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Department of Physiology, Development and Neuroscience




N. Sumru Bayin

Relevant References:

  • Bayin N.S+., Mizrak M., Stephen N.D., Lao Z., Sims P.A., Joyner A.L+. (2021) Injury induced ASCL1 expression orchestrates a transitory cell state required for repair of the neonatal cerebellum. Science Advances, 7, eabj1598, +co-corresponding author
  • Bayin N.S., Wojcinski A., Mourton A., Saito H., Suzuki N., Joyner A.L. (2018) Age-dependent dormant resident progenitors are stimulated by injury to regenerate Purkinje neurons. eLife 2018;7:e39879. PMID:30091706
  • Wojcinski A., Lawton A., Bayin N.S., Lao Z. and Joyner A.L. (2017) Cerebellar Granule Cell Replenishment Post-Injury by Adaptive Reprogramming of Nestin+ Progenitors, Nature Neuroscience Oct;20(10):1361-1370 PMID:28805814

Age-dependent regenerative mechanisms in the brain


The cerebellum is important for motor behavior and cognitive functions. Its protracted development makes the neonatal cerebellum susceptible to injury around birth. The neonatal CB can recover from the loss of at least two types of neurons, making it a powerful model system to uncover regenerative responses and study progenitor plasticity. When the granule cell progenitors are ablated, a subpopulation of the ventricular zone-derived nestin-expressing progenitors (NEPs) that normally generate glia undergoes adaptive reprograming and replenishes some of the lost granule cell progenitors. Using single cell RNA-seq, fate mapping and loss of function studies, we uncovered molecularly diverse NEP subtypes and identified a transitory cellular state that is required for the adaptive reprograming. Importantly, the regenerative potential of the neonatal cerebellum dramatically decreases once development ends, despite the presence of NEP-like cells in the adult cerebellum. NEP-like cells are able to respond to injury by increasing their numbers but only some astrocytes are produced. This project involves performing comparative genomic analyses of neonatal NEPs and adult NEP-like cells in order to identify signaling pathways and gene regulatory networks that enable regeneration in neonates and others that inhibit repair in the adult. The goal is to identify and test signals that can be activated in the adult CB upon injury to facilitate regeneration.

Riccardo Beltramo

Relevant References:

  • Branco T. & Redgrave P., The Neural Basis of Escape Behavior in Vertebrates. Annual Review of Neuroscience, 2020, 43:417-439.
  • Beltramo R. & Scanziani M., A collicular visual cortex: Neocortical space for an ancient midbrain visual structure. Science, 2019 Jan 4;363(6422):64-69
  • 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.

Aversive learning across the visual and navigational systems

When confronted with potential dangers, animals display adaptive fear-induced reactions that promote survival(1). Some of these behaviours are innate, such as escaping upon detection of distant predators; others are learned, such as freezing in response to stimuli previously associated with aversive outcomes. Environmental cues are often ambiguous and do not always univocally signal a clear danger. Therefore, correctly identifying and discriminating potentially hazardous stimuli is crucial for the survival of organisms.

This project aims to determine how aversive stimuli are perceived and processed across the visual and navigational systems to generate avoidance behaviours. 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 centre 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. Through chronic calcium imaging, large-scale electrophysiology, optogenetics and innovative behavioural tasks, we will dissect the neural circuits that assign emotional value to sensory information, and the network that weights potential threats against previously learned associations. The project will involve close collaborations with the Engineering Department and computational neuroscientists.

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 (LaChance et al., 2019), is perfectly placed at the interface between the cortical and collicular visual streams and the hippocampal formation.

Working in close collaboration with the Engineering Department and computational neuroscientists, we will combine electrophysiological, imaging, and opto/chemogenetic approaches to study the interactions between parallel visual pathways in sensory processing and spatial navigation.

Clare Buckley

Relevant References:

  • Liang X, Weberling A, Hii C-Y, Zernicka-Goetz M, Buckley CE (2022) E-cadherin mediated Apical Membrane Initiation Site localisation. EMBO J (in press)
  • Symonds ACE1, Buckley CE1†, Williams C, and Clarke JDW†. Coordinated assembly and release of adhesions builds apical junctional belts during de novo polarisation of an epithelial tube. Development 2020 147:dev191494 †corresponding authors 1Equal contribution
  • Buckley CE, Moore RE, Reade A, Goldberg AR, Weiner OD and Clarke JDW. Reversible Optogenetic Control of Subcellular Protein Localization in a Live Vertebrate Embryo. Dev Cell (2016) Jan 11:36(1): 117-26 DOI: 10.1016/j.devcel.2015.12.011

Building and breaking the Neural Tube

My group’s primary goal is to uncover how apical-basal polarity level sculpts the development of the CNS. We investigate how symmetry is broken at a single cell level during secondary neurulation, which occurs via de novo apical-basal polarisation within the centre of an initially solid tissue (How do epithelial tubes polarise?). We are also interested in how apical-basal polarity, signalling and morphogenesis interrelate during secondary neural tube opening and later cell differentiation (how do epithelial tubes open?). These questions have relevance both for understanding polarity-associated diseases and for directing organ bioengineering approaches.

We use high resolution imaging, CRISPR and optogenetics approaches in vivo, within the developing zebrafish neural tube. This enables us to image the behaviour of cells before, during and after a precise manipulation in polarity or signalling deep within the brain of a vertebrate organism. In addition, we use in vitro multicellular mouse embryonic stem cell (mESC) culture to compare the fundamental mechanisms of de novo polarisation in a non-neural epithelial context. We aim to understand how single cells respond to and affect their neighbours to build whole organs and to directly test what role apical-basal polarity dysregulation plays in the initiation of disease. Through this work, we hope to unravel parallel mechanisms of epithelial tube development and disease.

We are currently particularly interested in understanding the links between cell-cell adhesion, actomyosin contractility and cellular mechanics in relation to polarity initiation and morphogenesis of epithelial tubes. We are also interested in determining the effects of aberrant PI3K signalling on cellular behaviour and epithelial tube morphogenesis.

Angeleen Fleming

Relevant References:

  • Autophagy in Neuronal Development and Plasticity. Fleming A, Rubinsztein DC. Trends Neurosci. 2020 Oct;43(10):767-779. doi: 10.1016/j.tins.2020.07.003.
  • Unexpected Phenotype Reversion and Survival in a Zebrafish Model of Multiple Sulfatase Deficiency. Fleming A, Xuan LZ, Sanchez-Elexpuru G, Williams SV, Windell D, Gelb MH, Herbst ZM, Schlotawa L, Rubinsztein DC. Front Cell Dev Biol. 2022 Jun 2;10:843079. doi: 10.3389/fcell.2022.843079.

The role of protein clearance pathways in childhood neurodegenerative disorders

Childhood neurodegenerative disorders are characterised by both structural and functional changes in the CNS that typically result in progressive neurological dysfunction and often in early death.  Although there are over 600 of these rare diseases, a large number are caused by genetic mutations in protein clearance pathways or lysosomal digestive enzymes.  Our lab uses zebrafish models to study protein clearance pathways in health and disease.

Knockout studies of genes in the autophagy pathway have shown that this can lead to defects in neurogenesis and neuronal plasticity.  However, there are conflicting results from both experimental studies and from clinical data on patients with recessive mutations in autophagy genes.  Hence, it is unclear whether neurological defects arise as a result of deficits in protein/organelle clearance (autophagy) or from non-canonical roles of the encoded protein.  To date, most studies have been performed in vitro or from the post-mortem analysis of knockout mice.  Zebrafish offer a unique opportunity to study these processes in vivo.  We have developed a range of knockout, hypomorph and reporter lines, as well as models where we can up- and down-regulate key autophagy genes with tissue-specific drivers and with temporal control.  The project will use a range of imaging techniques as well as biochemical and genetic analysis to investigate the role of autophagy in neurogenesis and to determine whether autophagy or the non-canonical roles of these proteins accounts for the neuronal defects associated with childhood neurodegeneration.

Angeleen Fleming

Relevant References:

  • Seeing is believing: methods to monitor vertebrate autophagy in vivo. Lopez A, Fleming A, Rubinsztein DC. Open Biol. 2018 Oct 24;8(10):180106. doi: 10.1098/rsob.180106.

The role of autophagy in maintaining neuronal homeostasis

Autophagy is an intracellular clearance pathway that delivers cytoplasmic contents to the lysosome for degradation. It plays a critical role in maintaining protein homeostasis and providing nutrients under conditions where the cell is starved. It also helps to remove damaged organelles and misfolded or aggregated proteins.  Using the zebrafish, Danio rerio as a model system, this project seeks to expand our understanding of the role of autophagy in maintaining neuronal homeostasis.

Work in the Fleming laboratory focuses on the roles of toxic aggregate-prone proteins in the pathogenesis of neurodegenerative diseases and the clearance of aggregated proteins via autophagy.  From in vitro studies, we have a good understanding of the intracellular events that occur during autophagosome formation and of the signaling pathways that control this process.  However, little work has been done to determine the rate and regulation of autophagy in different tissue and cell types in vivo, for example, how this contributes to degeneration in neurons.  The ability to quantify and manipulate autophagic flux in vivo is an essential part of our studies and to this end, we have developed a transgenic zebrafish line in which we can observe autophagic flux in vivo.  Zebrafish are an ideal model for these investigations since larvae are small and transparent hence investigations can be performed in real time, in vivo using non-invasive confocal microscopy.  In addition, we have developed a range of genetic tools to temporally control and manipulate autophagy in different tissues.  The aim of this proposal is to investigate how manipulation (up and down-regulation) of autophagic flux affects pathology in a range of zebrafish neurodegenerative disease models using these newly developed tools.

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] Mandairon et al., ‘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.
  • [3] Erskine et al., ‘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.

Activity-dependent neuronal plasticity in the mouse olfactory bulb

In all living organisms the ability to sense and react to the environment is fundamental to survival. Animals must constantly sample the ever-changing environment via their sensory organs, and compute the resulting information to generate an appropriate behavioural output. How is this behavioural flexibility achieved, and which are the underlying brain computations? Neurons can modify themselves in response to environmental changes in a process called neuronal plasticity, which is thought to be the basis of adaptation and learning. In the lab we plan to address this important question by studying how mice adapt to olfactory stimulation and learn new olfactory tasks, and how this is sustained by flexible computations in the part of their brains that processes odours.

In this project we will perturb the olfactory landscape to trigger adaptive responses by subjecting the mice to either sensory deprivation (=nose blockage, like a mild cold)[1] or olfactory enrichment (=overexposure to odours, like when humans enter a perfume shop)[2]. We will take advantage of the mouse genetic toolbox to label neurons that respond to specific odours, and we will use immunohistochemistry and patch-clamp electrophysiology, to investigate how neurons in the olfactory bulb plastically change their synaptic connections, shape and intrinsic excitability, after deprivation or enrichment of different durations. Using automated behavioural testing [3], we will then probe the mice’s ability to sense and discriminate odours to test if and how adaptive plasticity influences learning.

Elisa Galliano

Relevant References:

  • [4] Lledo, et al., ‘Adult neurogenesis and functional plasticity in neuronal circuits’, Nat. Rev. Neurosci., vol. 7, no. 3, pp. 179–193, Mar. 2006, doi: 10.1038/nrn1867.
  • [5] Galliano et al., ‘Brief sensory deprivation triggers cell type-specific structural and functional plasticity in olfactory bulb neurons’, bioRxiv, p. 2020.05.10.086926, Jan. 2020, doi: 10.1101/2020.05.10.086926.
  • [6] Galliano et al., ‘Embryonic and postnatal neurogenesis produce functionally distinct subclasses of dopaminergic neuron’, eLife, vol. 7, Apr. 2018, doi: 10.7554/eLife.32373.

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

A crucial aspect of brain development and function is that neurons can structurally and functionally modify themselves and the strength of their connections with other neurons in response to certain stimulus patterns. These changes pertain to three main classes of plasticity: synaptic intrinsic, and structural. In the olfactory circuit, structural plasticity is taken to an extreme: not only neurons can change size and shape of neuronal sub compartments, but quite a few neuronal subpopulations can regenerate throughout life, adding and removing entire elements of the circuit [4]. Among these regenerating cells are olfactory sensory neurons in the nasal epithelium, dopaminergic cells and granule cells in the olfactory bulb, and interneurons in the olfactory cortex. While adult-born neurons have long been believed to be a like-for-like replacement of embryonic-born ones, recent work focusing on bulbar dopaminergic neurons has challenged this view. Indeed, embryonic and postnatally-born dopaminergic cells differ in morphology, function and activity-dependent plasticity [5], [6]. Using transgenic mouse models, immunohistochemistry, electrophysiology, and behavioural testing, this project wants to expand on these findings. Specifically it wishes to investigate (a) whether these differences based on birth date seen in the dopaminergic population can be generalized to the other regenerating populations in the olfactory system, and (b) what behavioural roles do embryonic and regenerating cells play in olfactory processing.

Dino Giussani

Relevant References:

  • Reynolds RM, Allan KM, Raja EA, Bhattacharya S, McNeill G, Hannaford PC, Sarwar N, Lee AJ, Bhattacharya S, Norman JE. Maternal obesity during pregnancy and premature mortality from cardiovascular event in adult offspring: follow-up of 1 323 275 person years. BMJ 347: f4539, 2013
  • 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. 6(34):eabb1929, 2020
  • 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 76(4):1195-1207, 2020

Maternal Obesity: Translatable Programmed Cardiovascular Dysfunction in Offspring

Maternal obesity during pregnancy is an increasingly alarming health care issue with short and long-term detrimental consequences for both mother and child. In her 2019 annual report, then as Chief Medical Officer, Dame Sally Davies highlighted that over half of women in the UK are over-weight or obese 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 physical and mental wellbeing of mothers and children.

The current 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 risk of heart disease in the offspring and provide invaluable information on what interventions during pregnancy can prevent this effect.  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 translational animal model to address these questions and make the research more relevant to the human clinical situation.

We will adopt an integrative approach, combining experiments of in vivo cardiovascular physiology (echocardiography and chronically instrumented preparations), with those at the isolated organ (Langendorff and myography), cellular (stereology and histology) and molecular (PCR, Western blot) levels. You will join an experienced team studying the physiology of the mother, the fetus and the adult offspring.

Dino Giussani

Relevant References:

  • Badran M, Yassin BA, Lin DTS, Kobor MS, Ayas N, Laher I.  Gestational intermittent hypoxia induces endothelial dysfunction, reduces perivascular adiponectin and causes epigenetic changes in adult male offspring. J Physiol. 597(22):5349-5364, 2019
  • Giussani DA. Breath of Life: Heart Disease Link to Developmental Hypoxia. Circulation 144(17):1429-1443, 2021
  • Skeffington KL, Beck C, Itani N, Niu Y, Shaw CJ, Giussani DA. Hypertension Programmed in Adult Hens by Isolated Effects of Developmental Hypoxia In Ovo. Hypertension 76(2):533-544, 2020

Obstructive Sleep Apnoea During Pregnancy and Early Origins of Heart Disease

Obstructive sleep apnoea (OSA) is characterized by episodes of intermittent hypoxia (IH), which promote oxidative stress and increase the risk of heart disease in affected patients. In turn, human pregnancy is associated with OSA, which is aggravated by obesity, the rates of which in the UK, including in women of reproductive age, are reaching epidemic proportions.  However, the effects of maternal IH due to OSA during pregnancy on the cardiovascular health of the offspring are largely unknown.  A recent study reported that IH in a mouse model of OSA during pregnancy programmed cardiovascular dysfunction in the adult offspring.  However, mechanisms remain uncertain because the partial contributions of IH on the mother, placenta and fetus are difficult to disentangle.  This project will study the effects of IH in the chicken embryo, an established model system that permits isolation of the direct effects of developmental challenges on the cardiovascular system of the offspring, independent of effects on the mother and/or the placenta.

Fertilised eggs will be exposed to normoxia or IH (Oxycycler, BioSpherix). At day 19 of the 21-day incubation period, the heart will be isolated and mounted onto a Langendorff preparation to determine effects on cardiac function during basal conditions and in response to a period of ischaemia-reperfusion (IR).  Cardiac IR injury will be determined by infarct size.  In another cohort of embryos, hearts will be frozen or fixed of molecular and histological analysis, respectively.  Embryos will be genotyped for sex to permit sex-dependent analyses.  Another group of fertilised eggs will be allowed to hatch, and birds will be raised to adulthood (6 months).  At 6 months, experiments performed in the embryo will be repeated in the adult. 

David Keays (Co-supervisor Ewa Paluch)

Relevant References:

  • Dogterom M, Koenderink GH. Actin-microtubule crosstalk in cell biology. Nat Rev Mol Cell Biol. 2019 Jan;20(1):38-54
  • Bodor DL, Pönisch W, Endres RG, Paluch EK.Of Cell Shapes and Motion: The Physical Basis of Animal Cell Migration.Dev Cell. 2020 Mar 9;52(5):550-562.
  • Keays DA, Tian G, Poirier K, Huang GJ, Siebold C, Cleak J, Oliver PL, Fray M, Harvey RJ, Molnár Z, Piñon MC, Dear N, Valdar W, Brown SD, Davies KE, Rawlins JN, Cowan NJ, Nolan P, Chelly J, Flint J.Mutations in alpha-tubulin cause abnormal neuronal migration in mice and lissencephaly in humans.Cell. 2007 Jan 12;128(1):45-57.

Tubulin Mutations and Neuronal Cell Shape

Following the birth of neurons in the proliferative ventricular zones, they embark on a cellular journey that requires dramatic changes in cell shape. As the migrate out of the subventricular zone they undergo a multipolar to bipolar transition, extending their leading process into the emerging cortical plate. The microtubule organising center provides the force necessary to translate the nucleus, as the cell migrates towards the surface of the brain squeezing past neurons in deeper layers of the cortex. On reaching their final destination, neurons begin a dramatic change in cellular morphology as their leading process extends to far flung anatomical locations, coupled with extensive dendrite formation and synaptogenesis. These changes in cell shape are dependent on functional crosstalk between the microtubule and actin cytoskeleton, which interact with each other through specialised proteins. Mutations in the tubulin gene family are known to cause a spectrum of neurodevelopmental diseases, collectively referred to as the tubulinopathies. Little is known, however, of the effect of these pathogenic variants on cell shape or on the actin cytoskeleton. Using iPSCs from patients with mutations in TUBA1A, TUBB2B and TUBB2A, this project will exploit advances in 2D and 3D organoid culture and advanced light imaging to assess the effect of tubulin mutations on cell shape and the dynamics of microtubule-actin interaction.

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) A conserved molecular cascade initiates trophectoderm differentiation in human, bovine and mouse embryos prior to blastocyst formation. Nature, 587: 443-447.
  • 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.
  • Blakeley P., Fogarty N.M., Del Valle I., Wamaitha S.E., Hu T.X., Elder K., Snell P., Christie L., Robson P. and Niakan K.K. (2015) Defining the three cell lineages of the human blastocyst by single-cell RNA-seq. Development, 142(20): 3151-3165.

Understanding the molecular mechanisms that control early human epiblast development

The goal of our 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. 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 and components of key signalling pathways 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 together with mathematical modelling and advanced statistical analysis. 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 integrated stem cell-based models of human development. Altogether, we seek to make significant advances in our understanding of the molecular programs that shape early human embryogenesis. The methods we develop will be applicable to other challenging to study primary human cellular contexts or in species that are historically challenging to study to understand evolutionarily conserved and divergent mechanisms.

Kathy Niakan

Relevant References:

  • Ross and Boroviak. (2020) Origin and function of the yolk sac in primate embryogenesis, Nature Communications,
  • 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) A conserved molecular cascade initiates trophectoderm differentiation in human, bovine and mouse embryos prior to blastocyst formation. Nature, 587: 443-447.
  • Bergmann S, Penfold CA, Slatery E, Siriwardena D, Drummer C, Clark S, et al. Spatial profiling of early primate gastrulation in utero. Nature. 2022;

Understanding the molecular mechanisms that control human yolk sac progenitor cell development

We seek to understand the molecular mechanisms that regulate early human development. Very little is known about the mechanisms that regulate the initiation and maintenance of extraembryonic lineages (such as the hypoblast and placental trophectoderm) despite their importance in early nutrient exchange and patterning of the epiblast-derived embryo proper.  The hypoblast lineage plays a pivotal role for axis formation, gastrulation and yolk sac formation in human embryogenesis. Moreover, the extraembryonic lineages that are derived from the hypoblast have been suggested to differ in their origin in human and non-human primate embryo development compared to the mouse. This PhD project will investigate the functional requirement of transcription factors in stem cell models of the hypoblast including 2D stem cell lines and 3D integrated stem cell models of embryos. Initially, candidate transcription factors will be screened in 2D cell lines using a genome editing approach which has been optimised in the Niakan and Boroviak labs. We have expertise in CRISPR/Cas9 genome editing, advanced light microscopy, single-cell spatial transcriptome profiling, multi-omics analysis, integrated stem cell models of embryos (blastoids), and human embryo culture methods. The PhD student will have access to stem cell lines from human, marmoset, rat and mouse for cross-species comparisons and embryos from these species to determine the phenotype of a selected factor in vivo. The student will also have an opportunity to acquire bioinformatics analysis skills and will work closely with statisticians and computational biologists to refine our methods to predict transcription factor interactions in the early embryo.

Ole Paulsen

Relevant References:

  • 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:
  • Brzosko Z, Mierau S and Paulsen O (2019) Neuromodulation of spike timing-dependent plasticity: Past, present, and future. Neuron 103: 563-581.

State-dependent synaptic plasticity in the mouse hippocampus

We are interested in the relations between network oscillations and synaptic plasticity in hippocampus-dependent memory. Using a combination of whole-cell recording, multi electrode recording, calcium imaging and optogenetics, both in vitro and in vivo, we aim to understand the rules that govern memory formation, consolidation and retrieval. This project would investigate synaptic plasticity rules in different neuromodulatory states, first in mouse hippocampal slices and subsequently in a reward-location memory task. 

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

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 GABAergic inhibitory interneurons in visual learning

The brain is continuously bombarded with visual input but has limited processing capacity. Learning to selectively process visual features relevant for behaviour is therefore crucial for optimal decision-making and thought to rely on activity of GABAergic inhibitory interneurons. Altered inhibition is linked to perceptual and learning impairments and associated with neurodevelopmental disorders including schizophrenia and autism.

The aim of this project is to understand the precise role of different types of GABAergic inhibitory interneurons in visual learning. Mice have a similarly 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 in visual cortex in specific cell types using 2-photon imaging and electrophysiology and use optogenetics to activate or inactivate activity of specific interneuron cell types. We will also apply two new innovative methods to optically measure the inhibitory neurotransmitter GABA (developed in the Looger lab, UCSD) and to locally pharmacologically manipulate GABA levels in the brain (Malliaras and Proctor labs, Dept of Engineering, Cambridge) during visual learning.

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 mice and humans at different scales, from local circuits to global brain networks.

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 variables to higher cognitive function remains poorly understood, although it is becoming increasingly clear that altered perception and motor behaviours profoundly alter cognitive performance.

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 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 during learning 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.


Eleanor Raffan

Relevant References:

Obesity – from genetic discovery to mechanistic insight via the atypical animal models.

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 often start with canine genetics - dogs are an excellent animal model for genetic studies because selective breeding means their genetics are particularly condusive to the studies we do. Recent work is extending into horse and production animal genetics. To follow up genetic findings, we use cellular experiments to understand the consequences of mutations on metabolism at a molecular level, focussing on neuronal development, cell signalling and adipocyte biology. And in pet dogs volunteered by their owners we study energy expenditure and eating behaviour to understand the whole-body physiological consequences of mutations of interest. Eleanor is a vet and we also have a clinically focussed research stream looking at the management of obesity in pet dogs and cats. I am happy to design PhD projects to suit the interests of each student. In the lab currently graduate students are working on clinical projects, cell biology, physiology and statistical genomics. This is an opportunity to have a true multidisciplinary scientific training in a friendly and supportive group.

Eleanor Raffan

Relevant References:

Genetics of a tasty steak – comparative genetic studies of fat distribution in production animals and human fat distribution patterns.

In humans, a tendency to store fat around the viscera instead of subcutaneously is associated with the development of insulin resistance, diabetes and other obesity related complications.  We know genes are central to determining fat deposition patterns but understanding how they have that effect has proven difficult.

In farm animals, selective breeding has directed fat deposition patterns in different species and breeds, often to the extreme. For instance, fat in the muscles (‘marbling’) is heavily selected for in beef cattle breeds and some pigs, whereas chicken and most pork is considered most desirable when very lean.  There is a wealth of data about what genes/genetic regions are likely responsible and we hypothesise that genes that promote particular fat distribution patterns in animals may overlap with human insulin resistance genes – either the exact genes, or related function.

This project will draw on publicly available data and prospectively collected animal tissue to identify loci associated with fat distribution in production animal species to find candidate genes and mutations. Comparative analyses with human GWAS data sets will be used to focus on shared candidate genes. Molecular studies of gene expression and function will be used to link genetic loci to mechanism.

As with my other projects, this can be adapted to fit your interests and skills – just get in touch to discuss before applying. 

Milka Sarris

Relevant References:

  • Kolaczkowska, E. & Kubes, P. Neutrophil recruitment and function in health and inflammation. Nat. Rev. Immunol. 13, 159–175 (2013).
  • Oishi, Y. & Manabe, I. Macrophages in inflammation, repair and regeneration. International Immunology (2018) doi:10.1093/intimm/dxy054.
  • Netea, M. G. et al. Defining trained immunity and its role in health and disease. Nat Rev Immunol 20, 375–388 (2020).

The elusive migration journeys and fates of inflammatory cells after microbial encounter

Inflammation is our body’s primary response to injury, ensuring tissue defence from invading microbes. Furthermore, dysfunctional inflammation is implicated in many diseases, from autoimmunity to cancer. It is critical therefore to fully understand the migratory response of leukocytes, which is at the heart of inflammation. The first cells to infiltrate damaged tissues are neutrophils and macrophages (‘myeloid cells’), which eliminate microbes and promote repair. The function of these cells is often assumed to end at inflammatory lesions. However, recent evidence challenges this view and indicates that myeloid cells can also disseminate from these sites (i.e. spread to other tissues in the body). Such emigration could potentially influence secondary inflammation elsewhere as myeloid cell function can be conditioned by prior microbial experience. Given these findings, it is important to discover what happens to myeloid cells post-infection: what journeys they take and what influence they have on inflammation resolution and on subsequent immune challenges. Answering these questions requires functional tracing of single cells in the entire animal. As this is challenging in large organisms, we propose to exploit disease models in zebrafish, coupled to state-of-the-art microscopy. Our general objective is to map the unexplored journeys of myeloid cells after microbial encounter and determine how they shape subsequent inflammatory responses.

Milka Sarris

Relevant References:

  • Palomino-Segura, M. & Hidalgo, A. Immunity: Neutrophil Quorum at the Wound. Curr. Biol. 30, R828–R830 (2020).
  • Poplimont, H. et al. Neutrophil Swarming in Damaged Tissue Is Orchestrated by Connexins and Cooperative Calcium Alarm Signals. Current biology: CB 30, 2761-2776.e7 (2020).
  • Kienle, K. & Lämmermann, T. Neutrophil swarming: an essential process of the neutrophil tissue response. Immunol. Rev. 273, 76–93 (2016).

The role of neutrophil group signalling in building inflammatory responses

Immune cells are remarkably capable of moving through tissues and locating sites of microbial threat during inflammatory responses. Research so far has largely concentrated on identification of chemical factors guiding leukocyte motion to target sites. However, fundamental, mechanistic questions remain about how immune cells are guided within complex tissues. One poorly understood aspect is how neutrophils coordinate their accumulation at sites of tissue damage. Recent research has revealed that after a few ‘pioneer’ neutrophils reach the site of injury they can produce secondary chemical signals that attract more neutrophils. This is an important amplification step that determines the magnitude of the neutrophil inflammatory response. It remains unclear how neutrophils generate an effective chemical concentration gradient capable of reaching other cells far away. Based on our recent work, we hypothesise that a certain number of neutrophils has to assemble into a cluster and closely coordinate the production of chemical signal within. We will employ mathematical modelling and novel optogenetic tools to manipulate attractant production in single cells. This will allow us to test different ways in which neutrophils can coordinate production of chemical signals. This work will help us understand how inflammatory responses are escalated and controlled, which is ultimately important for manipulating inflammation in disease settings.

Elena Scarpa (Co-supervisor TBC)

Pushing through: understanding cell division under in vivo physical confinement

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. To address this, we use Zebrafish. Zebrafish embryos are translucent, enabling visualisation of migrating cells in an intact animal. We investigate a population of 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 while confined in the interstitial spaces. These cells undergo mitotic errors during chromosome segregation with significantly higher frequency (up to 25%) than cells that divide before beginning migration. Cells dividing in the migratory path also display cortical blebbing at metaphase, a phenotype caused by mechanical compression in vitro. 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 mutants or laser optical manipulations to manipulate forces exerted by the surrounding tissues on the dividing TNC in vivo.

Amanda Sferruzzi-Perri

Relevant References:

  • Napso T, Zhao X, Ibañez Lligoña M, et al. Unbiased placental secretome characterization identifies candidates for pregnancy complications. Bioarchives. 2020.
  • Aykroyd BRL, Tunster SJ, Sferruzzi-Perri AN. Igf2 deletion alters mouse placenta endocrine capacity in a sexually-dimorphic manner. J Endocrinol. 2020;246(1):93-108.
  • Aykroyd BRL, Tunster SJ, Sferruzzi-Perri AN. Loss of imprinting of the Igf2-H19 ICR1 enhances placental endocrine capacity via sex-specific alterations in signalling pathways in the mouse. Development. 2022;149(1).
  • Lopez-Tello J, Khaira J, Kusinski LC, et al. Fetal and placental phosphoinositol 3-kinase (PI3K) p110α have distinct contributions in regulating resource allocation to the growing fetus. eLIFE. 2019;8.

Role of the placental malfunction in the programming of offspring and maternal disease risk

During pregnancy, nutrients must be supplied to the fetus for growth, but also to the mother to maintain the pregnancy. This nutrient balance depends on the placenta, an organ that develops during pregnancy to transfer nutrients to the fetus and that secretes hormones into the mother with metabolic effects. Impaired placental function disrupts the materno-fetal nutrient balance and results in major pregnancy complications, including gestational diabetes. preeclampsia and abnormal birthweight with both immediate and long-lasting effects on maternal and offspring health and cardio-metabolic disease risk. However, our understanding of the importance of placental endocrine function in the control of pregnancy wellbeing and long-term health of the mother and offspring is unknown. To address this knowledge gap, we have developed new molecular techniques1 and robust models of genetically-induced placental endocrine malfunction in mice (achieved by cell-specifically altering the expression of imprinted growth genes that control placental endocrine cell formation and function2,3). A PhD project could therefore utilise these new models and a range of in vivo physiological, molecular, cellular and histological techniques to:

1.            Identify the effect of placental endocrine malfunction on fetal and offspring growth and health outcomes and explore the molecular mechanisms involved.

2.            Examine the effect of placental endocrine malfunction on maternal health during and after pregnancy and elucidate the molecular mechanisms involved.

3.            Identify which placental endocrine factors are most important for controlling materno-fetal nutrient balance during pregnancy and studying how they may elicit their modes of action.

Amanda Sferruzzi-Perri

Relevant References:

  • Fowden AL, Camm EJ, Sferruzzi-Perri AN. Effects of maternal obesity on placental phenotype Current Vascular Pharmacology. 2020;19:113-131.
  • Musial B, Vaughan OR, Fernandez-Twinn DS, et al. A Western-style obesogenic diet alters maternal metabolic physiology with consequences for fetal nutrient acquisition in mice. The Journal of physiology. 2017;595(14):4875-4892.
  • Fernandez-Twinn DS, Gascoin G, Musial B, et al. Exercise rescues obese mothers' insulin sensitivity, placental hypoxia and male offspring insulin sensitivity. Sci Rep. 2017;7:44650.

Placental hormones and pregnancy health in obese mothers

Obesity during pregnancy affects maternal and infant health both during pregnancy and for long afterwards. It raises the risk of health complications like maternal diabetes during pregnancy, and increases the susceptibility of the mother to develop metabolic syndrome in the years after delivery. It also leads to neonatal and later life health complications in their infants, such that infants are more prone to develop metabolic impairments themselves in later life. Despite this, the mechanisms operating during pregnancy that lead to these poor pregnancy outcomes in obese women, remain unknown. The placenta is the organ that produces hormones responsible for changing the metabolism of the mother to ensure sufficient nutrients are available for fetal growth during pregnancy. However, to date, little is known about the role of placental hormone production and its relationship to obesity-related factors (such as oxidative stress and inflammation), in the development of maternal metabolic complications in pregnancies where the mother is obese. A PhD project would aim to address this knowledge gap by combining established models of diet induced obesity and genetically-induced placental endocrine malfunction with a range of in vivo physiological, and in vitro molecular, biochemical, cellular and histological techniques.

Dr. Fengzhu Xiong

Relevant References:

  • Kunz D et al. (2021) Downregulation of Extraembryonic Tension Controls Body Axis Formation in Avian Embryos. BioRxiv DOI:10.1101/2021.02.24.432525.

Morphogenetic Robustness under Fluctuations of Tissue Tension

Early amniote embryos are mechanically supported by extraembryonic and maternal tissues. These structures contribute tissue forces that may be essential for normal development of the embryo. In avian embryos, for example, the gastrula is under tension sustained by the vitelline membrane that encloses the yolk. Recently, we found that this tension decreases over developmental time to facilitate stage-specific morphogenesis of the embryo body. Such changes appear to only take effect over long periods at persisted high or low levels. On shorter time scales, the tension fluctuates naturally as the eggs are moved and also in ex ovo experimental culture conditions. Interestingly, in contrast to persistent tension, the morphogenetic dynamics of embryonic tissues remain largely unaffected by these fluctuations. This project aims to identify the mechanism ensuring this robustness against mechanical stochasticity on the embryo. Using a combination of theory, imaging, and mechanical and molecular perturbations, we will profile the tension fluctuation and tissue soft matter properties and test the hypothesis that tissues distinguish true morphogenetic forces from random fluctuations by responding preferentially to stresses at long time scales.

Dr. Fengzhu Xiong

Relevant References:

Moon LD & Xiong F (2021) Mechanics of neural tube morphogenesis. Seminars in Cell & Developmental Biology. DOI: 10.1016/j.semcdb.2021.09.009.

Tissue Mechanics in Neural Tube Morphogenesis

The neural tube is a developmental precursor of the vertebrate central nervous system, including the brain and the spinal cord. It begins as a specified 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. The folding process happens in conjunction with the morphogenesis of neighboring tissues including the paraxial mesoderm and the surface ectoderm. The failure of this folding and closure process underlies the neural tube defects (NTDs) in human development. From a physics perspective, tissue folding must require driving forces generated by the neural cells and/or the neighboring tissues. In addition, the mechanical properties of the neural tissue may also be regulated to ensure correct tissue deformation progress under the driving forces. The origins and magnitudes of forces from different sources are not well understood, nor are the regulatory mechanisms of tissue rheological properties. Consequently, an integrated picture of biomechanical model of neural tube morphogenesis is missing. To address this challenge, our project will involve (but not limit to) the following approaches using the avian embryonic neural folds as a model system: 1. use imaging to quantify the shape dynamics of the neural plate as it folds towards a tube; 2. use soft gels, magnetic droplets and cantilevers to dissect the contributions from tissue intrinsic (e.g., apical constrictions, intercalations) and extrinsic (e.g., paraxial mesoderm, endoderm) forces to neural tube folding; 3. use molecular and genetic methods to test relevant factors (e.g., cell polarity, adhesion, folate pathway) in regulating tissue biomechanics.