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Postgrad topics in Genetics

Below are the updated project lists for 2021 entry:

Julie Ahringer - Genome architecture and transcription regulation in development

> Lab webpage

A fundamental property of a single animal genome sequence is the ability to give rise to diverse cell types. The control of chromatin activity and spatial arrangement of the genome - genome architecture - establishes gene expression programmes that drive cellular identity, and dysregulation can cause disease. We study how genome architecture is regulated in vivo to establish and maintain programmes of gene expression. We use the C. elegans animal model system, in which we can leverage genetics, conduct assays in specific cell types, and use microscopy and single cell profiling to study individual known cells. Our research combines multiple approaches, including high-throughput genomic assays, high-resolution imaging, genome editing, computational analyses, and RNAi screening for functional gene discovery. 

Specific projects would depend on student interest.

 

Richard Durbin - Evolutionary and Computational Genomics

> Lab webpage

In addition to potential applicants applying for general University studentship funds or with their own funding, it is possible to apply for a Cambridge NERC Doctoral Training Partnerships ( https://nercdtp.esc.cam.ac.uk/staff/prof-richard-durbin ) with me to work on Malawi cichlid evolutionary genetics. I also have one studentship available for October 2021 funded by the ALPACA Integrative Training Network to work on algorithmic approaches to pangenome representation and analysis, based on the PBWT framework, https://cordis.europa.eu/project/id/956229 .

 

Christine Farr - Vertebrate Chromosome Biology

> Lab webpage

Projects include:

  • The functional organisation of centromere domains
  • The role of toposiomerase II at the centromere and the influence of SUMOylation
  • The role of TOPBP1 and PICH in mitotic chromosome segregation
    [2015]

Anne Ferguson-Smith - The epigenetic control of genome function / Pre- and Post-natal mammalian developmental genetics

 Please refer to the Group's webpage for research interests. [2020]

Michael Imbealt - Transposable elements and the evolution of gene regulatory networks

> Lab webpage

Our lab is focused on describing how transposable elements in mammalian genomes have been domesticated to participate in the regulation of genes. Specifically, we are interested in a class of epigenetic repressors (KRAB zinc finger proteins) that is involved in heterochromatin formation - we are working on the hypothesis that they modify accessibility of transposable-element derived regulatory platforms that impact nearby gene expression in a cell-type specific manner.

We study evolutionary conserved KRAB zinc finger proteins to elucidate their precise biological functions - a few projects also pertain to their collective role in development and responses to environmental stimuli. At the crossroads between genetics and evolution, we use the most up-to-date next-generation sequencing techniques (ChIP-seq, RNA-seq) to obtain profiles of variations induced by CRISPR manipulation of various targets. It is best to contact us to get the most up-to-date information about potential projects.

 

Frank Jiggins - Host-Parasite Evolution and Genetics

> Lab webpage

There is enormous variation within populations of insects in their susceptibility to infectious disease. This variation is important as it determines the rate at which mosquitoes transmit disease, and whether beneficial insects like bees can survive infection. By studying this we can understand the evolutionary arms races between hosts and parasites. We offer projects on Drosophila and mosquito disease vectors, both of which combine genomics, classical genetics and evolutionary analysis

  • The first project is to investigate the causes of variation in susceptibility to infection by identifying the genes that cause variation in the resistance of Drosophila to viruses. Using whole-genome approaches we will identify polymorphisms controlling resistance. We can then go on to study how natural selection is acting on this variation in natural populations, which will provide insights into how parasites drive the evolution of their hosts
  • The second project aims to understand why the mosquito Aedes aegypti varies in its ability to transmit disease. Populations of this important disease vector vary in many key traits relating to disease transmission, including susceptibility to important human pathogens. This project would combine work in the insectary and large-scale genome sequencing to understand the molecular and evolutionary causes of this variation  [2016]#

 

Felipe Karam Teixeira - Molecular Mechanisms Controlling Germline Stem Cell Biology

> Lab webpage

Also see: https://www.gen.cam.ac.uk/research-groups/karam-teixeira

We study the development of the germline, the immortal cell lineage that provides the continuity of life. Using Drosophila as a model, we combine developmental, genetics, microscopy, high-throughput sequencing analyses (small RNA-seq, RNA-seq, Ribo-seq) to build a systematic and unbiased understanding of diverse aspects governing germline biology in vivo. In particular, we are interested in dissecting the mechanisms protecting the germline genome against selfish DNA modules such as transposons, as well as in using germline stem cells as a model for understanding the control of stem cell self-renewal, growth, and differentiation in vivo. Projects include:

- Protein synthesis regulation controlling stem cell self-renewal and differentiation

- Mechanisms safeguarding genome integrity during germline development

- Small RNA- and chromatin-mediated regulation of alternative splicing.

 

Hansong Ma - Mitochondrial genetics in Drosophila

> Lab website

We use Drosophila to study mitochondrial DNA (mtDNA), including its transmission, recombination, and interaction with the nuclear genome. We are also keen on developing more genetic tools to understand how mtDNA impacts health and wellbeing.  [2020]

 

Liria Masuda-Nakagawa - Circuit mechanisms for regulation of sensory discrimination in Drosophila larval brain

> Lab webpage

Discrimination of sensory stimuli is essential for animals to form and retrieve specific memories. I am interested in the neuronal circuitry of this process, using the Drosophila larva as a model, with powerful tools for targeted manipulation of neurons, optogenetics, calcium imaging, and connectomics. I use the sensory input region of the larval mushroom bodies, with low cellular redundancy but similar processing principles as in mammals. Of particular interest is how neuromodulatory inputs regulate the sensitivity and specificity of processing, and integrate it with other physiological states. [2016]

 

Erik Miska - Small Regulatory RNA

> Lab webpage

We are interested in all aspects of gene regulation by non-coding RNA. Current research themes include: miRNA biology and pathology, miRNA mechanism, piRNA biology and the germline, endo-siRNAs in epigenetic inheritance and evironmental conditioning, small RNA evolution and the role of RNAi in host pathogen interaction [Oct 2017]

 

Cahir O'Kane - Molecular Analysis of Synaptic Function and Membrane Traffic in Drosophila

> Lab webpage

Projects include:

  • Structure and function of axonal endoplasmic reticulum, and the interplay between axonal membrane traffic and axon degeneration
  •  Roles of Hereditary Spastic Paraplegia disease gene products in neuronal membrane traffic and organisation and signalling in Drosophila
  • Roles of axonal endoplasmic reticulum and its biophysical properties in neuronal and synaptic function [2020]

 

Steven Russell - Genomics and Systems Biology of Drosophila

> Lab webpage

We are using genomics and genome engineering approaches to understand aspects of developmental gene regulation and chromatin structure in Drosophila, with a particular focus on nervous system development and early segmentation. We are particularly interested in the function of Sox-domain transcription factors, exploring aspects of functional redundancy and evolutionary conservation.

Available projects include:

  • The genomics of Sox transcription factors
  • Sox redundancy in the developing CNS
  • Sox function in testis development
  • Conserved Sox function during invertebrate segmentation and nervous system development  

[2019]

 

Henrik Salje- Pathogen Dynamics Group

> Lab webpage

The Pathogen Dynamics Group studies the spread, maintenance and control of infectious diseases through analytical and empirical techniques. We are an interdisciplinary group that works closely with a wide range of different disciplines including field epidemiologists, laboratory scientists, ministries of public health, and hospitals. Much of our is in resource-poor settings, which often have a disproportionate burden from infectious diseases. Details of projects are available on the group website.

[2020]

 

Aylwyn Scally - Evolutionary Genomics

> Lab webpage

Projects include:

  • Investigating demography and speciation within the great apes and other primates using whole-genome sequence data
  • Development of computational approaches in evolutionary genomics
    [2015]

 

Marisa Segal - Cell Cycle Control of Spindle Polarity in Budding Yeast

> Lab webpage

Chromosomal segregation along an axis of cell polarity is a hallmark of asymmetric cell divisions throughout evolution. The budding yeast S. cerevisiae is a unique model to explore spindle orientation linked to cell polarity. In budding yeast, pole-derived astral microtubules target the spindle poles asymmetrically (bud versus mother cell) orienting the spindle to intersect the bud neck. Spindle pole components are evolutionary conserved and studies in yeast have effectively predicted similar centrosome asymmetry in stem cell self-renewing divisions. We seek to bridge the mechanisms of cell polarity, spindle orientation and cell fate under cell cycle control as is only attainable at this time using budding yeast to uncover fundamental principles for establishment of centrosome asymmetry.
[2016]

 

Daniel St Johnston - Epithelial polarity in flies and mammals

> Lab webpage

Cell polarity is essential for most cell functions and for several key developmental processes, such as cell migration, axis formation and asymmetric stem cell divisions, whereas a loss of polarity is a critical step in the formation of tumours. We are analysing how cells become polarised and how this polarity controls the organisation of the cytoskeleton and intracellular trafficking. Part of the group studies the Drosophila oocyte, since its polarity defines the anterior-posterior axis of the future embryo. The rest of the group  focus on epithelial polarity, where we are comparing secretory (the follicle cells) and absorptive epithelia (the adult midgut) in Drosophila with a typical mammalian epithelium  (mouse intestinal organoids). Much of our work depends on advanced imaging, ranging from live imaging of mRNA transport and protein secretion to super-resolution imaging of polarity factors using custom-built microscopes with adaptive optics.  [2017]

 

Ben Steventon - Tissue tectonics and the emergence of pattern during complex morphogenesis

> Lab webpage

As cells proceed through development, information contained in the genome is expressed in a context-dependent manner. This must be regulated precisely in both space and time to generate patterns of gene expression that set-up the spatial coordinates of tissue and organ primordia that build the embryo. Our current understanding of pattern formation relies on the concept of positional information, the idea that cells receive instructive signals that impart a spatial coordinate system to generate pattern. While this model works very well in static cell populations with minimal cell rearrangement, it becomes challenging when considering dynamic morphogenetic processes such as gastrulation. Furthermore, pattern formation in gastrulation is highly flexible to alterations in the size, scale and spatial rearrangement of cells in both experimental and evolutionary situations. 

Our lab are currently focussing on developing two new concepts in the field of developmental genetics that will help resolve these long-standing problems of pattern regulation, evolvability and self-organisation. Firstly, tissue tectonics emphasises the role that multi-tissue interactions play in relaying information from changes at the organ and organism level to the regulation of gene regulatory networks (GRNs) at the cell level. Secondly, pattern emergence considers how extracellular signals act to control the dynamics of autonomous GRN activity, rather than as instructive signals to direct cell fate transitions. In this sense, pattern formation should not be seen as a downstream output of organisers and their responding tissues, but rather as an emergent property of their dynamic interaction. 

We have a number of projects that explore these concepts in the context of zebrafish posterior body elongation, the self-assembly of multi-axial patterning within aggregates of early embryonic cells in vitro, and through the morphogenetic engineering of mammalian gastruloids.

 [2020]

 

David Summers - Microbial Genetics and Cell Signalling

> Lab webpage

Research in the Summers laboratory uses E. coli as a model to study the role of indole in bacterial cell signalling. We are interested in the role of indole in the response of bacteria to a range of environmental insults including temperature, antibiotics and oxidizing agents. We have recently described a novel mode of indole action (pulse signalling) that occurs during E. coli stationary phase entry. In the biophysical aspects of our work we collaborate closely with Ulrich Keyser’s group at the Cavendish Physics laboratory.

Projects available focus on the role of indole as an intra-cellular messenger regulating key aspects of the bacterial cell cycle. In particular we are interested in the role of indole-induced changes in trans-membrane potential as part of the signalling mechanism. We also have translational interests in the development of novel therapies that reduce the likelihood of chronic bacterial infection. We are seeking to achieve this by interfering with indole signalling.

[not taking on new students in 2021-2022]

 

John Welch - Molecular Evolution

> Lab webpage

Projects include:

  • Adaptive genome evolution of bacterial pathogens (particularly S. aureus, and the genus Rickettsia)
  • Interpreting genomic regions of enhanced differentiation (particularly in Mytilus mussels)
  • The evolution of reproductive isolation
    [2020]

 

More information on research

A full listing of Groups in the Department appears here, and a description of research by themes here, but please note that only the labs listed on this page are currently accepting Graduate students.

Doctoral Training Programmes

Some Group Leaders also participate in the NERC-DTP and the SBS DTP Studentships, programmes: follow the links on their pages for project listings.