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Results

Quantifying the development of neural progenitor polarisation 27 Apr 2017

Apicobasal polarity plays a fundamental role in the defining functional features of neural progenitors during the early stages of embryonic development. The apical pole in neural progenitors is specialized for multiple rounds of progenitor divisions, resulting in brain growth, where as the basal pole forms the environment where neuronal differentiation will occur. However, it is not well understood how the apicobasal polarity of neural progenitors is established. During the project, we will test a hypothesis which suggests that apicobasal polarity is progressively generated and can be monitored by quantifying a Cdh2 protein gradient along the apicobasal axis in neural progenitors. A key goal will be to determine the distribution of the Cdh2 protein over time during neural progenitor polarization. To do this we will make three-dimensional time-lapse movies of developing neural primordium in zebrafish embryos that express a transgene Cdh2-GFP. The transgene containing GFP will make it possible to visualize the distribution of the Cdh2-protein during progenitor polarization. Quantification will be done using FIJI image analysis software.

Amount: £0
Funder: The Wellcome Trust
Recipient: King's College London

Use of tDCS in traumatic brain injury patients to modulate brain network and cognitive function 27 Apr 2017

Good cognitive control requires efficient brain network activity. The posterior cingulate cortex (PCC) is an important node within the Default Mode Network (DMN). The DMN shows deactivation on functional MRI (fMRI) during tasks requiring externally directed attention. Abnormal activation of this area is observed in TBI patients, and is related to poor cognitive function >. However, this area is not homogenous in its function, with the dorsal PCC thought to be involved in coordinating task-relevant changes in brain network activity >. Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation technique. TDCS can modulate cognitive function and has also been seen to modulate brain network activity >. There have been no studies of its effects on brain network activity in TBI patients. This study will test whether tDCS can improve cognitive control in TBI patients and whether it does so by brain network function, specifically whether it differentially modulates activity within the PCC. Key goals - To test the hypothesis that: 1)tDCS in TBI patients can modulate cognitive function 2)tDCS in TBI patients can modulate brain network function 3)The modulations in brain network function are related to any modulates in cognitive function

Amount: £0
Funder: The Wellcome Trust
Recipient: Imperial College London

The Role of MYBL2 in DNA damage response to etoposide in mouse embryonic stem cells (ESCs) 27 Apr 2017

Embryonic Stem cells (ESC) share common characteristics with cancer cells such as immortality and the ability to bypass the normal cell cycle checkpoints somatic cells have to pass through. This allows both cells to continuously proliferate without changing their cellular features. These similarities shared between both ESCs and cancer cells may relate to common patterns and mechanisms of regulating gene expression. In fact, as demonstrated by Yamanaka fully differentiated fibroblast could reverse their state of differentiation and be induced towards an embryonic stem cell-like state (induced-pluripotent stem cells (iPSCs)) by introducing four transcription factors expressed in a pluripotency state. These observations highlighted the importance of transcriptional factors in determining cell fate and their possible role in the induction of cancer. In this project, I will be working with mouse ESCs and will be looking at the role of MYBL2, a transcription factor highly expressed in ESC and iPSC, which is involved in cell proliferation and maturation, and try to better understand its role in the maintenance of genome integrity. I will be exploring how low levels of this gene affect the cell response to topoisomerase II inhibitor etoposide, a therapy currently used in to treat cancer.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Birmingham

Use of a Drosophila model to study circadian control of metabolic health. 27 Apr 2017

Internal daily timekeeping systems known as circadian clocks are used by all types of organisms to regulate their metabolism. For example, the clock-controlled scheduling of food intake and use affects health and longevity in both mammals and insects. Time-restricted or nutrient-restricted feeding improves the health of both mice and fruit flies (Panda, Science 2016). The period gene, which plays a key role in the circadian clocks of animals, provides a link between daily timekeeping and metabolic health. Flies lacking the period gene store less glycogen and triglycerides in spite of ingesting more food and are, therefore, more sensitive to starvation. I propose to test where and how the period gene provides this metabolic function. In particular, I will ask whether its role in starvation resistance is due to its control of sleep/wake rhythms or its function in periperhal clocks of metabolic tissues such as the fat body. Moreover, Dr Wijnen's laboratory recently showed that the period gene is induced at colder temperatures (Goda et al., Proc Biosci 2014) and I will test whether period-mediated starvation resistance is found preferentially at colder temperatures.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Southampton

Deciphering copy number variation in susceptibility to testicular germ cell tumour 27 Apr 2017

Testicular germ cell tumour (TGCT) has a strong inherited basis with brothers of cases having a 6—10 fold increased risk of disease and heritability of >45%. Whilst GWAS studies have identified >25 loci associated with disease, the underlying causative variants and mechanisms for conferring susceptibility to the disease are poorly understood. Furthermore, whilst recent whole exome analysis had implicated rare variants in genes related to microtubule and ciliary function in familial TGCT, these rare variants only account for a modest proportion of disease heritability. To date there has been no exposition of the role of copy number variation in susceptibility to TGCT and it is plausible that copy number variants may contribute to the "missing heritability" of TGCT. Furthermore, identification of copy number variants implicated in TGCT susceptibility may be informative with regard to highlighting novel TGCT susceptibility genes located within the regions of copy number variation. In this project I shall deploy copy number-calling algorithms on (i) SNP array data on 7319 TGCT cases and 23082 controls and (ii) whole exome sequencing data on an overlapping set of 962 TGCT cases and 1644 controls.

Amount: £0
Funder: The Wellcome Trust
Recipient: Institute of Cancer Research

Investigating causal links between smoking behaviour and sleep using Mendelian randomisation 27 Apr 2017

Smoking is associated with sleep disturbance and difficulties. However, it is unknown whether this relationship is causal and if so, in which direction the association occurs. Inferring causality from observational data is difficult due to the problems of confounding and reverse causality. The aim of this project is to investigate causal relationships between smoking and sleep using a bidirectional Mendelian randomisation approach. This project will involve secondary data analysis of publicly available genomewide association study data. Genetic variants which associate with smoking behaviour (smoking initiation, smoking cessation and cigarettes smoked per day) will be used as proxies for smoking in analyses to investigate causal effects of smoking on sleep. Genetic variants which associate with sleep duration will be used as proxies for sleep in analyses to investigate causal effects of sleep on smoking behaviour. These analyses should be less affected by confounding than conventional observational analyses. Understanding the causal nature of the relationship between smoking and sleep is important for development of smoking cessation strategies as sleep may be a factor influencing relapse to smoking following a quit attempt.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Bristol

Exploring the role of Nesprin-2 upregulation mediated by CRISPR/Cas9 in breast cancer cell metastasis 27 Apr 2017

The purpose of the study is to elucidate the role of the nuclear membrane protein nesprin-2 expression in LINC complex formation and the subsequent effect on nuclear rigidity in breast cancer. Their invasive phenotype permits breast cancer cells to metastasize and move through collagen-rich environments. The cells are hallmarked by nuclear softening in breast cancer and it is hypothesized that decreased nuclear rigidity due to mutations in nesprins facilitates metastasis. Therefore, addressing nesprin-2 functions in cancer development by understanding novel mechanistic concepts in metastasis is the principal underpinning objective. The study involves contrasting cells exhibiting changes in nesprin-2 expression. Two breast cancer cell lines MDA-MB231 will be used one of which will be modified with a CRISPR/dCas9 activation plasmid to upregulate specifically the expression of nesprin-2. The consequent protein products will be compared by using standard immunoblotting. Effects on LINC complex formation and structure in cancer cells will be assessed by confocal microscopy. Finally, 3-D space-restrictive porous scaffolds will be used to examine the migratory behavior of nesprin-2 activated MDA-MB231 cells relative to parental cells, which will help to understand how LINC nuclear complex architecture influences metastatic cell migration. This would potentially aid in developing novel treatments for breast cancer.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Durham

Deconstructing Mathematical Problem Solving: Contributions of Cognition and Language 27 Apr 2017

Mathematical skills predict career outcomes, health literacy, and finance skills. Troublingly, almost half of the adult population in the UK have a mathematical skill level equivalent to primary education. In order to remediate this and design effective, early interventions, it is important that we first understand how mathematical skills develop. In particular, little is currently known about the cognitive skills underlying mathematical skills. We will focus on understanding word problems because this is the type of mathematical information people more commonly encounter in daily life. We are interested in how high-level cognitive skills (known as executive functions) and language skills help solve mathematical word problems in children ages 5 and 6 – the age at which children first start formal schooling. Furthermore, since little attention has been placed on different types of word problems, we propose to investigate specifically which cognitive skills 5 to 6 years-old children use while solving ‘consistent problems’ (word problems involving relational terms that are consistent with the required mathematical operator) and ‘inconsistent problems’ (relational terms conflicting with the required mathematical operator). Findings will contribute to our understanding of how children acquire complex problem-solving skills and offer guidance on where to focus educational and interventional effort.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Sheffield

Determining the temporal stability of an immunoscore in high grade serous ovarian cancer 27 Apr 2017

The importance of the immune system in determining the behaviour of a cancer is only now becoming clearly understood. Recent data in patients with ovarian cancer have shown a positive correlation between tumours that have pre-existing intraepithelial T cells at diagnosis and extended life span of the patient. Such information may have both prognostic and predictive implications but a key tool required for the unlocking of this knowledge is a robust immunoscore. Imunoscores are simple scoring systems based on the presence or absence of immune markers including CD4, CD3 and CD45RO. The aims of this research project are to evaluate the temporal stability of the immunoscore using paired samples measured at primary presentation and then after three cycles of chemotherapy thus informing how the immunoscore can be incorporated into clinical research and practice.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Manchester

Foveal and peripheral contributions to controlling fixation duration 27 Apr 2017

Human vision relies on rapid gaze shifts to obtain high quality foveal information about the environment. Information is acquired during periods of stable fixation. During a period of stable fixation, several decision processes occur: (i) foveal analysis: the observer has to analyse (identify) the currently fixated object(s); (ii) target selection: the observer has to decide where to look next; and (iii) fixation control: the observer has to decide when to go there. In the current project, we aim to assess the role of foveal analysis and target selection on the control of fixation duration. Investigating this interaction is vital to understanding the processes which govern an observer’s active visual sampling of the environment. The critical question we will address is to what extent fixation duration is controlled by foveal analysis and target selection, when the difficulty of these two decision processes is carefully controlled.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Bristol

Investigating the expression and role of the lncRNA EGFR-AS1 in lung cancer 27 Apr 2017

Targeted therapies, have led to significant improvements in our ability to treat non-small cell lung cancer (NSCLC). One of these targets is the EGFR receptor which if mutated at particular residues makes this receptor amenable to targeted therapies such as EGFR Tyrosine Kinase inhibitors (TKIs). Whilst this improves survival, at some point all patients will develop resistance to the existing therapies. long non-coding RNAs (lncRNAs), are known to play critical roles in resistance to chemotherapy and epithelial mesenchymal transition (EMT). One lncRNA, called EGFR-AS1 exists in an antisense orientation to the EGFR. The only study on this lncRNA is in hepatocellular carcinoma, where its expression was shown to be significantly related to patient prognosis, and its inhibition resulted in significantly reduced cellular proliferation and invasion in vivo. Nothing is known about the role of this lncRNA in NSCLC. Preliminary data from the PIs laboratory indicates that the expression of this lncRNA is significantly altered in cells carrying mutations which render them sensitive to EGFR TKIs. This aim of this project is to evaluate this possibility in NSCLC, and to test whether overexpression of this lncRNA increases sensitivity to EGFR TKIs in resistant cells and its effects on markers of EMT.

Amount: £0
Funder: The Wellcome Trust
Recipient: Trinity College Dublin

Exploiting whole genome tagging of trypanosomes to identify new ciliopathy candidate genes in humans 27 Apr 2017

Ciliopathies are a range of human genetic diseases in which the normal functions of cilia/flagella are disrupted or prevented entirely. Ranging from mild to embryonically lethal, these diseases are often difficult to investigate as many do not appear to have clear links with particular genes or molecular mechanisms. This project aims to identify potential ciliopathy protein candidates and their corresponding human ciliary/flagellar genes by identifying previously unrecognised ciliary proteins conserved across eukaryotic life using the human parasite Trypanosoma brucei as a model organism. To start with, I plan to use TrypTag, a major new data resource, to identify which proteins localise to the flagellum and cilium. I shall then use bioinformatics tools and human genetic disease databases to identify which are conserved in humans not yet linked to a ciliopathy. Having excluded known ciliopathy-related proteins, I will then screen T. brucei deletion mutants for defects in flagellum growth, motility or flagellar beat. Those with defective phenotypes have the potential to be involved in human ciliopathies when mutated. The intended goal is to create a list of these novel candidate genes for involvement in human ciliopathies, with evidence for localisation and function in the flagellum/cilium of T. brucei.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Role of Hypoxia Inducible Factors in Liver Fibrosis 27 Apr 2017

Hepatic fibrosis is a chronic liver disease associated with the accumulation of scar tissue caused by the excessive deposition of extracellular matrix (ECM) proteins. The Activation of hepatic stellate cells (HSCs) is the initiating event in liver fibrosis, and as such uncovering the molecular determinants behind this activation is of great importance in understanding the disease. The expression of UCHL1, a deubiquitinase enzyme, is dramatically elevated upon hepatic stellate cell (HSC) activation and is involved in the regulation of HSC proliferation, however the precise targets of UCHL1 in this context is unclear. UCLH1 has recently been identified as a HIF1 alpha deubiquitinase which causes increased HIF1 activity under normoxic and hypoxic conditions by disrupting the degradation of HIF1 alpha. Preliminary data has suggested that HIF1a levels are elevated in activated HSCs and this activation is dependent on UCHL1. This project aims to build on these findings with the following aims - 1. Examine relationship between UCHL1 and HIF1 exploring the contribution to the fibrotic phenotype. 2. Examine effects of elevated UCHL1 and HIF1 on cellular proliferation. 3. Analyse markers of fibrosis and HIF activity.

Amount: £0
Funder: The Wellcome Trust
Recipient: Newcastle University

Controlling phosphodiesterase activity in biofilm dispersal 27 Apr 2017

Biofilm formation and dispersal are controlled by the secondary messenger bis-(3’-5’) cyclic dimeric guanosine monophosphate (c-di-GMP); high levels are associated with biofilm formation, while a reduction induces dispersal. The enzymes catalysing formation of c-di-GMP are diguanylate cyclases, while phosphodiesterases catalyse the breakdown of c-di-GMP. Structural studies of the EAL type phosphodiesterases were observed in the host laboratory in the presence of substrate c-di-GMP, suggesting that these structures would require further steps to attain full catalytic activity. The host laboratory have recently demonstrated that dimerization and active site formation as well as formation of three metal binding sites are distinct activation steps required to tune the enzymatic activity of phosphodiesterases (Scientific Reports 2017). The proposed project deals with the motility regulator protein, MorA, and the mucoid alginate regulator, MucR, from Pseudomonas aeruginosa. Both proteins have dual activity as diguanylate cyclase and phosphodiesterase. Interestingly, the two linked catalytic domains influence each other's activity; different levels of activity are observed for the phosphodiesterases when comparing isolated domains with the linked conformation. The objective of the project is to purify these proteins and determine their catalytic activities, comparing the isolated domains, mixtures of the individual domains, and the cyclase-phosphodiesterase domains in linked conformation.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Southampton

Do abnormal blood vessels impact bone loss in osteoporosis? 27 Apr 2017

Vascular endothelial growth factor (VEGF) has important roles in the blood vessels of adult tissues and in disease. Dr Clarkins laboratory have found that deletion of VEGF by bone forming osteoblast (osteocalcin; Ocn expressing) cells results in severe bone porosity similar to osteoporosis. To investigate how vascular endothelial cell- factors contribute to this porous phenotype, further experiments from Dr Clarkins lab collected conditioned media (CM) from osteoblasts (OBs) of mice with VEGF removed and added to vascular endothelial cells. In the absence of VEGF, endothelial cells were found to upregulate inhibitors of mineralisation including sclerostin which may contribute to osteoporotic bones of VEGF KO mice. The goal of my studentship project is to investigate how endothelial cells produce sclerostin, which is important as sclerostin has previously been reported to be secreted only by bone cells. I will investigate this by immunolabelling of sections of VEGF KO and WT long bones for sclerostin and a blood vessel marker CD31. I will also treat endothelial cells with CM from VEGF WT and KO cells and undertake Western blotting for sclerostin. Inhibiting blood vessel anti-mineralisation factors could provide a new a means to treat degenerative bone disease such as osteoporosis.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Southampton

A CRISPR/Cas9-Based Screen for Novel Actin Dynamic Factors 27 Apr 2017

The project will focus on understanding critical aspects involved in the biology of the apicomplexan parasite Toxoplasma gondii (T. gondii), an obligate intracellular parasite that can infect every warm-blooded animal including humans. T. gondii, the causative agent of toxoplasmosis, is of medical importance for human health as an infection can cause severe damage in the developing foetus and immunocompromised persons. In addition, T. gondii serves a model organism for Plasmodium falciparum, the aetiological agent of malaria. In order to invade the host cell apicomplexan parasites rely on their acto-myosin system. Furthermore, recent research highlights the importance of parasite actin during intracellular parasite development. It is thus important to identify and characterise factors involved in the regulation of actin dynamics. Here, cutting edge molecular tools including conditional CRIPSR/Cas9-systems will be applied to screen a subset of essential genes in T. gondii for novel factors involved in the regulation of actin dynamics. Investigating how the parasites regulate these filaments will give valuable insights into how apicomplexan parasites establish infections in their host.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Glasgow

Developing efficient xeno-free mechanoculture of stem cells for tissue engineering 27 Apr 2017

The aim of this project is to develop a completely xeno-free culture system for human mesenchymal stem cells (hMSCs), cultured on synthetic peptide hydrogels (PeptieGel Design, Ltd.) and ‘mechano-cultured’ in a simple wave tank bioreactor with dynamic hydrostatic pressure acting as a dominant stimulus to control cell growth and differentiation into active osteoblasts and chondrocytes. Our hypothesis is that the changing pressure (which replicates the loading experienced during anabolic exercise) will stimulate mechanotransduction pathways in the cell that promote the growth, asymmetric division and subsequent differentiation of hMSCs by enhancing the signal transduction of autocrine and paracrine growth and transcription factors. Our project goals therefore are to: Combine a simple wave tank bioreactor with our hydrostatic pressurisation system. Culture hMSCs in synthetic peptide hydrogels as encapsulated 3D microcarrier beads. Compare growth of conventionally cultured (T-flasks) hMSCs to the bioreactor cultured hMSCs Switch to differentiation media (chondrogenic and osteogenic) to determine how hMSCs differentiate during the end stages of mechanoculture. A summary of these goals is attached in the supporting document (fig. 1.)

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Liverpool

In vitro characterisation of neurons and glia derived from mouse ES cells having Y chromosome gene deficiencies 27 Apr 2017

The brain is a sexually dimorphic organ, which can explain why many psychiatric disorders are gender-biased. While it has been thought that fetal sex hormones play a crutial role in brain sexual differentiation, emerging evidence indicates that genetic and/or epigenetic factors encoded by sex chromosome genes are also involved. Here, we focus on several Y-linked genes expressed in the male brain, which may act in a dominant manner. Sry, Uty and Smcy genes, whose products can participate in histone modification, are of particular interest. However, their functions in the brain remain unknown mainly because of difficulties in conventional gene-targeting of Y loci in embryonic stem cells (ESCs). In this project, we will take advantage of Crispr/Cas genome-editing technology that allows us to modify Y-linked genes. Mutant alleles of these three genes in ESCs were created and then differentiation will be induced of neurons and glia from the mutant ES cells. Differential gene expression between wild-type and mutant cells will be analysed by RT-RCR and bisulfite PCR, and subsequently epigenetic status of these differential genes will be elucidated. The project will reveal influences of Y-linked genes on sex-specific epigenetic modification and lead to better understanding of gender-biased psychiatric disorders.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Aberdeen

Investigating the role of histone demethylation in the timing and epigenetic alterations of X chromosome inactivation in embryonic stem cells 27 Apr 2017

Epiblast cells within the inner cell mass of the blastocyst will differentiate to form the three germ layers during mammalian embryo development. Extracting these cells, known as embryonic stem cells, from mouse embryos has been a useful research tool as they are totipotent. This research works to understand gene-dosage compensation whereby one X chromosome (XC) is heterochromatically silenced in female embryonic cells and inactivated at blastocyst development. A series of epigenetic alterations through post-translational modifications to the XC’s histones are fundamental in this process. It has been established a reduction in acetylation occurs at histone level during inactivation and adding histone acetylase inhibitors can prevent XC silencing. However, timing is key as if the inhibitor is added too early or too late during differentiation it is ineffective. Other histone modifications, such as methylation, are as important as there is complex interaction between them. Using a range of biochemical techniques, including immunofluorescence microscopy, the extent of acetylation and methylation on the inactive XC at varying histone demethylase inhibitor concentrations will be measured. This research will work to define the inhibitor-sensitive time window of XC inactivation more clearly.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Birmingham

The role of inheritance and the EGF pathway in mis-segregation of chromosomes during mitosis. 27 Apr 2017

I am proposing to research how the mis-segregation of whole chromosomes during mitosis impacts future cell divisions and how this is coupled to spindle assembly pathways and epidermal growth factor (EGF) signaling. During this project I will investigate whether a gain or loss of a chromosome, due to mis-segregation, predisposes daughter and grand-daughter cells to further segregation errors. Additionally, I will research whether the inhibition of EGF signaling will exacerbate chromosomal mis-segregation. The research will be carried out on non-small cell lung cancer (NSCLC) cell lines, which will be transfected with GFP-CENP-A, marking kinetochores, or GFP-tubulin, marking the spindle, and treated with SiR-DNA, allowing visualisation of chromosomes. These fluorescent reporter constructs will allow chromosomal mis-segregation and spindle geometry to be observed during live cell imaging. The live-cell imaging experiments will then be repeated in the presence of Gefitinib, allowing observations to be made whilst EGF signaling is inhibited. The primary goals of this research are firstly being able to provide key insight into how the EGF pathway regulates chromosomal instability (CIN) and cell fates in NSCLC, and secondly to be able to establish how the mis-segregation of whole chromosomes impacts future cell divisions.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Warwick