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Department of Physiology, Development and Neuroscience




Maria P. Alcolea


Relevant References:

  • Colom B, Herms A, Hall MWJ, Dentro SC, King C, Sood RK, Alcolea MP, Piedrafita G, Fernandez-Antoran D, Ong SH, Fowler JC, Mahbubani KT, Saeb-Parsy K, Gerstung M, Hall BA, Jones PH. Mutant clones in normal epithelium outcompete and eliminate emerging tumours. Nature. 2021 Oct;598(7881):510-514.
  • Herms A#, Fernandez-Antoran D#, Alcolea MP#, Kalogeropoulou A, Banerjee U, Piedrafita G, Abby E, Valverde-Lopez JA, Ferreira IS, Dentro SC, Ong SH, Colom B, Murai K, King C, Mahbubani K, Saeb-Parsy K, Lowe AR,  Gerstung M,  Jones PH. “Epithelioids: Self-sustaining 3D epithelial cultures to study long-term processes”
    PREPRINT, bioRxiv, 2023, 522589, doi:
  • Alcolea MP, Greulich P, Wabik A, Frede J, Simons BD, Jones PH. Differentiation imbalance in single Oesophageal progenitor cells causes clonal immortalization and field change. Nat Cell Biol. 2014 Jun;16(6):615-22.




The role of tissue mechanics during early tumour formation

The recent realisation that tissues accumulate cancer-associated mutations with age has revolutionized the cancer field. We now know that genetic alterations do not represent the sole cause of cancer and that other non-genetic factors may play a significant role during early tumour formation. Supporting this notion, unpublished data from the Alcolea lab demonstrates that stromal cells respond to epithelial mutations by creating a fibrotic microenvironment that promotes tumorigenesis. These exciting results offer the provocative idea that the early tumour ECM is more than just a scaffold, and that interactions between cells and ECM play a significant role during the most incipient stages of tumour initiation and development.

In this interdisciplinary project, we will make use a new 3D organ culture approach, cell tracing methods, single-cell RNA sequencing and genetic screenings to study how the mechanical properties and forces of the ECM impact tumour formation and progression in vivo.

The long-term vision of this project is to establish the clinical relevance of the early tumour ECM; as a benchmark to identify new targets of potential use in early cancer diagnostics and therapeutics, as well as to develop strategies to prevent the onset of this aggressive disease in the first place.

Additionally, exploring the mechanobiology of early tumours in vivo will offer new insights into how the physical properties drive biological processes in complex 3D tissues, filling existing gaps in current understanding.

Maria P. Alcolea


Relevant References:

  • Bejar MT#, Jimenez-Gomez P#, Moutsopoulos I, Colom B, Han S, Calero-Nieto FJ, Göttgens B, Mohorianu I, Simons BD, Alcolea MP*. Defining the transcriptional signature of esophageal-to-skin lineage conversion.
    PREPRINT, bioRxiv, 2021, 431899, doi:
  • Doupé DP*, Alcolea MP*, Roshan A, Zhang G, Klein AM, Simons BD, Jones PH. A Single Progenitor Population Switches Behavior to Mainta in and Repair Esophageal Epithelium. Science. 2012 Aug 31;337(6098):1091-3.
  • Ge, Y. & Fuchs, E. Stretching the limits: from homeostasis to stem cell plasticity in wound healing and cancer. Nat Rev Genet 19, 311-325, doi:10.1038/nrg.2018.9 (2018).

Mechanisms regulating cell fate plasticity in epithelial organoids.

Despite decades of intense research, modern medicine still faces a critically unresolved question. How can cell fate be manipulated to increase the regenerative capacity of adult tissues? The emerging notion that epithelial cells present a high degree of plasticity in response to injury, rewiring their fate in order to preserve tissue integrity, offers the possibility to explore the ill-defined processes modulating cell behaviour in response to regeneration. Here we propose to identify and to characterise the common mechanisms regulating cell plasticity across epithelial tissues, as a way to unearth the generic and tissue specific rules dictating the regenerative capacity of epithelial cells.

To address this ambitious but critical aspect of epithelial stem cell biology, we will grow organoids from different human and mouse epithelial tissues under comparable regenerative conditions. For this, we will implement a unified approach that uses the exact same conditions for all tissues. The transcriptional signature and inferred Gene Regulatory Networks defining organoid-derived cells will be investigated using single-cell RNA sequencing approaches, and the mechanisms of action will be dissected by implementing genetic screenings.

This study will identify shared and specific mechanisms driving epithelial cell plasticity; providing a novel perspective on cell fate decision-making and offering a benchmark to develop shared multi-organ regenerative strategies.

Riccardo Beltramo


Relevant References:


Neural pathways for vision-based spatial navigation

A critical requirement for survival is the ability to navigate in the environment. This skill is believed to rely on internal spatial representations of the surroundings, such as the “spatial maps” found in the hippocampus and parahippocampal cortex.

Sensory inputs are fundamental for shaping these internal spatial representations. In particular, visual cues are considered essential factors that guide navigation. However, how visual input is converted into spatial maps is still poorly understood.

Mammals have two coexisting brain structures that process visual information: the ancient “superior colliculus” and the phylogenetically newer “visual cortex”. This Ph.D. project aims to determine the roles played by these parallel visual systems in spatial navigation.

We have recently discovered that the superior colliculus has a dedicated space in the visual cortex: the postrhinal area (POR) (Beltramo & Scanziani, 2019; Beltramo, 2020). POR, whose responses rely on collicular activity and are critically involved in spatial navigation (Brenner, Beltramo et al., 2023), is perfectly placed at the interface between the cortical and collicular visual streams and the hippocampal formation.

Combining electrophysiological, 2photon imaging, and opto/chemogenetic approaches, we will study the interactions between ancient and modern visual pathways in sensory processing and spatial navigation.

Riccardo Beltramo


Relevant References:

  • [1] Dunsmoor J. & Paz R., Fear Generalization and Anxiety: Behavioral and Neural Mechanisms.
    Biol Psychiatry, 2015 Sep 1;78(5):336-43.
  • [2] Beltramo R. & Scanziani M., A collicular visual cortex: Neocortical space for an ancient midbrain visual structure.
    Science, 2019 Jan 4;363(6422):64-69.
  • [3] Burgess C.R., Rohan N. Ramesh R.N., Sugden A.U., Levandowski K.M., Minnig M.A., Fenselau H., Lowell B.B,1, Andermann M.L., Hunger-dependent enhancement of food cue responses in mouse postrhinal cortex and lateral amygdala.  Neuron, 2016 Sep 7; 91(5): 1154–1169.

Sensory processing and fear overgeneralization in stress-induced anxiety, across the visual system

Anxiety disorders stem from dysfunctions in the circuits that process aversive stimuli1. When confronted with potential dangers, animals must select the appropriate behavioral response. In an environment full of complex stimuli, sometimes threat cues are ambiguous, making it challenging to distinguish dangerous from irrelevant stimuli. The ability to generalize across similar stimuli is an adaptive strategy that protects animals from fatally missing a potentially deadly environmental cue. In other words, “better safe than sorry”. However, an exaggerated generalization of fear to harmless stimuli (i.e. “fear overgeneralization”) is maladaptive and considered a hallmark of numerous anxiety disorders[1].

The cellular and circuit mechanisms mediating fear overgeneralization are largely unknown. This PhD project investigates the development of fear overgeneralization at the level of the sensory circuits that process aversive information.

Using the mouse visual system as a model, we will focus on a visual cortex selectively activated by innately fearful stimuli[2], targeted by the amygdala[3], and driven by a midbrain center that triggers avoidance behaviors[2]. We will determine how changes in the neural sensory representations of dangerous and safe visual stimuli affect the animals’ ability to discriminate them. Given the critical role of preexisting stress in the pathogenesis of numerous anxiety disorders, we will test the hypothesis that emotional distress changes how sensory stimuli are encoded during learning, leading to fear overgeneralization. Through chronic 2photon imaging, large-scale electrophysiology, and innovative behavioral tasks, we will determine the effects of severe stressors on early sensory processing, during the development of stress-induced anxiety.

Thorsten Boroviak


Relevant References:

  • Bergmann S, Penfold CA, Slatery E, Siriwardena D, Drummer C, Clark S, Strawbridge SE, Kishimoto K, Vickers A, Tewary M, Kohler TN, Hollfelder F, Reik W, Sasaki E, Behr R, Boroviak TE. Spatial profiling of early primate gastrulation in utero. Nature, 2022.
  • Connor R. and Boroviak T, Origin and function of the yolk sac in primate embryogenesis, Nature Communications, 2020
  • Munger C, Kohler TN, Slatery E, Ellermann AL, Bergmann S, Penfold CA, Ampartzidis I, Chen Y, Hollfelder F, Boroviak TE. Microgel culture and spatial identity mapping elucidate the signaling requirements for primate epiblast and amnion formation. Development, 2022



Functional interrogation of human gastrulation in embryo models

How do complex body patterns emerge in the early embryo? The first signs of the human body axis can be traced back to the second week of gestation. To get to this point, the fertilised egg has implanted and established a small sheet of cells, the embryonic disc. Deeply embedded within extraembryonic tissues, gastrulation transforms the EmDisc into three germ layers and organizes the body plan. All of these events are essential for healthy embryo development, but in human they have been notoriously hard to study for ethical and technical reasons.

Our lab revealed the signalling landscape between implantation and gastrulation of primate embryos in vivo (Bergmann et al., Nature 2022). In this project, we will emulate human gastrulation by generating blastoids from pluripotent stem cells and allowing them to implant on an endometrial/stromal attachment matrix. Primitive streak formation in blastoid-derived postimplantation cultures will be analysed by immunofluorescence and single-cell transcriptome profiling for direct comparison to human and non-human primate embryo gastrula stages. In a second step, we will use knockout and reporter cell lines to pinpoint the individual effects of AVE candidate regulators to devise a conceptional framework for human gastrulation.

Stem-cell-based embryo models elucidating the crosstalk between embryonic and extraembryonic tissues will be critical to understand human implantation failure and how errors in gastrulation can lead to congenital malformations. Ultimately, this research holds the transformative potential to establish patient-specific organogenesis in a dish.

Albert Cardona


Relevant References:

Changes to the brain connectome in a disease model

Mental health impacts the life of millions of people world wide. How the brain's circuits change under disease remains poorly understood. Here, we propose to map and analyse the synaptic wiring diagram, or connectome, of brains of animal models for disease. One such model is Parkinson's, inducible in Drosophila by the targeted expression of alpha-synuclein in its dopamine neurons. Notably, affected animals present behavioural signatures of the disease, yet remarkably continue to function and live. Understanding how the brain circuits have been altered could show the path towards devising effective palliative treatment. To this end, you will map and analyse neural circuits using volume electron microscopy and techniques for connectomics, and compare the connectome with that of the wild type to identify changes in neural circuit architecture that could explain the observed behavioural phenotypes.

Albert Cardona


Relevant References:

  • Winding M, Pedigo BD, Barnes CL, Patsolic HG, Park Y, Kazimiers T, Fushiki A, Andrade IV, Khandelwal A, Valdes-Aleman J, Li F. The connectome of an insect brain. Science. 2023 Mar 10;379(6636):eadd9330
  • Jovanic T, Schneider-Mizell CM, Shao M, Masson JB, Denisov G, Fetter RD, Mensh BD, Truman JW, Cardona A, Zlatic M. Competitive disinhibition mediates behavioral choice and sequences in Drosophila. Cell. 2016 Oct 20;167(3):858-70
  • Lappalainen JK, Tschopp FD, Prakhya S, McGill M, Nern A, Shinomiya K, Takemura SY, Gruntman E, Macke JH, Turaga SC. Connectome-constrained deep mechanistic networks predict neural responses across the fly visual system at single-neuron resolution. bioRxiv. 2023:2023-03

Bringing life to the wires: computational modeling of a brain

We now have the ability to map synaptic wiring diagrams, or connectomes, of whole brains, such as that of the Drosophila melanogaster larva and adult. On the basis of the known wiring diagram, inferred neurotransmitter signatures of each neuron, and abundant transcriptomic data, the question of how the brain works can now be tackled with computational modelling. In this project, you will devise in silico models of brain function, derive hypotheses of the role of specific neurons and circuit motifs in signal processing, memory establishment and extinction, and action selection, and then test these hypotheses experimentally.

Elisa Galliano


Relevant References:

  • [1]  Galliano et al., ‘Brief Sensory Deprivation Triggers Cell Type-Specific Structural and Functional Plasticity in Olfactory Bulb Neurons’, J. Neurosci. Off. J. Soc. Neurosci., vol. 41, no. 10, pp. 2135–2151, Mar. 2021, doi: 10.1523/JNEUROSCI.1606-20.2020.
  • [2]  Erskine,  Bus, Herb, and  Schaefer, ‘AutonoMouse: High throughput operant conditioning reveals progressive impairment with graded olfactory bulb lesions’, PloS One, vol. 14, no. 3, p. e0211571, 2019, doi: 10.1371/journal.pone.0211571.
  • [3]  Huang , Hardyman, Edwards , and Galliano E (2023) Deprivation-induced plasticity in the rodent’s early visual, auditory, and olfactory circuits. bioRxiv 2023.09.04.556170.


Activity-dependent neuronal plasticity in the mouse olfactory bulb

The ability to sense and respond to the environment is critical for the survival of all organisms. This process involves gathering sensory information and using it to generate appropriate behaviors, a feat achieved through neuronal plasticity. This includes structural, synaptic, and intrinsic changes in neurons. However, these mechanisms are often studied in isolation, and their collective impact on behavior remains unclear. In our lab, we seek to bridge this knowledge gap by examining how mice adapt to olfactory stimuli. For this project we will manipulate their olfactory environment, subjecting them to sensory deprivation (similar to a mild cold) or olfactory enrichment (resembling exposure to a perfume shop). Using advanced genetic tools, we label neurons responsive to specific odors. Our approach combines immunohistochemistry and patch-clamp electrophysiology to investigate how olfactory bulb neurons adapt their synaptic connections, morphology, and intrinsic properties in response to different durations of sensory changes. We complement these cellular investigations with automated behavioral testing to assess the mice's ability to detect and differentiate odors and to understand the influence of adaptive plasticity on the learning process. Our comprehensive studies aim to provide deeper insights into the complex neural mechanisms that underlie behavioral adaptability in response to changing olfactory stimuli.

Elisa Galliano


Relevant References:

  • [1]  Lledo, Alonso, and Grubb, ‘Adult neurogenesis and functional plasticity in neuronal circuits’, Nat. Rev. Neurosci., vol. 7, no. 3, pp. 179–193, Mar. 2006, doi: 10.1038/nrn1867.
  • [2] Galliano et al., ‘Embryonic and postnatal neurogenesis produce functionally distinct subclasses of dopaminergic neuron’, eLife, vol. 7, Apr. 2018, doi: 10.7554/eLife.32373.
  • [3] Mandairon, Stack, Kiselycznyk, and Linster, ‘Broad activation of the olfactory bulb produces long-lasting changes in odor perception’, Proc. Natl. Acad. Sci. U. S. A., vol. 103, no. 36, pp. 13543–13548, Sep. 2006, doi: 10.1073/pnas.0602750103.

Embryonic and adult neurogenesis: do different birth dates lead to functional diversity?

An essential aspect of brain development and function is the ability of neurons to adapt structurally and functionally in response to specific stimuli. This adaptation involves changes in the strength of connections, morphology, and intrinsic properties and falls under three main categories: synaptic, intrinsic, and structural plasticity. In the olfactory system, structural plasticity is particularly striking, with several neuron subpopulations regenerating throughout an organism's lifespan. This includes olfactory sensory neurons, dopaminergic cells, and granule cells.

Recent research has unveiled differences between embryonic and postnatally-born dopaminergic cells, challenging the notion that they are like-for-like replacements. Using transgenic mouse models, immunohistochemistry, electrophysiology, and behavioral testing, our project aims to expand on these findings. Specifically, we investigate whether the distinctions based on birth date seen in dopaminergic neurons extend to other regenerating populations in the olfactory system. Additionally, we seek to unravel the behavioral roles played by embryonic and regenerating cells in olfactory processing. By addressing these questions, our research contributes to a more comprehensive understanding of the intricate dynamics within the olfactory circuit and the broader implications of neuronal plasticity for brain function and behavior.

Dino A. Giussani


Relevant References:

  • Botting KJ, Skeffington KL, Niu Y, Allison BJ, Brain KL, Itani N, Beck C, Logan A, Murray AJ, Murphy MP, Giussani DA. Translatable mitochondria-targeted protection against programmed cardiovascular dysfunction. Sci Adv. 2020;6(34):eabb1929;
  • Allison BJ, Brain KL, Niu Y, Kane AD, Herrera EA, Thakor AS, Botting KJ, Cross CM, Itani N, Shaw CJ, Skeffington KL, Beck C, Giussani DA. Altered Cardiovascular Defense to Hypotensive Stress in the Chronically Hypoxic Fetus. Hypertension. 2020;76(4):1195-1207.
  • Brain KL, Allison BJ, Niu Y, Cross CM, Itani N, Kane AD, Herrera EA, Skeffington KL, Botting KJ, Giussani DA. Intervention against hypertension in the next generation programmed by developmental hypoxia. PLoS Biol. 2019;17(1):e2006552.

Maternal obesity during pregnancy:  Early Origins of Heart Disease in Progeny

Summary of project

Maternal obesity during pregnancy is an alarming health care issue with detrimental consequences for mother and child. In her 2019 report, then as Chief Medical Officer, Dame Sally Davies highlighted that over half of women in the UK are over-weight during pregnancy. She stressed that a focus on the health of the pregnant woman and of her offspring and interventions to improve it offers a new and important opportunity to ensure the wellbeing of mothers and children. The PhD project addresses this issue directly using a well characterised sheep model of maternal obesity during pregnancy.  It will define mechanisms by which obesity during pregnancy influences the risk of heart disease in progeny and provide invaluable information on potential intervention.  In contrast to rodents, such as mice and rats, which are born highly immature, in sheep and humans, the fetal heart and blood vessels mature their structure and function at similar rates during development.  Therefore, sheep are the ideal animal model to address these questions and make the research more relevant to the human clinical situation.

Goal of research

This project will mimic the human situation of obesity during pregnancy in sheep and determine how maternal obesity can harm the baby’s heart and circulation.  It will test a specific antioxidant drug as potential treatment during obese pregnancy to prevent this.  The project will take advantage of the sheep model to test fetal cardiovascular function in vivo under basal and stimulated conditions, experiments that cannot be done in other species.  The project will then relate cardiovascular functional outcomes in the fetus to molecular pathways, including oxidative stress signalling and miRNA dysregulation.

Dino A. Giussani


Relevant References:

  • Giussani & Davidge. J Dev Orig Health Dis. 4(5):328-37, 2013
  • Itani et al. J Pineal Res. 60(1):16-26, 2016
  • Giussani. Circulation 144(17):1429-1443, 2021.

Obstructive Sleep Apnoea and Early Origins of Heart Disease

Obstructive sleep apnoea (OSA) is characterised by intermittent hypoxia (IH), which promotes an increased risk of heart disease in patients. In turn, human pregnancy is associated with OSA, which is aggravated by obesity, the rates of which in the UK are reaching epidemic proportions.  However, the effects of maternal IH during pregnancy on the cardiovascular health of the offspring are unknown. This project will study the effects of IH in the chicken embryo, an established model system that permits isolation of the direct effects of IH on the developing cardiovascular system, independent of effects on the mother and/or the placenta.

Fertilised chicken eggs will be exposed to normoxia or IH (Oxycycler, BioSpherix). At day 19 of the 21-day incubation period, hearts will be isolated.  In one cohort of embryos, the heart will be mounted onto a Langendorff preparation to determine effects on cardiac function.  In another cohort of embryos, cardiac mitochondrial respiratory capacity and substrate preference will be determined by permeabilised cardiac muscle fibre respirometry. Other cohorts of embryos will be perfusion fixed at term to determine alterations in cardiac wall remodelling and cardiomyocyte number, size and nuclearity.  A final cohort of embryos will be reserved for freezing hearts at term to determine underlying signalling pathways by molecular biology and miRNA analysis.

Subsequent phases of the PhD project will target intervention with mitochondria-targeted antioxidants, such as MitoQ.  Finally, embryos will be sexed by genotyping and cardiovascular functional, cellular, mitochondrial and molecular data will be analysed in a sex-dependent manner.

Courtney Hanna


Relevant References:

  • Andrews et al. 2023 Mechanisms and function of de novo DNA methylation in placental development reveals an essential role for DNMT3B. PMID: 3669062
  • Policarpi et al. 2021 Epigenetic editing: Dissecting chromatin function in context. PMID: 33724509


The impact of DNA methylation on gene regulation in placental development

DNA methylation is an epigenetic modification that exerts its function through the recruitment of epigenetic repressors or interfering with transcription factor binding to silence gene expression. DNA methylation is dramatically reprogrammed during early development in both the embryonic and extra-embryonic lineages. During this reprogramming event, the placental genome only becomes about half as methylated as most other cell types, a feature that is maintained throughout pregnancy and is conserved across mammalian species. Despite this atypical patterning, using transgenic mouse models, we have recently demonstrated that DNA methylation is essential for placental development and function. Yet, it remains unknown which genomic loci are responsive to DNA methylation in the placenta and what changes in gene expression underpin the developmental phenotypes.

To address these questions, this PhD project will use multi-omics techniques to identify regulatory elements that become de-repressed upon loss of DNA methylation in placental cells. Using CRISPR epigenetic editting techniques, the impact of region-specific changes in DNA methylation on gene regulation and trophoblast differentiation can then be functionally tested in cultured trophoblast stem cells.

Allan Herbison


Relevant References:

  • McQuillan HJ, Clarkson J, Kauff A, Han SY, Yip SH, Cheong I, Porteous P, Heather AK, Herbison AE (2022) Definition of the estrogen negative feedback pathway controlling the GnRH pulse generator in female mice. Nature Commun 13, 7433.
  • Clarkson J, Han SY, Piet R, McLennan T, Kane G, Ng J, Porteous R, Kim J, Colledge WH, Iremonger KJ, Herbison AE (2017) Definition of the hypothalamic GnRH pulse generator in mice. Proc Natl Acad Sci (USA) 114, E10216-E10223.
  • Herbison AE (2016) Control of puberty onset and fertility by gonadotropin-releasing hormone neurons. Nature Rev Endo, 12, 452-466.

Serotonin modulation of the GnRH pulse generator controlling fertility

The cells responsible for generating pulsatile reproductive hormone secretion have now been identified to be a population of kisspeptin neurons located in the arcuate nucleus of the hypothalamus (Clarkson et al., 2017). These neurons act as a central pattern generator to drive the pulsatile secretion of gonadotropin-releasing hormone (GnRH) that controls pituitary hormone release. A wide range of environmental and internal homeostatic factors modulate the frequency of the GnRH pulse generator and, hence, the fertility of an individual (Herbison, 2016).  The serotonin neurons of the brainstem project throughout the forebrain and convey multiple types of information including that of stress, mood, and arousal state on neuronal activity.  This project will use the latest in vivo GCaMP imaging, chemogenetic, and in vivo CRISPR gene editing approaches (McQuillan et al., 2022) in a suite of genetically modified mice to explore the role of brainstem serotonin neurons in modulating the activity of the kisspeptin GnRH pulse generator.  The studies are aimed at understanding the core neural network responsible for controlling reproductive hormone secretion with a view to improving the treatment of infertility in the clinic.

David Keays


Relevant References:

  • Cushion TD, Paciorkowski AR, Pilz DT, Mullins JG, Seltzer LE, Marion RW, Tuttle E, Ghoneim D, Christian SL, Chung SK, Rees MI, Dobyns WB. De novo mutations in the beta-tubulin gene TUBB2A cause simplified gyral patterning and infantile-onset epilepsy. Am J Hum Genet. 2014 Apr 3;94(4):634-41.
  • Lancaster MA,  Renner M, Martin A,  Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger J, Jackson AP, Knoblich JA.Cerebral organoids model human brain development and microcephaly. Nature. 2013 Sep 19;501(7467):373-9.
  • Keays DA, Tian G, Poirier K, Huang G, Siebold S, Cleak J, Oliver P, Washbourne R, Fray M, Harvey RJ, Molnar Z, Pinon M, Dear N, Brown SD, Rawlins JP, Davies KE, Cowan NJ, Patrick Nolan P, Chelly J, Flint J. Mutations in α-tubulin cause defects in neuronal migration in mice and lissencephaly in humans. Cell. 2007 Jan 12;128(1):45-57.

Modelling Human Neurodevelopmental Disease with Cerebral Organoids

The human brain is arguably the most complex structure in biology. It’s construction is dependent on a complex cascade of cellular events that include mitotic division, relocation of migrating neurons, and the extension of dendrites and axons. These processes are reliant on a dynamic and functionally diverse microtubule cytoskeleton. Microtubules form the mitotic spindle enabling the separation of sister chromatids, they facilitate translocation of the nucleus and extension of the leading process during neuronal migration, and microtubule polymers extend and maintain large and longstanding axons in mature neurons. Reflecting their importance mutations in genes encoding for tubulin subunits and microtubule associated proteins cause severe neurodevelopmental disorders. For instance, variants in TUBA1A are known to cause lissencephaly and cerebral palsy, mutations in TUBB2A cause cortical malformations, and substitutions in MAST1 cause microcephaly, autism and corpus callosum phenotypes. To study the underlying molecular and cellular mechanisms of these diseases the Keays laboratory is exploiting iPSCs and advanced 2D and 3D neuronal cultures. This project will utilise our recently created biobank of patient derived iPSCs (, coupled with CRISPR-cas9 genome engineering to generate isogenic controls. This project with focus on TUBB2A which is known to cause abnormal cortical gyration, microcephaly,  and/or autism. Following the generation of cerebral organoids the student will study how disease causing mutations influence the properties of the microtubule cytoskeleton, and the cellular events necessary for brain formation.

David Keays


Relevant References:

  • Isrie M, Breuss M, Tian G, Hansen AH, Cristofoli F, Morandell J, Kupchinsky ZA, Sifrim A, Rodriguez-Rodriguez CM, Dapena EP, Doonanco K, Leonard N, Tinsa F, Moortgat S, Ulucan H, Koparir E, Karaca E, Katsanis N, Marton V, Vermeesch JR, Davis EE, Cowan NJ, Keays DA, Van Esch H. Mutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type. Am J Hum Genet. 2015 Dec 3;97(6):79. 
  • Lancaster MA,  Renner M, Martin A,  Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger J, Jackson AP, Knoblich JA.Cerebral organoids model human brain development and microcephaly. Nature. 2013 Sep 19;501(7467):373-9.
  • Breuss, M., Heng, JI., Poirier, K., Tian, G., Jaglin, XH., Qu, Z., Braun, A., Gstrein, T., Ngo, L., Haas, M., Bahi-Buisson, N., Moutard, ML., Passemard, S., Verloes, A., Gressens, P., Xie, Y., Robson, KJ., Rani, DS., Thangaraj, K., Clausen, T., Chelly, J., Cowan, NJ., Keays, DA. (2012). Mutations in the β-tubulin gene TUBB5 cause microcephaly with structural brain abnormalities. Cell Rep. 2(6):1554-62.


The role of EB2 in Neurodevelopment and Disease

Circumferential skin creases Kunze type (CSC-KT) is a rare disease characterised by intellectual disability, circumferential skin creases, cleft palate, a reduction in brain size, and facial dysmorphism. It is colloquially known as the “Michelin tire baby syndrome”. In collaboration with the Van Esch laboratory we have shown that this intriguing syndrome is caused by mutations in genes that encode for either EB2 or TUBB5. EB2 is a protein associated with the microtubules that is critical for apico-basal epithelial differentiation, whereas TUBB5 is a beta tubulin that is broadly expressed in the developing central nervous system. Our goal is to understanding how, at a molecular and cellular level, mutations in these two proteins lead to this usual human disease. We predict that mutations that cause CSC-KT perturb the structure or function of the microtubule cytoskeleton, altering the proliferative output and/or survival of cells in the brain and skin. To explore this hypothesis the student will use iPSCs, which harbour a human disease causing mutation to generate both 2D and 3D neuronal cultures. This study will provide insight into the pathophysiological mechanisms that cause CSC-KT, and shed light on a growing spectrum of disease states that are associated with the microtubule cytoskeleton.

Sepiedeh Keshavarzi


Relevant References:

  • Keshavarzi S, Bracey EF, Faville RA, Campagner D, Tyson AL, Lenzi SC, Branco T, Margrie TW, Multisensory coding of angular head velocity in the retrosplenial cortex. Neuron 2022, 110(3): 532-543.
  • Keshavarzi S, Velez-Fort M, Margrie TW, Cortical integration of vestibular and visual cues for navigation, visual Processing, and perception. Annual Review of Neuroscience 2023, 46: 301–320.
  • Campagner D*, Vale R*, Tan YL, Iordanidou P, Pavon AO, Claudi F, Stempel AV, Keshavarzi S, Petersen RS, Margrie TW, and Branco T, A cortico-collicular circuit for orienting to shelter during escape. Nature. 2023, 613(7942):111-119.

Investigating the Role of Thalamo-Cortico-Thalamic Circuits in Spatial Orientation

To successfully navigate the environment, animals must keep track of their heading direction and orientation relative to the surrounding scene. The brain computes spatial orientation by combining self-motion signals with information about the environment’s layout. However, how these distinct types of information reach the brain's navigation system and integrate to perform orientation computations remains unclear.

The proposed project seeks to address these questions by dissecting the organisation and function of neural circuits that connect the anterior thalamus and the retrosplenial cortex (RSC). Both RSC and the anterior thalamus are closely associated with the head direction network and contribute to spatial navigation. The project aims to answer the following questions:

1.            What is the role of anterior thalamic inputs in orientation computations in the RSC?

2.            How do RSC corticothalamic pathways influence orientation computations?

3.            To what extent do these thalamocortical and corticothalamic circuits contribute to spatial orientation abilities?

The project utilises large-scale electrophysiological recording (Neuropixels), circuit manipulation involving optogenetics and chemogenetic tools combined with viral tracing techniques, and sophisticated behavioural paradigms to assess spatial orientation abilities in mice. This research involves close collaboration with software and hardware engineers to assist with research and development solutions.

Sepiedeh Keshavarzi


Relevant References:

  • Keshavarzi S, Bracey EF, Faville RA, Campagner D, Tyson AL, Lenzi SC, Branco T, Margrie TW, Multisensory coding of angular head velocity in the retrosplenial cortex. Neuron 2022, 110(3): 532-543.
  • Keshavarzi S, Velez-Fort M, Margrie TW, Cortical integration of vestibular and visual cues for navigation, visual Processing, and perception. Annual Review of Neuroscience 2023, 46: 301–320.
  • Velez-Fort M*, Bracey EF*, Keshavarzi S*, Rousseau CV, Cossell L, Lenzi S, Strom M, Margrie TW, A circuit for integration of head- and visual-motion signals in layer 6 of mouse primary visual cortex. Neuron 2018, 98(1):179-191.

Unravelling Cortical Processing of Self-Motion: Insights into Head Motion Coding

Accurate perception of one's own movements is vital for successful navigation and comprehending the world around us. For instance, angular head velocity (AHV) cells, a class of neurons that encode the direction and speed of head movements, are thought to be pivotal for updating an individual's sense of direction during navigation. Recent studies within the retrosplenial cortex (RSC), a core component of the brain's navigation system, have shown that the AHV signal in the cortex predominantly relies on vestibular inputs, with enhanced accuracy through the addition of vision (optic flow). However, the pathways through which vestibular and optic flow information reaches the cortical AHV network, the mechanisms of vestibulo-visual integration in the local cortical circuits, and how they shape AHV computation remain unknown.

This project aims to bridge these knowledge gaps by exploring the influence of various cortical and subcortical inputs on the generation of the AHV signal in the RSC and dissecting the contributions of distinct cortical cell types to this computation. The study will employ in vivo electrophysiological recordings (Neuropixels) and two-photon calcium imaging in head-fixed mice during vestibular and visual stimulation, together with circuit manipulation techniques. Additionally, it will utilise patch-clamp recordings in brain slice preparations with optogenetic stimulation of identified inputs. This research involves close collaboration with software and hardware engineers to assist with research and development solutions.



Andrew Murray


Relevant References:

  • N Verma, M Liao, H Ly, A Loria, KS Campbell, H Bush, PA Kern, PA Jose, H Taegtmeyer, DM Bers, S Despa, LB Goldstein, AJ Murray, F Despa. Diabetic microcirculatory disturbances and pathologic erythropoiesis provoked by deposition of amyloid-forming amylin in red blood cells and capillaries. Kidney International, 97:143-155, 2020.
  • KA O’Brien, BD McNally, AP Sowton, A Murgia, J Armitage, LW Thomas, FN Krause, LA Maddalena, I Francis, S Kavanagh, DP Williams, M Ashcroft, JL Griffin, JJ Lyon, AJ Murray. Enhanced hepatic respiratory capacity and altered lipid metabolism support metabolic homeostasis during short-term hypoxic stress. BMC Biol. 19:265, 2021.
  • N Verma, G Velmurugan, E Winford, H Coburn, D Kotiya, N Leibold, L Radulescu, S Despa, K Chen, L van Eldik, P Nelson, D Wilcock, G Jicha, A Stowe, L Goldstein, D Powel, J Walton, M Navedo, M Nystoriak, AJ Murray, GJ Biessels, C Troakes, H Zetterberg, J Hardy, T Lashley, F Despa. Aβ efflux impairment and inflammation linked to cerebrovascular accumulation of amyloid-forming amylin secreted from pancreas. Comms Bio 6:2, 2023.


Pancreatic Amylin and Cardiac Metabolism in Diabetes: Signal, Saviour or Silent Assassin?

Amylin, also known as islet amyloid polypeptide (IAPP), is a pancreatic hormone co-secreted with insulin following meals, and has canonical roles as a satiety signal and inhibitor of gastric emptying and glucagon secretion. In pre-diabetic insulin resistance, amylin levels rise alongside insulin. Amylin exerts physiological effects through heterodimeric receptors of the calcitonin receptor and receptor activity-modifying proteins (RAMPs). Amylin receptors are highly expressed in cardiomyocytes, yet the role of amylin signaling in the heart remains unknown. Human amylin is also amyloidogenic and forms pancreatic amyloid, a pathological hallmark of type 2 diabetes. This key feature of amylin biology is overlooked in most models of diabetes since rodent amylin has a much-reduced propensity to aggregate. Recent work from our group and collaborators, used a modified rat model which expresses human amylin in pancreatic β-cells (HIP rat). We found that pre-diabetic hypersecretion of amylin results in its deposition in extra-pancreatic tissues, including heart, brain and renal tubules. In kidney, this resulted in hypoxia-inducible factor (HIF) pathway activation and pathological erythropoiesis, suggestive of tissue hypoxia. More recently, we found activation of HIF signaling in association with altered mitochondrial respiration in the heart and liver of HIP rats. It remains unclear whether this represents a novel, signaling role for amylin or a stress-induced pathological consequence of its aggregation. This project will therefore aim to elucidate the role of amylin in cardiac metabolism, using in vitro approaches and a novel inducible, mouse model in which expression of human amylin can be fine-tuned to establish temporal aspects of amylin biology alongside dietary stress.

Kathy Niakan


Relevant References:

  • Gerri C., McCarthy A., Alanis-Lobato G., Demtschenko A., Bruneau A., Loubersac S., Fogarty N.M.E., Hampshire D., Elder K., Snell P., Christie L., David L., Van de Velde H., Fouladi-Nashta A.A. and Niakan K.K. (2020) Initiation of a conserved trophectoderm program in human, cow and mouse embryos. Nature, doi: 10.1038/s41586-020-2759-x
  • Wamaitha S.E., Grybel K.J., Alanis-Lobato G., Gerri C., Ogushi S., Mahadevaiah S.K., Healy L., Lea R.A., Molina-Arcas M., Elder K., Snell P., Christie L., Downward J., Turner J.M.A. and Niakan K.K. (2020) IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche. Nature Communications, 11: 764.
  • Fogarty, N.M.E., McCarthy, A., Snijders, K.E., Powell, B.E., Kubikova, N., Blakeley, P., Lea, R., Elder, K., Wamaitha, S.E., Kim, D., Maciulyte, V., Kleinjung, J., Kim, J.-S., Wells, D., Vallier, L., Bertero, A., Turner, J.M.A. and Niakan K.K. (2017) Genome editing reveals a role for OCT4 in human embryogenesis. Nature, 550(7674): 67-73.


Investigating the function of transcription factors in the establishment or maintenance of the human embryonic epiblast

The goal of the Niakan Laboratory is to understand the molecular mechanisms that control early human development. The mechanisms that regulate early cell fate decisions in human development remain poorly understood, despite their fundamental biological importance and wide-reaching clinical implications.

The PhD project will investigate when and how human embryonic epiblast cells are established and maintained and understand the molecular mechanisms that distinguish these pluripotent cells from extra-embryonic (placenta and yolk-sac progenitor) cells during embryogenesis. We have recently identified several transcription factors that are highly expressed in epiblast cells of the developing human embryo, which we hypothesize are required for the development of these pluripotent cells. We seek to understand the function requirement of these factors using a range of methods including cutting-edge single cell, imaging and genome editing techniques.

The knowledge gained from this project will provide fundamental insights into human biology and facilitate the development of conditions for the further refinement of implantation models and the establishment of novel human stem cells and stem cell-based models of development.

Research techniques used in the laboratory include: molecular biology, advanced microscopy and image quantification, live embryo imaging, human and mouse preimplantation embryo culture and micromanipulation, proteomics, genome modification (i.e. CRISPR-Cas9), TRIM-Away protein depletion,  genome-wide techniques (i.e. single-cell multi-omics combining RNA-seq, DNA-seq and methylomics analysis), generation of human stem cell-based models of development and human trophoblast, embryonic and induced pluripotent stem cell derivation.

Ole Paulsen


Relevant References:

  • Brzosko Z, Mierau S and Paulsen O (2019) Neuromodulation of spike timing-dependent plasticity: Past, present, and future. Neuron 103: 563-581. DOI:
  • Fuchsberger T, Jarzebowski P, Clopath C, Brzosko Z, Wang H, Paulsen O (2022) Reactivation of hippocampal neurons enables associative plasticity of temporally discontiguous inputs. eLife. DOI:
  • Jarzebowski P, Hay YA, Grewe BF, Paulsen O (2022) Different encoding of reward location in dorsal and intermediate hippocampus. Curr Biol 32: 834–841. DOI:

Spatial memory and state-dependent synaptic plasticity in the mouse hippocampus

Synaptic plasticity is a leading cellular model to explain behavioural learning and memory. However, the relationship between the fast timescale of induction of plasticity and the much slower timescales of behavioural learning is not well understood. There is strong experimental evidence that synaptic plasticity is under control by neuromodulators, including acetylcholine and dopamine, which may alter synaptic learning rules both prospectively and retrospectively (Brzosko et al., 2019). This project would test the idea that the neuromodulatory state of the network at different phases of memory encoding could help explain how memories are bound together at different timescales. To this end, the student would use whole-cell patch-clamp recording in brain slices (Fuchsberger et al., 2022), and multi electrode recording, calcium imaging and optogenetics in behaving animals (Jarzebowski et al., 2022), to understand hippocampal encoding of reward-location in a reward-based spatial memory task. 

Interested students are encouraged to contact the supervisor for more detailed discussion of potential PhD projects.

Dr. Jasper Poort


Relevant References:

  • Poort, J., Wilmes, K., Chadwick, A., Blot, A., Sahani, M. Clopath, C., Mrsic-Flogel, T., Hofer, S., Khan, A., (2022). Learning and attention increase visual response selectivity through distinct mechanisms. Neuron,
  • Khan, A.G, Poort, J., Chadwick, A., Blot, A., Sahani, M., Mrsic-Flogel, T., Hofer, S. (2018). Distinct learning-induced changes in stimulus selectivity and interactions of GABAergic interneuron classes in visual cortex. Nature Neuroscience,
  • Poort, J., Khan, A.G., Pachitariu, M., Nemri, A., Orsolic, I., Krupic, J., Bauza, M., Sahani, M., Keller, G., Mrsic-Flogel, T.D., and Hofer, S.B. (2015). Learning Enhances Sensory and Multiple Non-sensory Representations in Primary Visual Cortex. Neuron



The role of different cell types at low and high levels of the cortical hierarchy in visual learning

Our brain is constantly overloaded with visual information. Learning to selectively process visual features relevant for behaviour is therefore crucial for optimal decision-making and has been linked to activity of GABAergic inhibitory interneuron cell types. Altered inhibition is linked to perceptual and learning impairments and associated with neurodevelopmental disorders including schizophrenia and autism. However, the computational roles in visual learning of neurons in low-level brain areas, specialized in processing specific visual features, and neurons in higher-level brain regions, more closely linked to visual decision-making, are not yet understood.

               The aim of this project is to understand the precise role of different cortical cell types in and projections between low- and high-level visual brain areas, in visual learning. Mice have a similarly hierarchically organized visual cortex and show complex decision-making behaviours. Mouse brain circuits can be measured and manipulated during behaviour in ways not possible in humans.

Our approach is to train head-fixed mice, including pharmacological and genetic mouse models of neurodevelopmental disorders and healthy controls, in visual decision-making tasks. We measure activity at the bottom (primary visual cortex) and top (posterior parietal cortex) of the visual cortical hierarchy in specific cell types using 2-photon imaging and electrophysiology and use optogenetics to activate or inactivate activity of cell types.

The PhD project is associated with a Wellcome Trust funded collaborative programme with a cross-disciplinary international research team to investigate the role of GABAergic inhibition in visual learning in mice and humans at different scales, from local circuits to global brain networks.

Dr. Jasper Poort


Relevant References:

  • Poort, J., Wilmes, K., Chadwick, A., Blot, A., Sahani, M. Clopath, C., Mrsic-Flogel, T., Hofer, S., Khan, A., (2022). Learning and attention increase visual response selectivity through distinct mechanisms. Neuron,
  • Meyer, A.F., O’Keefe, J.,, and Poort, J. (2020). ‘Two Distinct Types of Eye-Head Coupling in Freely Moving Mice’. Current Biology. 
  • Meyer, A.F., Poort, J., O’Keefe, J., Sahani, M., Linden, J.F. (2018) A Head-Mounted Camera System Integrates Detailed Behavioral Monitoring with Multichannel Electrophysiology in Freely Moving Mice’. Neuron

Dissecting perceptual and motor contributions to decision-making using novel computational tools for behavioural assessment and modelling of neural circuits

Mental disorders, including neurodevelopmental disorders, are characterized by complex dysfunctions in learning, attention, and decision-making. However, the contribution of perceptual and motor function to higher cognitive function remains poorly understood.

The first aim of this project is therefore to apply advanced computational methods for detailed characterization of visual and motor function in freely moving mice, including both genetic and pharmacological models of neurodevelopmental disorders, using novel deep learning methods to track eye, head and limb positions of freely behaving mice while they are learning and performing visually-guided decision-making tasks. We hypothesize that coordinated orienting eye and head movements are critical for both accurate learning and decision-making, and that alterations in mouse models explain important aspects of observed impairments. The second aim is to investigate neuronal responses in visual cortex during learning and task performance, followed by automated ex-vivo matching of cells and immunohistological characterization to identify cell types and projection targets of neurons to build computational circuit models of decision-making. We will test the hypothesis that learning-related changes in visual neurons and their interactions with higher-level brain areas are critical for rapid and accurate decision-making.

The PhD project is associated with a Wellcome Trust funded collaborative programme with a cross-disciplinary international research team to investigate the role of GABAergic inhibition in visual learning in mice and humans at different scales, from local circuits to global brain networks.

Eleanor Raffan


Relevant References:


Studying inter-species communication with EEGG in dogs and humans

Little is known regarding the neurobiological mechanisms of inter-species perception and communication. Growing evidence suggests apes may possess the "theory of mind" of other subjects, but whether different species share the same understanding of environmental stimuli and mental states remains controversial. One of the most striking examples of inter-species communication is the dog's domestication.

Human social neuroscience has adopted dual-electroencephalography (EEG) paradigms to study inter-brain synchronisation patterns during human-human interactions making it possible to track how two brains interpret the same speech signals or other environmental stimuli in time and how they influence each other. Dual EEG paradigms were recently adapted to study adult-infant communication.

This project will follow on from a current funded pilot project in which we are modifying existing dual EEG paradigms from adult-infant research to study human-dog interaction. Using portable EEG devices and a multi-camera setting, we will study interbrain synchronisation patterns between dog owners and their pets.

The proposed project is the first attempt to characterise inter-species inter-brain synchronisation patterns. It has the potential to uncover neural markers of communication between phylogenetically different species and provide foundations to develop social neuroscience of group behaviours within and across animal species. The project will benefit from collaboration with Dr Valdas Noreika (QMU) on EEG aspects.


Eleanor Raffan


Relevant References:

Obesity – from veterinary genetics to mechanism and human relevance

Why are some individuals prone to obesity and yet others stay lean in an obesogenic environment? Obesity is highly heritable as are related metabolic traits. We study obesity genetics 'in the round' starting from genetic discovery studies using GWAS and other epidemiological approaches working with 'big data'. Capitalising on my background as a vet, we start with animal genetics – dogs, horses and farm animals are excellent models because selective breeding means they show phenotypes of interest and their genomes are conducive to gene mapping. We follow up genetics with cell studies to understand mechanism, focussing on neuronal development, cell signalling and adipocyte biology, including with transcriptomics. We also study whole body physiology in pet dogs volunteered by their owners.

For this PhD I am happy for projects to be moulded to suit the interests of a student but, broadly, a genetics-focussed project would be most likely to involve performing a genome wide association study (GWAS) for obesity or related traits on existing or prospectively collected data from dogs or production (farm) animal species. Associated loci will be interrogated for genes of interest using a range of bioinformatics tools. Comparative genomics in humans and other animal breeds and species will be used to focus on causative genes and mutations of particular interest.  There may be the opportunity to do some ‘wet lab’ genetics as part of the downstream analysis and follow-on investigations into your data. Similarly, physiological studies of energy expenditure and/or eating behaivour may be possible for suitably qualified students. 

Emma Rawlins


Relevant References:

  • He et al., 2022. “A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates.” Cell 185: 4841-4860,
  • Lim et al., 2023 “Organoid modelling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease.” Cell Stem Cell, 30: 20-37,
  • Sun et al. 2021. “A Functional Genetic Toolbox for Human Tissue-Derived Organoids.” ELife 10 (October).

Determining the gene regulation networks controlling lung fibroblast identity

We, and others, have recently identified three major fibroblast lineages in the human lungs: airway, adventitial and alveolar. We have recently constructed a single cell RNAseq and ATACseq atlas for the developing human lung and predicted the differentiation trajectories (He et al. 2022), many of which differ to those seen in mice. Similar single cell RNAseq datasets exist for the adult human lung in normal and diseased states. We have also established a human foetal lung organoid system and methods for efficiently growing the fibroblast sub-types (Lim et al., 2023). This in vitro system provides an ideal, dynamic model to test hypotheses regarding lineage relationships and gene regulation networks during human lung development.

The aim of the project is to determine, and functionally test, the gene regulation networks controlling human lung fibroblast identity. We will predict the gene regulatory networks from the single cell data. We may also use targeted damID (Southall et al., 2013; Sun et al., 2022) to test some of the network predictions by identifying transcription factor binding sites. We will use fibroblast culture in conjunction with an effective genetic toolbox recently established in our lab for human organoids (Sun et al. 2021) to manipulate gene expression and functionally test the gene regulatory networks. We will also use this knowledge to manipulate gene regulatory networks in adult fibroblast cells, to test whether it could be possible to ameliorate disease states.

Angela Roberts


Relevant References:

  • Roberts, A. Annu. Rev. Psychol. 71, 357–387 (2020); Delgado, M.R. et al. Neuron 59, 829–838 (2008); Ironside, M. et al. JAMA Psychiatry 76, 71-78 (2019).

Intra-prefrontal interactions in emotion regulation

There has been considerable insight into the circuits by which prefrontal cortex provides higher-order control over behaviour through studies of its interactions both cortically and subcortically. These have included prefronto-parietal, prefronto-temporal, prefronto-striatal and prefronto-amygdala interactions. However, functional interactions within the prefrontal cortex are far less studied but of enormous importance for gaining insight into the overall functional organisation of the central executive and its control over cognition and emotion.  Here, we will investigate those interactions, focussing in particular on the interplay between dorsolateral prefrontal cortex, particularly area 46 and area 32 in the medial wall, in respect to the regulation of emotion. Using chemogenetics, we have already established a role for area 46 in the regulation of both threat and reward related behaviours. Here we will test the hypothesis that these emotion regulatory functions of area 46 are instantiated by its bi-directional connectivity with area 32.

Angela Roberts


Relevant References:

  • Arnsten, A.F.T., Joyce, MK.P., Roberts A.C.  (2023)  Neuroscience and Biobehavioral Reviews 145, 105000; Cao, X., Deng, C., Su, X. & Guo, Y. Frontiers in Psychiatry vol. 9 413 (2018); Aupperle, R. L., Melrose, A. J., Francisco, A., Paulus, M. P. & Stein, M. B. Hum. Brain Mapp. 36, 449-462 (2015).

Functional asymmetry in dorsolateral prefrontal cortex

Dorsolateral prefrontal cortex is a target for transcranial magnetic stimulation (TMS) treatment strategies for depression; with the left hemisphere rather than the right hemisphere being the primary target. Despite this bias in treatment strategy, there is limited evidence from functional neuroimaging studies of functional hemispheric asymmetry within dorsolateral prefrontal cortex and thus little explanation for such treatment asymmetry. Recent studies in our lab have identified functional asymmetry following inactivation of area 46, a major subregion of dorsolateral prefrontal cortex. Harnassing chemogenetics and pathway specific interventions this project will determine the extent of the functional asymmetry across the range of cognitive and emotional functions known to be dependent upon area 46 and the implications for overall prefrontal functional organisation.

Alberto Rosello-Diez


Relevant References:

  • (1) A Body Weight Sensor Regulates Prepubertal Growth via the Somatotropic Axis in Male Rats. Jansson J. O. et al. Endocrinology 162 (2021). PMID: 33693673.
  • (2) The imprinted Igf2-Igf2r axis is critical for matching placental microvasculature expansion to fetal growth. Sandovici, I. et al. Dev Cell 57, 63-79 e68 (2022). PMID: 34963058.
  • (3) Diffusible signals, not autonomous mechanisms, determine the main proximodistal limb subdivision. Rosello-Diez A, et al. Science. 2011 May 27; 332(6033):1086-8. PMID: 21617076.

Inter-species chimeras to study the control of organ size and body proportions, including limb-brain and limb-placenta communication.

Body size and proportions vary vastly between species but are very tightly controlled within species, which is critical for efficient locomotion and interaction with the environment. This tight control is only beginning to be understood, with studies suggesting that body weight can be sensed by the brain, impacting the hypothalamus-pituitary growth-hormone production (aka somatotropic) axis (1), and that the placenta adapts to fetal growth demands (2). Our group uses sophisticated approaches to study the intrinsic and extrinsic mechanisms that control body size and proportions, with a focus on the limbs. We have previously shown that the signal environment can alter limb size and pattern(3). Therefore, one powerful approach to study the regulation of organ size is to generate inter-species chimeras, where the organ of interest from a given species develops within the signal environment (i.e., the body) of another species differing in size and/or proportions. In this project, we will generate for the first time chimeric animals in which rat stem cells will give rise to the limb connective tissues in the context of a mouse host that would be limbless otherwise. We will assess whether mechanical loading and other extrinsic signals can modulate the genetically-encoded limb size and proportions. Gene expression and chromatin accessibility will be compared for the donor limb cells in their endogenous vs. chimeric context, to uncover the key molecular events underlying this modulation. In addition, via collaborations, we will study a) the impact that this developmental challenge (limbs with different growth demands) has on placental structure, expression and function; b) whether the potentially different weight-sensing properties of the rat limbs impacts the somatotropic axis.

Alberto Rosello-Diez


Relevant References:

  • (1) Compensatory growth and recovery of tissue cytoarchitecture after transient cartilage-specific cell death in foetal mouse limbs. H’ng CH, Amarasinghe S, Zhang B, Chang H, Powell D, Rosello-Diez A. bioRxiv. 2023 June 20. doi: 10.1101/2023.06.20.545035.
  • (2) Cell-nonautonomous local and systemic responses to cell arrest enable long-bone catch-up growth in developing mice. Rosello-Diez A#, Madisen L, Bastide S, Zeng H, Joyner AL#. PLoS Biol. 2018 Jun 26;16(6):e2005086. doi: 10.1371/journal.pbio.2005086. PMID: 29944650. #Co-corresponding authors.
  • (3) The effect of experimental epiphysiodesis on growth in length of the rabbit's tibia. Hall-Craggs, E. C. J Bone Joint Surg Br 50, 392-400 (1968). PMID: 5651349.

Exploring the sizostat, a thermostat-like mechanism to sense and control limb size during growth and repair

How do organs know how much they must grow to attain and maintain species-specific body proportions? To address this question, our group studies the molecular and cellular mechanisms by which growth perturbations are detected and compensated for. We use transgenic mice and chicken to obtain a holistic view of intra- and inter-organ cell communication during organ development and repair, focussing on the long bones in the limbs (1,2). Bone elongation is driven by a transient cartilage structure that is continuously produced, destroyed and replaced by bone. A hot question in the field is how cartilage progenitor cells (CPs) integrate intrinsic and extrinsic information so that growth is maintained for a certain amount of time and then stops. One powerful approach to study the regulation of organ size is analysing the recovery of a normal growth trajectory after a developmental insult (aka catch-up growth). Of note, when one of the two cartilage ends in a bone is damaged, the other can partially compensate for its absence (3), suggesting that there is a target bone size for age, and that a feedback mechanism informs CPs of bone size. We posit that bone elongation leads to steady increase of a mechanical signal that is transduced into a biochemical one, which in turn affects the activity of CPs. We think that it works like a thermostat for size (sizostat): there is an age-dependent threshold for the mechano-transduced signal, and when this signal approaches the threshold, growth is stalled, and vice versa. We are using a combination of physical manipulation, unbiased genomics and functional genetics in chicken and mouse embryos to unravel these mechanical and biochemical signals. Long-term, this knowledge may allow manipulating individual bone length in livestock and humans

Bénédicte Sanson


Relevant References:

  • Higashi T, Chiba H. 2020 Molecular organization, regulation and function of tricellular junctions. Biochim Biophys Acta Biomembr. doi: 10.1016/j.bbamem.2019.183143. EpPMID: 31812626.
  • Finegan TM, Hervieux N, Nestor-Bergmann A, Fletcher AG, Blanchard GB, Sanson B. 2019 The tricellular vertex-specific adhesion molecule Sidekick facilitates polarised cell intercalation during Drosophila axis extension. PLoS Biology. doi: 10.1371/journal.pbio.3000522. PMID: 31805038
  • Bosveld F, Wang Z, Bellaïche Y. Tricellular junctions: a hot corner of epithelial biology. 2018 Curr Opin Cell Biol. doi: 10.1016/ PMID: 29843079.



Investigating how tricellular junctions act as organisers of epithelial morphogenesis

Epithelial sheets are remarkably dynamic: during embryonic development, cells constantly exchange position when cell sheets grow and change shape, while in adult epithelia, the homeostatic balance between cell renewal and loss also leads to cells rearranging. Cell rearrangements are a challenge for epithelia, as cell-cell junctions need to remodel when cells change position, while at the same time preserve barrier function and mechanical strength to maintain the integrity of the cell sheet. Recently, tricellular junctions, where three cells meet, are emerging as potential organisers of cell-cell junction remodelling during morphogenesis. Specialised components at tricellular junctions appear to influence the tension, length, and behaviour of bicellular junctions during cell rearrangements and modulate selective barrier function, but mechanistic evidence is lacking. This PhD project aims to i) elucidate the composition and organisation of tricellular junctions at the nanoscale and ii) solve the mechanisms by which tricellular junctions control junctional dynamics during cell rearrangements. To do so, we will take advantage of a simplified model epithelium in vivo, in early Drosophila embryos, where only tricellular adherens junctions (tAJs) are present. We will capitalize on our recent discovery of the cell surface molecule Sidekick, which uniquely localises at tAJs in Drosophila epithelia and is required in several tissues for normal cell rearrangements, including during axis extension. We will use Sidekick as a molecular entry point to elucidate tAJs organisation and their role in junctional dynamics during cell rearrangements. This will in turn advance understanding of tricellular junction function in higher organisms and more generally of epithelial cell mechanics.

Milka Sarris


Relevant References:

  • (1) Kolaczkowska, E. & Kubes, P. Nat. Rev. Immunol. 13, 159–175 (2013).
  • (2) Wang, J. et al.. Science 358, 111–116 (2017).
  • (3) Netea, M. G. et al. Nat Rev Immunol 20, 375–388 (2020).

Visualising neutrophil migration during resolution of infection

Bacterial elimination requires rapid recruitment of leukocytes to sites of infection. A key type of cell that infiltrates infection loci is the neutrophil. These cells fight bacteria by phagocytosis, secretion of extracellular antimicrobial compounds and structures (such as ‘neutrophil extracellular traps’). However, their inflammation must also be resolved, to ensure tissue homeostasis and prevent chronic inflammation. Contrary to the initial view that resolution of neutrophil accumulation arises solely from local apoptosis in infected loci, recent evidence suggests a number of recruited neutrophils can also disseminate from these sites. It remains unclear what the mechanisms and functional implications of these migratory patterns are. The aim of the project will be to perform live imaging and tracing of neutrophils in order to discover, i) what are the tissue destinations of experienced neutrophils, ii) what is the lifespan of these cells after infectious challenge, iii) to what extent these cells disseminate via the blood or lymphatic vasculature after bacterial infection ii) to what extent they form interactions with other cells, for example other innate immune cells like macrophages, or hematopoietic progenitor cells, and what are the functional consequences of such interactions in homeostasis or immunity. The project will exploit established state-of-the art live confocal imaging techniques and zebrafish reporter lines allowing the visualisation of neutrophils and other relevant cell types.

Elena Scarpa


Relevant References:


  • Richardson, J. et al. Leader Cells Define Directionality of Trunk, but Not Cranial, Neural Crest Cell Migration. Cell reports 15, 2076–2088 (2016).
  • Alhashem, Z. et al. Notch controls the cell cycle to define leader versus follower identities during collective cell migration. Elife 11, e73550 (2022).
  • Alhashem, Z., Camargo-Sosa, K., Kelsh, R. N. & Linker, C. Trunk Neural Crest Migratory Position and Asymmetric Division Predict Terminal Differentiation. Frontiers Cell Dev Biology 10, 887393 (2022b).



The consequences of a big squeeze.

Cells move through our bodies squeezing into tiny spaces. This can stress them, damaging their DNA or causing errors during cell division, which can promote cancer. We use neural crest cells, which move through narrow spaces in the trunk of Zebrafish embryos, as a model for cell migration under physiological mechanical stress. Trunk neural crest cells (TNCs) move through narrow spaces, squeezing between the neural tube, notochord and somites. These cells will form a chain of single cells, with a larger and faster leader cell at the front of the chain (Richardson et al 2016) and several follower cells. Leader/follower identities are specified by Notch signalling (Alhashem 2022), and cells acquire differential fates depending on their position in the migratory chain (Alhashem 2022b), with leader cells preferentially becoming neurons and followers acquiring glial or pigment cell identity (Alhashem 2022b). Our lab has observed that TNCs experience significant nuclear deformation during their in vivo migration. Recent studies have highlighted that nuclear deformations occurring upon mechanical stress in cultured cells can cause changes in chromatin organization (Nava et al.,  2020) that protect the genome against damage but also cause  functional changes in gene expression and cellular behaviours (Jain and Vogel, 2018). However still little is known about how dynamic changes in nucleus shape affect genome organisation, gene expression and cell fate decisions in vivo in an intact organism. In this proposal we will ask how nuclear deformation experienced by different subpopulations of neural crest cells during their physiological developmental migration affect their subnuclear organization, gene expression and fate decisions in vivo.

Elena Scarpa


Relevant References:

  • Richardson, J. et al. Leader Cells Define Directionality of Trunk, but Not Cranial, Neural Crest Cell Migration. Cell reports 15, 2076–2088 (2016).

  • Taubenberger, A. V., Baum, B. & Matthews, H. K. The Mechanics of Mitotic Cell Rounding. Front. Cell Dev. Biol. 8, 687 (2020).


To bleb or not to bleb? Investigating the dynamics of mitosis under mechanical stress in vivo

Cells dividing or migrating in tissues must push against other cells or squeeze through tight spaces. In vitro studies on single cells have shown that physical compression causes mechanical stress, leading to mitotic errors. However, whether compressive forces also cause errors during cell division in vivo has not yet been investigated. Using translucent, that enable visualisation of migrating cells in an intact animal,  we will investigate a population of well characterized embryonic multipotent stem cells, neural crest cells. In the trunk of the Zebrafish embryo, trunk neural crest cells (TNCs) move through narrow spaces squeezing between the neural tube, notochord and somites.  We have observed that TNCs can divide half-way through their migration while confined in the interstitial spaces. These cells display  cortical blebbing at metaphase, a phenotype caused by mechanical compression in vitro. Using  fluorocarbon oil microdroplets to measure mechanical stress in the Zebrafish embryo we observe strongly suggest that TNCs experience significant compressive stress during their developmental migration. To assess whether mitotic errors of TNC correlate with physical confinement, we will quantify timings and location of these aberrant mitosis events and measure the dimensions of these cells. To understand the dynamics of mitotic metaphase blebbing in dividing TNC, we will image and quantify myosin-GFP and utrophin-mCherry fluorescence. To determine if compression from the embryonic microenvironment alters mitotic fidelity in vivo, we will make use of genetic and mechanical manipulations to perturb forces exerted by the surrounding tissues on the dividing TNC in vivo.

Keita Tamura


Relevant References:

  • Tamura K, Takeda M, Setsuie R, Tsubota T, Hirabayashi T, Miyamoto K, Miyashita Y. Conversion of object identity to object-general semantic value in the primate temporal cortex. Science 357: 687-92 (2017a). DOI: 10.1126/science.aan4800.
  • Tamura K, Ohashi Y, Tsubota T, Takeuchi D, Hirabayashi T, Yaguchi M, Matsuyama M, Sekine T, Miyashita Y. A glass-coated tungsten microelectrode enclosing optical fibers for optogenetic exploration in primate deep brain structures. J Neurosci Methods 211: 49-57 (2012). DOI: 10.1016/j.jneumeth.2012.08.004.
  • Esmaeili V=1,†, Tamura K=1,† (=1, equal contribution; †, corresponding), Muscinelli SP, Boscaglia M, Lee AB, Modirshanechi A, Oryshchuk A, Foustoukos G, Liu Y, Crochet S, Gerstner W, Petersen CCH†. Rapid suppression and sustained activation of distinct cortical regions for a delayed sensory-triggered motor response. Neuron 109: 2183-2201.e9 (2021). DOI: 10.1016/j.neuron.2021.05.005.


Dissecting visual cognition into distinct neuronal circuits for perception and memory

Whenever we see an object, we not only perceive its physical appearance but also experience a non-physical impression like ‘familiarity’ such that distinguishes a friend from strangers, a vegetable from inedible plants, etc. On the other hand, we can ‘see’ the physical details of familiar objects more easily than those of novel objects. Thus, perception and memory are closely interrelated in visual cognition, and we will encounter a substantial difficulty if this ability is impaired in such situations as dementia and dyslexia. Dissociable neuronal circuits for perception and memory would be a seed for innovative stimulation therapies to guide visual cognition, but such circuits remain totally unknown. We have previously demonstrated using optogenetic techniques in macaque monkeys that activation of a particular brain area in the medial temporal lobe (perirhinal cortex) causes monkeys to judge any presented visual objects as ‘seen before i.e., familiar,’ even when it was novel (Tamura et al., Science 2017). This result indicates that perirhinal cortex outputs a cognitive signal that steers memory judgements. In this project, the student will investigate common marmosets and rodents to identify projection pathways from the perirhinal cortex, and distinguish which pathway shifts the memory judgements, and which pathway modifies the perception of objects. Through the project, the student will develop and acquire various cutting-edge techniques including psychophysics, high-density electrophysiology, and optical measurements and manipulation, and develop themselves into an innovative systems neuroscientist who can lead the future innovation towards the circuit-based brain healthcare, along with the rapidly expanding global trend towards the primate neuroscience.

Fengzhu Xiong


Relevant References:

  • Kunz D, Wang A, Chan CU, Pritchard RH, Wang W, Gallo F, Bradshaw CR, Terenzani E, Muller KH, Huang YYS, Xiong F, (2023) “Downregulation of Extraembryonic Tension Controls Body Axis Formation in Avian Embryos”, Nature Communications
  • Chan CU*, Xiong F*, Michaut A, Vidigueira JMN, Pourquie O, and Mahadevan L., (2023) “Direct Force Measurement and Loading on Developing Tissues in Intact Avian Embryos”, (*equal contribution), Development
  • Moon LD, Xiong F, (2022) “Mechanics of Neural Tube Morphogenesis”, Seminars in Cell and Developmental Biology


How do the brain and the spinal cord get their shape?

The neural tube is the developmental precursor of the vertebrate central nervous system, including the brain and the spinal cord. It begins as a flat epithelial tissue called the neural plate, which then drastically deforms by bilaterally folding towards the midline. As the folds move to meet dorsally, they fuse to close the neural tube with an internal lumen. Under the pressure of the lumen, the brain and spinal cord expand differentially to lay down the initial shapes of these organs. The folding and expansion processes happen in conjunction with the morphogenesis of neighboring tissues. The failure of this folding, closure or inflation process underlies a variety of neural tube defects (NTDs) in human development. From a physics perspective, tissue shape change must require driving forces generated by the neural cells and/or the neighboring tissues. In addition, the mechanical properties of the tissue may also be regulated to ensure correct tissue deformation progress under the driving forces. Recently, our team discovered that the brain roof plates are a lot more deformable than the spinal cord counterpart, which underlies their drastically different expansion. In this project we will identify the mechanisms by combining interdisciplinary approaches inlcuding imaging of the neural tube morphogenes; using soft gels, magnetic droplets, cantilevers and pressure controllers to dissect the contributions from tissue intrinsic (e.g., apical constrictions, intercalations) and extrinsic (e.g., lumen, paraxial mesoderm, endoderm) forces; and molecular and genetic methods to test relevant factors (e.g., cell polarity, adhesion, extracellular matrix, folate pathway) in regulating cell behaviours and tissue biomechanics.

Fengzhu Xiong


Relevant References:


  • Chan CU*, Xiong F*, Michaut A, Vidigueira JMN, Pourquie O, and Mahadevan L., (2023) “Direct Force Measurement and Loading on Developing Tissues in Intact Avian Embryos”, (*equal contribution), Development
  • Xiong F, Ma W, Benazeraf B, Mahadevan L, Pourquie O, (2020) "Mechanical Coupling Coordinates the Co-elongation of Axial and Paraxial Tissues in Avian Embryos", Developmental Cell
  • Mongera A*, Michaut A*, Guillot G, Xiong F, Pourquie O, (2019). “Mechanics of Anteroposterior Axis Formation in Vertebrates”, Annual Reviews of Cell and Developmental Biology

How does the body axis stay straight during elongation?

Bilateral symmetry is a fundamental feature of the external body plan of >99% of existing animal species. The formation and breaking of this symmetry are among the most important questions in developmental biology and attracts wide general interest. The backbone of the symmetric feature is a straight head to tail (or antero-posterior) body axis that grows in length during development. In vertebrates, this straight spine is first laid out during and post gastrulation in early embryonic development. At these stages, a progenitor domain (node/tailbud in amniotes) progressively produces body axis tissues including the notochord, neural tube and paraxial mesoderm in an anterior to posterior manner. This process and the subsequent growth and morphogenesis of these tissues extend the animal body by several folds in a short time. How the body axis stays straight during this drastic elongation is unclear, particularly considering that the axis is also thinning significantly at the same time, sharply reducing its bending stiffness. This question also has implications on body axis related developmental abnormalities, such as scoliosis and neural tube defects. In this project we take an interdisciplinary approach to test the hypothesis that an increasing stress against bending produced by the paraxial mesoderm prevents axis bending. We hypothesize that the paraxial mesoderm functions as active guard rails of the elongating midline tissues through inter-tissue forces. We will use the newly developed Tissue Force Microscopy (TiFM) and image analysis to test the variabilities of symmetry and tissue responses to curvature. These new results combining quantitative force dynamics and molecular perturbations (e.g., FGF signaling) will lead to a new physical model of axis symmetry.