NIHRDataInsights/HRCSData huggingface dataset:
Title: Investigation of lncRNAs regulated by ELK-1 and AP-1 transcription factors
Funder: Wellcome Trust

Abstract: Recent studies of global genome transcription indicate that majority of the DNA is transcribed into RNA molecules. Since protein coding genes occupy approximately 3% of human genome, the function of remaining transcripts is unknown. Recent evidence indicates that a large fraction of those unknown transcripts might be long non-coding RNAs (lncRNAs). The lncRNAs are a varied class of genomic element whose only common features seem to be their length (>200 nucleotides) and lack of obvious protein coding potential. In the courseof PhD project, we will study the lncRNAs by investigation of their expressionregulation. Our recent study showed that ELK-1 and AP-1 transcription factors interact with genomic regions which are distant from known protein-coding genes. This observation raised question whether those transcription factors might regulate other unknown genomic elements (such as lncRNAs) which are present in their proximity. In the course of the project we will combine latest technologies such as RNA-Seq and ChIP-Seq together with well-established molecular biology techniques and bioinformatics approaches to identify and descibe properties and functions of IncRNAs potentially regulated by ELK-1 and AP-1 transcreiption factors. We hope that this project would progress scientific understanding of the role the IncRNA play in the cell.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Decoding the interplay between chromatin structure and transposable element insertion in Drosophila
Funder: Wellcome Trust

Abstract: Transposable elements (TEs) are mobile DNA elements that account for substantial proportions of the genomes of most organisms. For example, TEs make up approximately 45% of the human genome. TEs have been shown to generatemutations leading to Mendelian diseases and cancers in humans. Despite their abundance and importance, the mechanisms that regulate TE insertion in eukaryotic genomes remain largely unknown. The overall aim of this project is to investigate the interplay between chromatin structure and TE insertions in eukaryotes using the model species, Drosophila melanogaster, to address several objectives: Objective 1. Decode the chromatin features that influence promoter targeting of the Drosophila melanogaster P element during artificial mutagenesis experiments. Objective 2. Identify chromatin features associated with de novo insertion sites of naturally occurring TEs using population-resequencing data. Objective 3. Investigate the chromatin properties of TE insertions in the Drosophila melanogaster reference genome. Objective 4. Develop robust software for the identification of de novo TE insertions in next generation sequencing data. This work will lead to important insights about the basic mechanisms of TE integration that can be used to interpret patterns of TE insertion in eukaryotes and potentially to harness TEs as vestors for genetic engineering or gene therapy.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: The role of de nova protein synthesis in mitosis
Funder: Wellcome Trust

Abstract: Transcription and translation are largely suppressed during mitosis, a notion re-enforced by the fact that the vast majority of mitotic control is mediated via phosphorylation and ubiquitin-mediated proteolysis. However, it transpiresthat some proteins are synthesized de novo during mitosis, including cyclin B1and Cdc20, two key mitotic regulators. It appears that this de novo mitotic synthesis is mediated by the cytoplasmic polyadenylation mechanism, as opposedto canonical cap-dependent translation. However, exactly why these proteins are synthesized de novo is unclear. Our hypothesis is that both cyclin B1 and Cdc20 are "topped up" during a prolonged mitotic arrest, with de novo synthesis of cyclin B1 maintaining the mitotic state, and de novo synthesis ofCdc20 ensuring that cells can efficiently exit mitosis upon completion of chromosome alignment. To test this hypothesis, I will use gene targeting to mutate the 3' UTRs in the cyclin B1 and Cdc20 genes in order to disrupt the cytoplasmic polyadenylation mechanism while leaving the canonical cap-dependent pathway. This will create cell lines that cannot synthesise these proteins specifically during mitosis. I will also set up novel biosensors to investigate cytoplasmic polyadenylation-dependent translation during mitosis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Mitochondrial redox regulation
Funder: Wellcome Trust

Abstract: Recent reports have highlighted the important regulatory functions played by the glutathione (GSH) and thioredoxin systems in maintaining cellular redox homeostasis during normal and stress conditions. These systems are conserved throughout evolution, yet despite their key roles in redox regulation, little is known regarding their roles in the compartmentalized regulation of mitochondrial redox homeostasis. We will address the mechanisms by which cellsuse compartment-specific redox regulation to protect mitochondria against oxidative damage, focussing on two Specific goals: To characterize the regulation of the mitochondrial thioredoxin system, focussing on its role in growth and apoptosis. Our preliminary data indicate that oxidation of the mitochondrial thioredoxin correlates with increased rates of apoptosis and we will use the yeast system as a model to identify the functional links between mitochondria, reactive oxygene species and apoptosis. The mitochondrial intermembrane space (IMS) ery (Mia40/Erv1). The recent omaintains its own redox environment and contains an(Trx1 and Trr1) and glutatessential disulfide bond formation machinery MS is


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Integrated Structural Biology Approach to the Regulation of PI-Phospholipase CGamma.
Funder: Wellcome Trust

Abstract: The overall aim of the project is to investigate the structure and regulation of the ã-isoforms of phospholipase C (PLC ã), in the context of the interaction with activating growth factor receptors and its interaction with membrane-embedded substrate. Specifically the project will attempt to validate a model for the receptor recruitment to, activation by, and subsequent release from the fibroblast growth factor receptor that has been developed by the co-supervisors of this project [1]. Importantly the work will attempt to determine whether the model, developed using experimental data obtained for PLCã1, is also applicable to PLCã2 for which mutations cause immune deficiency disorders in human patients.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: The role of the homeobox gene Hesx1 in stem cell fate.
Funder: Wellcome Trust

Abstract: The elucidation of the transcriptional mechanisms underlying cell stemness is an important goal of modern cell biology and a vast amount of research has revealed the functionof several transcription factors in the maintenance and induction of pluripotency. Hesx1,encoding a transcriptional repressor, is a critical homeobox gene during normal vertebrate development and its absence leads toforebrain and pituitary defects in all species analysed, including humans. Despite the fact that Hesx1 was initially cloned from mouse ES cells 27 years ago, there is no information on its function in these cells. Preliminary research from the hostlab has shown that Hesx1-deficient ES cells have a similar molecular signature to epiblast stem cells (EpiSC), suggesting that HESX1 may beinvolved in the maintenance of ES versus Epi cellfates. In addition, Sara has identified from microarray data available in theliterature, that the core pluripotency factors SOX2, OCT4, Nanog and TCF3 are bound to the promoter region of Hesx1. Finally, we have preliminary data indicating that Hesx1 is expressed in the inner cell mass of the 3.5-4.5 days post coitum (dpc) mouse blastocyst. In addition she will identify HESX1 transcriptional targets in order to understand at the molecular level the function of HESX1 in these cells.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Understanding the cellular and molecular mechanisms by which the complement factor C9 can control neural crest migration and invasion.
Funder: Wellcome Trust

Abstract: Research regarding Neural Crest (NC) migration is important for understanding the development of many organs and systems. Increasing evidence of similarities between NC migration and cancer metastasis have also attached an additional importance to this area of study. Preliminary investigations have suggested a novel role for the complement cascade in early development with the finding that several complement factors (i.e. C3a, C9) are not only expressed in NC but also required for the migration of this tissue. The proposed project aims toinvestigate the cellular and molecular mechanisms by which complement factor C9 controls NC migration and invasion. We will perform high-resolution time-lapse video analysis of NC migration and invasion in vitro and in vivo, comparing control and C9 deficient NC cells. Several candidates will be testedas possible targets of C9 activity such as alterations in cell adhesion, proliferation and apoptosis. Further study will also aim to identify the domain ofC9 important for this function within NC. Collectively these results should allow us to elucidate a completely novel function for complement factor C9 in NC migration and invasion, which could also be relevant for cancer metastasis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Prediction of Protein Structure and Function Using Graphical Learning Biology Techniques.
Funder: Wellcome Trust

Abstract: The accurate prediction of biological function on a genome-wide scale promiseswide-ranging benefits in understanding complex biological processes. Such understanding will be a key stepping stone in the development of techniques and pharmaceuticals to target genes associated with disease and their products. Historically, structural insights have provided the most detailed information on biological function, highlighting, for example a specific catalytic mechanism or interactions with partner proteins or other molecules. An in-depth analysis of key functional regions such as those in enzyme active sites, protein-protein binding sites, metal binding sites, and ligand binding clefts, as well as interacting regions between proteins is likely to add significantlyto the repertoire of tools currently available. In this project we will apply some new techniques we have developed to allow correlated mutations in protein families to be detected to the joint problem of protein structure and function By detecting pairs of sites which appear tochange in concert across the evolutionary tree we can infer the possible fold of the protein, residues involved in protein-protein interactions, and residues involved in ligand binding. From this information we hope to recognise a wide range of ligand binding sites, including DNA, RNA, A(TD)P, G(TD)P, sugars, cofactors and even other proteins. For the function prediction work, we may focus initially on predicting DNA and RNA binding sites which are of interest in Dr Savva's lab.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Investigating the Structure of Intrinsically Disordered Proteins Using Bioinformatics and CD Spectroscopy.
Funder: Wellcome Trust

Abstract: Intrinsically disordered proteins are composed of regions where there is no regular secondary structure; they have been proposed to play an important rolein signalling, intermolecularinteractions, molecular recognition and control processes. These roles arise from the functional advantages these proteins exhibit, i.e. promiscuity, one-to-many binding, increased radius and speed of interactions (Uversky and Dunker, 2012). Intrinsically disordered proteins are often a mixture of conformers lacking stable secondary or tertiary structure, which cannot readily be characterized by NMR or crystallographic methods that rely on the presence of defined regular and persistent structures (Uversky andLonghi, 2010). The proposed project would focus on developing and using bioinformatics t predmethods to: improve of DISOPRED (Ward, 2004) and enhance its current predictive capabilities of DISOPRED (Ward, 2004) and enhance its the functionality torder (Dunker et al., 2008), as well as method to identify and design natively disordered polypeptides with the potential for undergoing disorder-to-order (and order-to-disorder) transitions. After this step, molecular biology techniques are going to be used to clone and express the designed proteins, and then the method of circular dichroism (CD) spectroscopyto enable the identification of the nature and quantification of the different types of intrinsic disorder found in proteins and changes when they bind partner compounds to form complexes, or are exposed to alternative environments.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Mechanism of Helicase Unwinding Studied Using Magnetic Tweezers.
Funder: Wellcome Trust

Abstract: 1) Establish basic techniques for single molecule assays 2) Create protein and DNA template preparations 3) Perform single molecule mechanical studies using magnetic tweezers 4) Develop combined magnetic tweezers and TIRF imaging 5) Use of optical tweezers/AFM to study mechanics and structure at higher temporal and spatial resolution 6) Write up thesis


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Synthetic Biology and Chemoenzymatic Pathways to Isoquinoline Alkaloids.
Funder: Wellcome Trust

Abstract: The enzyme norcoclaurine synthase (NCS) which catalyses the key step in benzylisoquinoline alkaloid (BIA) biosynthesis will be manipulated to increaseits ability to accept non-natural substrates and create novel compounds. The mutant enzymes will also provide information on the catalytic mechanism. Enzymesystems that can generate the aldehyde substrates of NCS in situ will be developed in order to create synthetic pathways in vitro and in vivo to generate novel biologically active compounds. Enzymes that can modify the BIA products of theengineered NCS will also be investigated to extend further the ability tomake new biologically active compounds. The synthetic pathways will be built in E. coli with the aim of having bacterial systems that could be used to synthesise realistic quantities of pharmacologically active compounds. BIA's have diverse biological activities such as antimicrobial, eukaryotic receptor binding (e.g. dopamine, opiod), acetylcholesterase inhibition, anxiolytic, phosphodiesterase inhibition and calcium channel blockade to list only a few of their activities. The antimicrobial activities of some of the novel BIA's will be tested in the project and other activities will be investigated via collaborations.


Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: GENERIC HEALTH RELEVANCE
Title: Courtship of Drosophila: vibratory signals by the male and their receipt by the female.
Funder: Wellcome Trust

Abstract: Animal development is an everyday miracle that many take for granted. In the last 100 years great progress has been made in understanding one key question: How do cells know where they are in the body information they need to make the right part of the body in the right place (eye, nose, heart). But there is another aspect of animal design which is just as important but remains mysterious. If a some cells make a finger, they need to build it in the right alignment, to attach it to the hand corr ectly and point it in the right direction. To do this each cell needs to know its orientation within the whole; a property known as planar cell polarity. Planar polarity is most obvious in oriented structures, such as the whorls of hair on a baby's head. However it is probably even more important inside the body; for example in orienting nerve outgrowth so as to wire the nervous system correctly. Our project is to understand the mechanism of planar polarity. We use the fruitfly because the mecha nisms are universal, the same genes being used in flies and in us, and because the fruitfly is excellent for genetic experiments.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Structural probing of the sodium-hydantoin transporter Mhp1 in action.
Funder: Wellcome Trust

Abstract: Secondary-active trans-membrane transporters facilitate the movement of substrates, such as neurotransmitters or metabolites, across the cell membrane. Disruption of these vital processes may cause severe disease in humans, for example Parkinson's disease or kidney disorders. The aim of this project is to elucidate the structural basis of the transportmechanism of secondary-active transporters using the bacterial sodium-hydantoin transporter Mhp1 as a model system. Currently, static crystal structures of Mhp1 in various intermediate states along the transport cycle provide only limited insights into its mechanism. In order to bridge thegaps between these structures, we will develop and apply complementary time-resolved X-ray techniques, including X-ray crystallography, small-angle X-ray scattering and hydroxyl radical footprinting. These experiments will require the construction of instruments such as rapid mixing and substrate delivery devices, followed by integration onto synchrotron beamlines.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: A deeper understanding of enzymatic reactions: development of methodologyfor the direct photocaging of proteins for time resolved studies.
Funder: Wellcome Trust

Abstract: The study of structural changes occurring in proteins during function allows for a deeper understanding of mechanisms and structure-activity relationships. In order toobserve the small conformational changes and transient statessampled by enzymes during catalysis, high­resolution, time-resolved, biophysical techniques must be used, but the applicability of these methods is currently very limited. We will develop new, widely applicable methods for protein photocaging to provide temporal control over reaction initiation using small molecule cross­ linkers to restrict protein dynamics essential for function. Mobile regions within the enzyme will be "pinned" to lock the enzyme in non-catalytic, but substrate-binding conformations preventing turnover before release using photolysis. These tools will promote thewidespread usage time-resolved techniques for the study of biomolecules.· We will apply this methodology to gain unique insight into catalytic reactions in real-tirne, obtaining high-resoulution structures of the different conformations adopteby the enzymes along the reaction pathway using time-resolved X-ray crystallography and spectroscopy.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: Investigating the structure of amyloid using high resolution imaging techniques.
Funder: Wellcome Trust

Abstract: A large number of human diseases are associated with the deposition of amyloid-like aggregates. As amyloid species associated with different diseasesshare structural properties, it is hypothesised a generic mechanism of cytotoxicity may be the underlying cause for many different diseases pathology. The projects key goals are; 1) Elucidate structural information on amyloid fibril ends Ends of fibrils have been shown to interact with synthetic membranes, and so elucidating the structure of fibril ends may provide insights into mechanism of interaction, which may be a pathway of fibril cytotoxicity. 2) Analyse how amyloid fibrils interact with membrane fractions of cells As fibrils have been shown to interact with synthetic membranes, we seek to analyse how they interact with membranes extracted from the cell such as lysosomal membranes. 3) Assess the structure of amyloid in the cellular environment and characterise the cell's response. We aim to image both fibrils and oligomers inside whole cells using high resolution imaging techniques including cryo-electron tomography, in order to characterise how the cell responds to amyloid exposure. These goals will help to elucidate underlying mechanisms of amyloid cytotoxicity, providing insights into the pathology of diseases such as Alzheimer's disease, Parkinson's disease and haemodialysis related amyloidosis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Structural and Dynamical Characterization of Flexible Macromolecules CombiningMultiple Low-Resolution Data
Funder: Wellcome Trust

Abstract: The determination of protein structures is still a lengthy and costly process,success of which cannot be predicted in advance. The discovery of an increasing number of highly dynamic, less structured, or even fully disordered proteins makes the structure determination of such proteins impossible. These proteins are often involved in important biological processes. KNowing the ensemble of structures adopted by such systems would be useful to understand their function as well to design new drugs able to inhibit them. X-ray crystallography or NMR is unsuitable for large flexible systems presenting different coexistingstates.Alternative, low-resolution methods, such as small-angle X-ray scattering (SAXS), hydrogen-deuterium exchange probed by mass spectrometry (HD-MS), provide of which information on the ensemble of structures populated. Suchinformation is too sparse for it to be used as restraints to generate by molecular simulation the real ensemble of conformations populated by the protein. By deriving a coarse-grained molecular model that simultaneously agrees with HD-MS and SAXS data we aim to determine free energy landscapes of proteins with important biomedical interest, such as the transcription factor ó54 and the disordered protein p27.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Creating Diverse Libraries of Bicyclic Peptides Functionalised as Carrier Molecules.
Funder: Wellcome Trust

Abstract: We aim to develop a new class of antibody mimetic based on bicyclic peptides. We will develop chemical methods to create novel bicyclic scaffolds containing two variable loops. The scaffolds will be conjugated to drug molecules or imaging reagents to allow applicationin selective drug delivery or diagnostic purposes. Phage display libraries of these scaffolds will be produced and screened against selected targets. Targets have been selected to investigate a range of potential applications - delivery of drugs or imaging reagents to specific cells, diagnostics and biosensor use. Hits from the screening process will be resynthesized on a large scale and tested in vitro to assess cell entry,specificity and sensitivity.


Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: GENERIC HEALTH RELEVANCE