiries about the project please contact Prof Sue Vaughan: svaughan@brookes.ac.uk or Dr Jack Sunter: jsunter@brookes.ac.uk
Requirements:
Applicants should have a first or upper second class honours degree from a Higher Education Institution in the UK or acceptable equivalent qualification in biological science or related discipline. EU Applicants must have a valid IELTS Academic test certificate (or equivalent) with an overall minimum score of 7.0 and no score below 6.0 issued in the last 2 years by an approved test centre.
How to apply:
Applications should be sent to:hlsapplications@brookes.ac.uk and should include the following application form:
/documents/research-opportunities/phd-studentship-application-jan-14/
The Oxford Interdisciplinary Bioscience Doctoral Training Partnership
The Oxford
Interdisciplinary Bioscience Doctoral Training Partnership (DTP) programme is a 4-year DPhil*/PhD programme
that aims to equip a new generation of researchers with the skills and
knowledge needed to tackle the most important challenges in bioscience
research.
We
provide an innovative, individually-tailored training programme that includes
taught courses in interdisciplinary skills and the opportunity for students to
undertake two exploratory research projects with prospective supervisors in
their first year before choosing their main 3-year research project. Students
also undertake a 12-week professional internship to gain direct experience of
the areas of work into which they can apply their skills.
Oxford
Brookes University are
offering a place on the BBSRC funded DTP within the Department of Biological
& Medical Sciences in the areas of plant cell biology, virology, insect and
spider development, mammalian cell biology, molecular biology, metabolic
modelling/systems biology, parasitology and bioimaging. The successful
candidate will enjoy access to our state of the art facilities, including newly
refurbished laboratories and bioimaging suite.
In
addition to their choice of PhD project at Oxford Brookes University, the
student will be able to undertake their exploratory research projects at any of
the seven world-class research institutions that make up the DTP:
- University
of Oxford,
coordinators of the DTP
- Oxford
Brookes University, a
partner with the University of Oxford in developing regional excellence in
bioscience research
- Pirbright
Institute, the
UK’s national centre of research into viral diseases of livestock and viruses
that spread from animals to humans
- Diamond
Light Source, the
UK’s national synchrotron science facility
- ISIS, which provides national
capabilities for neutron science
- STFC Central
Laser Facility, which
provides state-of-the-art laser technology for experiments in physics,
chemistry and biology
- The
Research Complex at Harwell (RCaH), is a multidisciplinary laboratory specialising in
research using Diamond, ISIS and the Central Laser Facility at Harwell
- The Rosalind Franklin Institute is a new national
institute dedicated to bringing about transformative changes in life science
through interdisciplinary research and technology development.
The
programme is supported by the Biotechnology
and Biological Sciences Research Council (BBSRC) with additional support from
within the Partnership.
Please see
below for potential supervisors and instructions on how to apply.
If you wish
to apply to the DTP via Oxford Brookes University please complete the Faculty
of Health and Life Sciences PhD Research Studentship Application Form.
Application
and CV must be emailed to the address shown on the application form and CC’d to
dcarter@brookes.ac.uk
We have
many projects available which can be taken as a short term (3-month) rotation
or a full PhD project. The following supervisors are offering exciting
projects; for further information click on the link to visit their lab website.
Alison
Forhead Endocrine regulation
during fetal growth
Alistair
McGregor Evolution of animal
development and morphology
Andy
Jones Functional studies of insect nicotinic acetylcholine
receptors.
Barbara
Jennings Investigating the
mechanism of Groucho-mediated repression
Casper
Breuker Butterfly Ecological
Evolutionary Developmental Biology
Dave
Carter Extracellular Vesicle biology
David
Meredith Membrane Transporter
function
Dianne
Newbury The Genetics of Language Disorders
Hee-Jeon
Hong Microbial genetics and
antibiotic resistance
Isabel
Bermudez Molecular
Neuropharmacology
Jack
Sunter Understanding cell morphogenesis in Leishmania
Jon
Lees Deep Learning for protein function prediction
Jordi
Solana The use of single-cell RNA-seq to identify stem cells
Katja
Graumann Nuclear envelope in
plants
Korneel
Hens Next generation
technologies for gene regulatory network mapping
Linda
King Molecular Virology
Maike
Kittelmann Synapse formation in
neurons
Maria
Santos-Nunes Phenotypic evolution
and adaptation
Mark
Poolman Cell systems modelling
Michael
Gerth Evolution
of inherited microbial symbionts in insects
Paul
Potter Analysing critical factors in mitochondrial complex I
assembly
Ravinder
Kanda The Role of Endogenous
Retroviruses in Immunity
Ryan
Pink Cell signalling
Saad
Arif Evolutionary Genetics and Genomics
Sue
Vaughan Cell Biology of Trypanosomes
Verena
Kriechbaumer Endoplasmic reticulum
structure and function
Deadline
for receipt of applications is 12 noon on 22nd
January 2021
Eligibility
criteria: The
studentship covers bench fees, stipend, and ‘Home’ tuition fees only.
Start
date September/October 2021
Bursary
is approximately £15,609 for academic year 2021/22
Applicants
require a good Honours degree level equivalent to a UK degree BSc (minimum 2.1
or higher).
Any
queries please contact: Professor David Carter:dcarter@brookes.ac.uk