071B0DBF-D15E-4014-8A00-01FA5366F004Investigating the role of interoceptive mechanisms in the development of biobehavioural markers of drug addiction.Closed2274747StudentshipThe role of interoception, the ability to sense the internal state of the body, in adaptive and maladaptive behaviour remains elusive. The purpose of the present research project, is better to understand the role of the peripheral opiate systems in interoception and its role in maladaptive behaviours, such as those observed in compulsivity, a disease model of which is drug addiction.
Thus, an under-investigated characteristic of addiction is the dysfunction in interoception and the associated impairment in insight, manifested at several levels of integration of the brain, from sensory processing to emotion regulation and meta-cognition. Drug addicts display deficits in cost-benefit decision making tasks which rely on interoceptive mechanisms and its neural correlate, the insular cortex. Furthermore lesions of the insular cortex in smokers have led to an increased likelihood of cessation of smoking. In preclinical rodent models, cocaine methiodide (an analogue of cocaine that does not reach the brain) has been shown to maintain instrumental responses initially reinforced by cocaine demonstrating that the interoceptive properties of cocaine acquire reinforcing properties in individuals with a history of cocaine self-administration.
Despite the compelling evidence showing that interoception and its neural substrate, the insular cortex, contribute to the development of behavioural characteristics of drug addiction, evidence is poor on the underlying molecular and cellular mechanisms. The extent to which central versus peripheral (hence interoceptive) opioidergic mechanisms of opiates contribute to the formation of interoceptive cues and development of addiction-related behaviours for opiates remains to be established.
The aim of this project is to investigate the role of the peripheral opiate system in interoception and its contribution to the individual vulnerability to develop drug addiction. We will combine rodent models of drug addiction developed and refined in the Belin lab with correlational and causal interrogation of neural networks in behaving rats and post-mortem investigations of molecular correlates at the neural and circuit level.
We will initially investigate if rats can discriminate heroin from a vehicle with or without the presence of a peripheral opioid antagonist in a drug discrimination task. This will indicate the role peripheral opioid receptors play in the relaying of interoceptive information of heroin. Subsequently, using a self-administration paradigm, we will test if the blockade of peripheral opioid receptors affects the reinforcing properties of heroin. This will mean pre-treating rats with injections of selective antagonists of peripheral opioid receptors and looking at their effects on acquisition of self-administration and loss of control over heroin intake. Furthermore we will employ more complex self-administration paradigms to look at facets of drug-preparatory behaviour such as compulsive seeking.
Next we plan to use fibre photometry to investigate the cellular dynamics in the insular cortex during heroin-seeking behaviour; thus establishing neural correlates complementing the behavioural experiments. Furthermore, we aim to selectively manipulate neural circuits using optogenetics to functionally study the circuits and potentially investigate synaptic mechanisms. This will enable us to identify biobehavioural markers of the vulnerability to the abuse potential of drugs and better understand the role interoception plays in this process.2024-03-3047D1BADC-597A-4B3F-8462-4C3BF3018C12COVID2019-09-30INCOME_ACTUAL022747476CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified00082994-6774-4061-A06F-00EC3C928876Quantum Algorithms for Nonlinear Differential Equations - QuANDiEClosedEP/Y004663/2Research GrantAbstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.2025-03-30798CB33D-C79E-4578-83F2-72606407192CEPSRC2024-02-01INCOME_ACTUAL19022Please see responses under previous grant code.Please see responses under previous grant code.87568343-BEF7-4798-AF71-BD9AB469FFCF67c9e1dbcf85a1.21287543Aerospace Defence and MarineEnergyManufacturing including Industrial BiotechologyTransport6C378D32-A6E9-4D4A-A68A-4FF77BDB30A1Quantum algorithm for smoothed particle hydrodynamicsComputer Physics Communications5676fb70bcdf4b7d6324d89f78ad6f9bAu-Yeung R2024-01-0165bb80143a2c87.63162841E744FA78-0843-42B0-95FB-202A26D25FADQuantum smoothed particle hydrodynamics algorithm inspired by quantum walksPhysics of Fluids5676fb70bcdf4b7d6324d89f78ad6f9bAu-Yeung R2025-01-0169a6c464f19472.59804193EP/Y004663/2583F7D29-7A76-48E6-9A9C-82E905D0EB83EP/Y004663/129520.382023-05-312024-01-3100082994-6774-4061-A06F-00EC3C928876EP/Y004663/219022.82024-02-012025-03-306CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified07442042-F041-4416-86A3-01B9A875749AStereospecific arylation of organolithiums: synthetic, mechanistic and structural investigationClosedEP/F069103/1Research GrantThe discovery of new small molecules for use as drugs, agrochemicals, fragrances etc. relies on the availability of simple precursors that can be incorporated into more complex target molecules. The research we propose will lead to a simple and efficient way of making some classes of molecule currently considered difficult or even impossible to obtain, a limitation which means that some groups of potential targets are currently unavailable. It seeks to develop a transformation in which an aromatic ring becomes bonded to a lithium-bearing carbon atom in such a way that the shape of the starting material is remembered in the product. The products have the common feature of a highly hindered carbon atom carrying an O, N or S substituent - a feature difficult to construct by existing methods. The proposed reactions proceed by a remarkable mechanism, and by joint investigation involving both synthetic organic and structural inorganic chemists we propose to understand why the reaction works the way it does and to use this understanding to develop further related transformations.2012-06-29798CB33D-C79E-4578-83F2-72606407192CEPSRC2009-01-05INCOME_ACTUAL307704A59C9DD0-1F2E-4D9F-A8C2-53FE4B0588C2Geometry-selective synthesis of E or Z N-vinyl ureas (N-carbamoyl enamines).Organic letters53092b68ca12b903af331fe3c03c7c3cLefranc J2011-01-011523-7052doi_53d01b01bf6823a63774DA85-C8E4-4EE6-A86D-6631FFA76D94Amines bearing tertiary substituents by tandem enantioselective carbolithiation-rearrangement of vinylureas.Organic letters87d0a26c8ad740e63a7f7599d7c0cec0Tait M2013-01-011523-7052doi_55f95c95c94a1301EB6DD861-2778-4DCD-B952-BE8493AF4931Quaternary centres bearing nitrogen (a-tertiary amines) as products of molecular rearrangements.Chemical communications (Cambridge, England)d58d9d7946ebcbf18bb4cbaf0e60ff2dClayden J2011-01-011359-7345doi_53d02d02db8ba8f89282F88F-6180-4698-8768-31A0BDA0D54ELigand effects in the formation of tertiary carbanions from substituted tertiary aromatic amides.Chemistry (Weinheim an der Bergstrasse, Germany)caff8b2906fca05a928c341c8cf9e748Smith AC2011-01-010947-6539doi_53cfc2fc2f619d3dEP/F069103/117FABAB0-878A-49C2-8D3D-6B8F62B1A2F0100Chemical synthesis062ADC54-54DC-4D30-8D45-E6BCB95D1FF220Asymmetric Chemistry23B3EB33-7332-4E38-81A1-3B934872352620Biological & Medicinal Chem.35D9E755-0524-4F1F-8127-C728E8287E5560Chemical Synthetic Methodology074DC7C2-8D1F-48AA-A994-02229C8D90C4Past, present and future benefits from marine biogenic shellfish reef habitats (4463)Closed2785447StudentshipBiogenic shellfish reefs are complex seafloor habitats created by the presence of species such as oysters and mussels. They promote high biodiversity and provide important benefits to humans including improved water quality, food provision and cultural services such as recreational diving and fishing. These habitats were once highly abundant around the United Kingdom but were subsequently severely depleted. Because of the multiple benefits they provide to humans and marine biodiversity, biogenic reefs are of high conservation and restoration interest. However, we lack an understanding of the scale of past loss, the benefits they once provided and what benefits they could provide in the future if they were to be restored. We also need to understand who will benefit from restoration activities and what trade-offs will have to be made to keep these habitats healthy while coastal habitats continue to be heavily used.
To fill these knowledge gaps, this PhD will investigate the past, present and future of ecosystem service provision in biogenic shellfish reefs at a site in the South West of England, the Fal Estuary. A case study approach will allow for in-depth analysis and practical application. It will also develop methodological approaches and generate lessons for wider research and management.
This PhD will work closely with stakeholders and adopt natural and social scientific approaches to understand the implications of past loss and future regeneration of these habitats, and how the benefits and trade-offs of restoration action will be distributed across society. Supervised by experts based at the University of Exeter, Plymouth Marine Laboratory and Natural England, the student will develop a deep knowledge of the challenges facing marine managers while generating an interdisciplinary understanding of approaches to tackle these challenges head-on.
Recent governmental commitments in the 25 Year Environment Plan & Fisheries Act to an ecosystem approach to management, and commitment to a Net Gain approach to biodiversity, means this project has great potential to inform policy and management for biogenic reefs. The successful student will gain the ability to delve into ecological, historical and social science approaches to gain interdisciplinary research skills that they can build on in their future careers in academia, government or industry.2027-08-308A03ED41-E67D-4F4A-B5DD-AAFB272B6471NERC2023-01-09INCOME_ACTUAL027854476CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified034E8798-03A8-4AFF-9AB2-009D19A2EDBEUniversity of Dundee - Confidence in Concept 2014ClosedMC_PC_14099Partnership and ContributionAbstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.2017-09-29C008C651-F5B0-4859-A334-5F574AB6B57CMRC2015-03-01INCOME_ACTUAL700000MC_PC_140996CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified007662E8-5AFF-497A-A1FD-00246571593FProbing the structure and function of a super-rogue photosystem II complex involved in chlorophyll f synthesisClosedBB/V002007/1Research GrantThere is an urgent need to develop new strategies to improve crop yield to feed the ever-growing global population. Crop plants grow because they use the energy of sunlight to drive the conversion of atmospheric carbon dioxide into biomass. This process of photosynthesis is relatively inefficient with much less than 1% of the incident solar energy converted into stored chemical energy. One straightforward way to improve photosynthetic efficiency is to capture more of the sunlight in the first place. Plants rely on chlorophyll pigments (as well as some accessory pigments) to absorb light to drive photosynthesis. The chemical nature of the chlorophyll pigments found in plants necessarily means that photosynthesis is restricted to the visible region of the solar spectrum. In recent years, however, several strains of cyanobacteria, which perform plant-like photosynthesis, have been discovered that make modified forms of chlorophyll that absorb light in the far-red region of the spectrum. If these far-red chlorophylls could be made in plants and assembled correctly in the photosynthetic apparatus, the number of photons of light that could be used to drive photosynthesis could be increased by up to 19%, a considerable increase in efficiency. One of the far-red absorbing chlorophylls is chlorophyll f (Chl f). In order to make Chl f in plants, an important first step is to identify and characterise the cyanobacterial enzyme that synthesises Chl f. In a recent breakthrough, Don Bryant and colleagues in the USA showed that Chl f synthesis was dependent on the ChlF protein subunit which, somewhat surprisingly, was found to be related to one of the proteins present in the well-studied photosystem II complex which catalyses the light-driven oxidation of water to oxygen characteristic of plant photosynthesis. In follow-up work, we have discovered that ChlF does not act alone, as was originally thought, but is part of a new type of PSII complex, which we term the super-rogue PSII complex. The super-rogue PSII complex shows clear similarities to regular PSII but has evolved to make Chl f rather than split water into oxygen. Chl f is made from the Chl a pigment through an oxidation reaction involving molecular oxygen; but the chemistry involved in this process is currently unknown. In this application, we propose to study the structure and mechanism of the newly identified super-rogue PSII complex in unprecedented detail. We aim to investigate whether the super-rogue complex is photochemically active and will test the hypothesis that the super-rogue PSII complex activates molecular oxygen into a reactive form that oxidises a Chl a molecule bound to a specific site in the super-rogue PSII complex. The project involves a team of scientists with skills in microbiology, molecular biology, biochemistry and spectroscopy. Our experimental approaches are diverse and involve working on biochemically pure protein complexes as well studying cyanobacterial mutants expressing Chl f. Ultimately our studies will provide important new knowledge on a new type of photosystem II complex that will underpin future work producing Chl f in crop plants.Synthesis of chlorophyll f (Chl f) in cyanobacteria requires the expression of the ChlF subunit, a paralogue of the D1 subunit of oxygen-evolving photosystem II, but the mechanism remains unclear. In background work we have discovered that ChlF is able to substitute for D1 to form a modified PSII complex with a role in Chl f synthesis rather than water oxidation. We have named this complex the super-rogue PSII complex (or sr-PSII). We have also identified a QD sequence motif in ChlF that is important for Chl f synthesis and possibly the binding of Chl f. To clarify the role of sr-PSII in Chl f synthesis, we propose to: (1) determine the co-factor composition of the sr-PSII complex; (2) use time-resolved absorbance and fluorescence spectroscopies to characterize its photochemical activity; (3) probe the presence of the potential Chl f-binding site by monitoring changes in the optical properties of variant sr-PSII complexes in which the axial His ligand or the QD residues that are predicted to H-bond to the formyl group are mutated; (4) test the possible involvement of reactive oxygen species in Chl f synthesis (5) establish an in vitro system for Chl f synthesis using either the isolated sr-PSII complex or membranes containing sr-PSII to help assess catalytic parameters of the enzyme and (6) test whether heterologous production of Chl f is enhanced by expressing the native 'far-red' PSII subunits of Chroococcidiopsis thermalis which are known to bind Chl f. In parallel we will (7) isolate FLAG-tagged sr-PSII from C.thermalis to assess whether the native system contains additional protein components and then use mutagenesis to confirm the importance of the QD motif in the native system. Overall this work will provide new insights into the synthesis of Chl f which will be important for future work aiming to introduce Chl f into the photosynthetic apparatus of plants as a strategy to enhance photosynthetic efficiency.Understanding the details of Chl f synthesis might in the long-term lead to the development of microalgae and plants with more efficient photosynthesis, especially in far-red enriched environments, such as the lower regions of the canopy, or in dense cultures of algae. In the agricultural sector, beneficiaries could include: companies involved in modifying or selecting plants to maintain and or improve crop yields; farmers who wish to develop new practices for similar reasons; governments and policy-makers interested in developing novel strategies to achieve food security; and the public who will benefit from food security. In the biotechnology sector, beneficiaries include companies who wish to develop microalgae and other related photosynthetic organisms as solar biorefineries for the sustainable production of green chemicals and high-value products. In the bioenergy sector, beneficiaries include: companies wishing to develop alternatives to fossil fuels; governments and policy makers who are interested in new routes to energy security and for new energy sources for developing countries; the military who are looking for alternative fuels for specific and niche uses; environmentalists who need to focus on rational long-term alternatives to fossil fuels. In the environmental and ecological sector, beneficiaries include those wishing to understand more about the role of chl f-producing cyanobacteria in a changing environment. In the education sector, in museums and in the media, there will be benefits from publicising new advances in photosynthesis, one of the most fundamental biological processes and one that has been taught at secondary school and so readily familiar to the general public.
Staff hired for the project will obtain training in cutting edge research in world-leading research centres. Peter Nixon and James Murray are members of the Photosynthesis Research Lab at Imperial College which includes world leading experts in Photosynthesis including Bill Rutherford FRS and Jasper van Thor, with expertise ranging from femtosecond spectroscopy to cyanobacterial physiology. The PDRA and technical staff will be in an excellent position to progress their careers. They will have the benefit of the excellent intellectual environment of a leading university with a tradition of close ties with engineers and industry.2025-07-08198E4A3D-B2DC-45D4-8351-7CCEC4061876BBSRC2021-05-31INCOME_ACTUAL594088Photographs and video describing the 'Solar biobattery' were presented by Dr Marin Sawa at the Eco-Vision Plan Exhibition held in the Art Museum of the China Central Academy of Fine Arts, Beijing, China.Participation in an activity, workshop or similarInternational76F065F8-8D8B-492F-8A9E-2D7CAF590969The "Eco-Vision Plan-Sheng" exhibition involved 28 artists and designers from 15 countries and regions, including Imperial College London, Harvard University, Massachusetts Institute of Technology, and the Netherlands Museum of Architecture and Design, with 32 pieces of art and design projects of 45 species, in an attempt to explore the changes of "living", "habitat", "ecology" and "survival" through a brandnew perspective, so as to explore the visionary new opportunities behind the ecological crisis from the ecological context and cultural background of China, and to call for an international ecological dialogue across cultures, time and space, and fields.65f17f02c372d7.99989833falsePublic/other audienceshttps://mp.weixin.qq.com/s/W5FzwEHpHT57YQKKUOX-zg20235069750United KingdomGBPUnited Kingdomen_GBLong wavelength oxygenic photosynthesis2030-12-02Biotechnology and Biological Sciences Research Council (BBSRC)UKRI2820811C421B-F0C7-423A-B96E-B772EBEB1C6269a71afe26dd61.88535317Public2026-01-01We are studying the role of the newly discovered super-rogue photosystem II (srPSII) complex in the biosynthesis of the far-red absorbing chlorophyll f pigment. Ultimately, fundamental knowledge in this area might lead to the re-engineering of oxygenic photosynthesis so that plants, algae and cyanobacteria are able to improve their photosynthetic efficiency and their growth by harvesting solar radiation in the far-red region of the spectrum . Progress has been excellent. We have been able to improve expression of the srPSII complex in our model system, the cyanobacterium, Synechocystis 6803, so that we can produce up to 8% Chl f/Chl a, a value close to that seen in cyanobacteria that naturally produce Chl f (Qi et al 2025). Using this improved strain we have been able to isolate sufficient amounts of the srPSII complex to determine its structure by cryo-EM to a resolution of 2.46 Angstroms. This has allowed us to identify the binding sites of cofactors and changes in structure that might be linked to its role in Chl f synthesis (Objective 1). In collaboration with the groups of David Bina and Jasper van Thor we have now conducted detailed time-resolved absorption measurements to investigate energy and electron transfer within the complex (Objective 2). We have made mutants in CP43 that specifically affect ligation of a possible Chl f molecule in sr-PSII and have found that Chl f biosynthesis is blocked (Objective 3). Recent experiments have provided evidence that the isolated sr-PSII is able to produce singlet oxygen in the light, and so an excellent candidate for the oxidation of Chl a to Chl f (Objective 4). We have also made excellent progress re-engineering PSII to bind Chl f pigments (Objective 6, Qi et al in preparation) and will continue to collaborate with Dan Canniffe to isolate the srPSII complex from a native organism (Objective 7). Overall, we have achieved 5 out of the 7 objectives originally outlined in the proposal. In addition, during the course of the project we discovered a novel route for the synthesis of the far-red Chl d pigment in PSII (Qi et al, in preparation) and determined several cryo-EM structures of WT and variant srPSII complexes (Zhi et al, in preparation) which were not identified as objectives in the original proposal. Our work on the synthesis of Chl d and Chl f will continue through the award of a 5-year LoLa grant (January 2026- December 2030) to study long wavelength oxygenic photosynthesis.The knowledge gained in this award will provide us with important tools and insights to re-engineer the photosynthetic apparatus of plants and algae to bind Chl f.819C9792-79D8-4300-A874-54A84AD0E0CD65e9e63e75ded6.44979429Agriculture Food and DrinkEnergyEnvironmentManufacturing including Industrial Biotechology71D11936-620E-49ED-95A2-530733796411Enhancing the production of chlorophyll f in the cyanobacterium Synechocystis sp. PCC 6803.Physiologia plantarumddee18ca7eee38c7151f3bc96c583608Qi M2025-01-010031-931767e835a202b47515C1BA3-BF93-4D48-A968-5AFD71F7316FChloroplast alchemy: rewriting the chloroplast genome with high precision.Trends in plant science8ddc4f2aa0e381f4865faac43d0c603eAhmad N2025-01-011360-1385678b71eb7c95cE5B46907-EE5D-4FA1-84A4-98F516E9B593Harnessing the potential of chloroplast-derived expression elements for enhanced production of cellulases in Escherichia coli.PeerJde8bbbd2f23d85097d4f688b6e3fb00bSiddiqui A2025-01-012167-8359679f0f1fb036aDF87C782-BE64-4A97-83B3-DE78453A8559The biogenesis and maintenance of PSII: Recent advances and current challenges.The Plant cell682fbc570b4b7004cf4e63d405ec287bKomenda J2024-01-011040-465166776babc1b5f3.81438547F89D70A1-0E93-464F-A1D2-756384F9A375Accumulation of Cyanobacterial Photosystem II Containing the 'Rogue' D1 Subunit Is Controlled by FtsH Protease and Synthesis of the Standard D1 Protein.Plant & cell physiologyf02c021074de23ceff430d6ed7c73adaMasuda T2023-01-010032-078165d273c983a3c4.7150702751E95953-61AC-4DF1-9821-0A53B435B467The Photosynthetic Electron Transport Chain of Oxygenic PhotosynthesisBioelectricityddee18ca7eee38c7151f3bc96c583608Qi M2023-01-01644a963cdd9fd9.04894541BB/V002007/12D9083F0-05FA-4726-9EB2-3FCC293CAAF948Biomolecules & biochemistry4CCA4C04-0C28-41BE-8869-FA6391A7F00524Microbial sciences52C19A61-0A59-4643-A8D3-583E9A7F811A24Plant & crop science6997E843-AD07-4064-B67D-D4A928309DB448Biochemistry & physiology3D51C146-5AFC-42C5-93BB-17CC751DE0DA24Bioenergetics19F550D7-1AE6-4B86-87B9-2C2934306C3424Environmental Physiology07828D21-A20E-4368-9D88-015A30686E6FRole of avian dendritic cellsClosedBBS/E/I/00001302Institute ProjectAbstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.The UK poultry industry faces many challenges to remain sustainable, including moves to more extensive rearing systems; withdrawal of antibiotics and other drugs such as anti-coccidials; resistance and residue problems with anti-helminthics. These will all impact on poultry health, but also the potential to impact on human health. Increased incidence of zoonotic pathogens in chickens, such as avian influenza, could lead to an increase in these diseases in man. One approach to these challenges is to develop novel and more effective vaccines. For this to be a realistic and sustainable approach, we need a better understanding of host-pathogen interactions in chickens. This proposal seeks to build on our unique capability to grow dendritic cells (DC) in a non-mammalian species. DC in mammals are professional antigen presenting cells, providing a link between innate and adaptive immune responses, driving the adaptive response to that necessary to clear infection with a particular pathogen. In mammals, antigen presentation takes place primarily in lymph nodes (LN). The chicken, like most non-mammalian vertebrates, lacks LN but antigen presentation still occurs. This proposal forms part of our efforts to understand antigen presentation in a species lacking LN. This proposal aims to understand DC biology in the chicken in more depth. Firstly, we wish to define the phenotype of DC, both immature DC and those matured in vitro under different conditions, in more depth. In mammals and presumably in the chicken, DC travel to the site of infection, and thence to the site of antigen presentation, under the influence of chemokines. We intend to determine which chemokines have functional effects on chicken DC. Preliminary data suggests that DC can be matured to either a Th1 or TH2 phenotype. We will determine if DC can bias T cells to a Th1 or Th2 phenotype in vitro. We then want to characterise ex vivo-isolated DC, and finally begin to analyse chicken DC migration in vivo.unavailable2010-05-13198E4A3D-B2DC-45D4-8351-7CCEC4061876BBSRC2007-05-14INCOME_ACTUAL191535BBS/E/I/000013026CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0355D174-E641-4AEC-A421-00DB6DF1D88BDisruption to the development of maternal sensitivity: the impact of depression and alcohol use during pregnancy on mother-infant interactions.ClosedES/I004823/1Research GrantAbstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.2011-09-294A6A6A2B-EA26-4C59-867B-B531CEFE8374ESRC2010-09-30INCOME_ACTUAL80573Disruption to the development of maternal responsiveness?Participation in an activity, workshop or similarAE7FB033-8B82-46A8-AAA7-074D244936DCPresentation and discussion of findings at Oxford University seminar series, Department of Psychiatry, April 2011r-3963555352.72839982ab347c2falseReduced maternal responsiveness in depressed mothers may explain the negative impact of depression on child development. Antenatal depression is also associated with poor child development, independently of later depression. However, the mechanism to explain this is unclear. One explanation is that antenatal depression leads to poorer child outcomes by disrupting the preparation of maternal responsiveness to infants as it develops during pregnancy.
We used longitudinal data from a UK cohort study (ALSPAC), to investigate whether antenatal depression is associated with reduced maternal responsiveness, independently of depression close to the time maternal responsiveness was measured. The study included measurements of antenatal and postnatal depression and an observation of the mother interacting with their infant at 12 months. The complete case sample comprised 875 mother-infant pairs.
Women with high depression scores during mid pregnancy, even if they had low scores at the time of the maternal responsiveness measurement, had reduced maternal responsiveness compared to women with consistently low depression. The results suggest that antenatal depression may disrupt the development of maternal responsiveness. Therefore, maternal responsiveness remains impaired in antenatally depressed women even if their depression improved.
Due to the importance of maternal responsiveness for child development, we investigated other exposures during mid pregnancy that may disrupt its development. We found that women who drank >=1 glass of alcohol a week during pregnancy showed reduced maternal responsiveness after birth.
This study provides evidence that factors during pregnancy can effect later responsiveness of a mother to their infant.Further research into the antenatal development of maternal sensitivity.CB1D6D51-6AE8-4C25-9D40-96A09F9302E9r_4738116383b2f2d75aCommunities and Social Services/PolicyHealthcare11E82523-EC2F-4E69-AB67-B1F29120472FThe association between observed non-verbal maternal responses at 12 months and later infant development at 18 months and IQ at 4 years: a longitudinal study.Infant behavior & developmentf5da9cfdd5d9ce7e846f3e468641c368Pearson RM2011-01-010163-6383pm_53cbfefbfef24b780F9987261-B43B-4E88-8F82-08DA005CF0EEThe impact of alcohol use during pregnancy on maternal responses after birth.Archives of women's mental healthf5da9cfdd5d9ce7e846f3e468641c368Pearson RM2012-01-011434-1816pm_53cc012c012118e1943F62DDC-5E3C-49BA-8800-DC78C6DB15DCDisruption to the development of maternal sensitivity : the impact of depression during pregnancy on mother-infant interactions00b96264b0b32fd80b5a302577788391Rebecca Pearson (Speaker)2011-01-01r_3747621307cb14e778ACBF18CE-2FD7-402A-9340-DAF9CDB2A855Disruption to the development of maternal sensitivity? : the impact of antenatal depression on mother-infant interactions after birth94955bfabda867be00dbc6fa16850345Rebecca Pearson (Author)2011-01-01r_1061726182cb42511896FFD089-3593-4C5B-AE7E-5EE223935714Disruption to the development of maternal responsiveness? The impact of prenatal depression on mother-infant interactions.Infant behavior & developmentf5da9cfdd5d9ce7e846f3e468641c368Pearson RM2012-01-010163-6383pm_53cc013c013a58dd3ES/I004823/157835945-1CF3-4554-A46B-1504261EB208100Psychology57835945-1CF3-4554-A46B-1504261EB208100Psychology035A5424-F902-4927-9457-01FCF86F5E46Development of a modelling and simulation framework to optimize layered bearing architecturesClosed2629596StudentshipPlain half shell journal bearings are used in a wide range of turbomachinery shaft applications, including marine, automotive and power generation applications. These bearings have to be conformable and fatigue resistant under quite complex service loading conditions. Complex layered architectures may offer a tuneable approach to optimizing fatigue performance in terms of controlling initiation behavior and growth behavior (sometimes these two effects may play out in opposing ways). Currently a somewhat empirical approach is employed by manufacturers to identify the number, thickness and type of the different layers in the thin overlay coating. Work at Southampton University has now identified a consistent way in which to track the initiation and early stages of fatigue growth (using thermography techniques) and provided a detailed assessment of crack initiation and growth in the various layered constructions provided to date (using FIB and other advanced microscopy techniques). A follow-on PhD is now planned to apply these newly developed and validated techniques (mechanical testing, strain analysis, thermography and advanced microcopy characterization) to a systematic set of variations in overlay coating architecture (spacing, thickness, separation etc of hard and soft layers). These will be produced by the student via electroplating approaches at the sponsor company's new purpose built laboratory and they will then evaluate this systematic set of parametric explorations in terms of how this controls fatigue behavior. An important component of the PhD will be to develop and validate a materials modeling and simulation framework based on these findings to investigate optimization of the layered architecture for fatigue performance.2020-09-29798CB33D-C79E-4578-83F2-72606407192CEPSRC2017-09-30INCOME_ACTUAL026295966CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0096EA78-5A08-49FA-9F1F-003344C4FA97Investigating the Regulation and Replication of R-loops at TelomeresActive2934080StudentshipEukaryotic chromosomes are capped at each end by specialised nucleoprotein structures called telomeres, which are mutated or altered in essentially all incidences of cancer. Telomeres are transcribed into a non-coding RNA called TERRA, which forms a three-stranded R-loop structure in which the RNA remains bound to the template. R-loops are particularly prevalent at telomeres in ALT-type cancer cells, where they are thought to prevent efficient replication of the chromosome end. This project will identify novel R-loop regulating factors at telomeres and examine how TERRA-based R-loops regulate and influence the telomere replication process.2028-10-05C008C651-F5B0-4859-A334-5F574AB6B57CMRC2024-10-06INCOME_ACTUAL029340806CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified07832667-2BC4-4857-A4FF-019CD66E6D4FA CELL ATLAS OF THE DEVELOPING HUMAN SENSORY NERVOUS SYSTEM: INVESTIGATING DEVELOPMENT TO UNDERSTAND DISEASEClosedMR/W000830/1FellowshipContext of the research:
Pain is the main reason that diseases of the muscles and joints lead to disability. In particular, for the tens of millions of individuals who suffer from Osteoarthritis (OA) , pain can be debilitating at end stages and be present even at rest, preventing the use of joints in the hand, hip and knees. Around the world, this tremendous societal and monetary burden is set to rise alongside an aging population. Currently, there is no cure for osteoarthritis and end stage disease is treated with joint replacement, a costly and major operation. Importantly, we lack effective pain-relief medications for OA.
Until recently, it was thought that wear-and-tear of the protective lining of the joint, and increased bone-to-bone contact is what leads to pain in disease. Interestingly, recent studies from various research groups have shown that new nerves sprout into the joint surface as part of the disease process of OA. These nerves appear to be present in individuals with painful OA, but is absent in those with less painful OA. In adulthood, nerves normally have limited capacity to grow, so this leads us to think that disease nerves are driven by processes similar to those that are active when we our nervous system begins to develop while an embryo in the womb.
The objective of this project is therefore to apply cutting edge technology to investigate the development of the human sensory nervous, comparing it to what happens in disease, with the aim of identifying novel ways of interfering with it, in order to treat pain.
Aims and objectives:
First, we aim to understand how the sensory nervous system forms in the developing human. To achieve this, we will use single-cell sequencing technologies. This will allow us to detect what drives different types of developing nerves, one by one. We aim to form a classification system for these nerves, sorting them by their function, for example, some nerves may sense touch and others may sense pain, and they might be driven by different signals to grow.
Secondly, we will map the distribution of these developing nerves in space, using a type of technology known as spatial transcriptomics. This will form an atlas of the nerves throughout the body and allow us to understand how nerves are queued to grow towards their destination during development.
Then, we will map nerves in the diseased human osteoarthritic knee joint in adulthood. We will apply innovative technologies to first identify areas where nerves are present, and then sequence the genes activated within these areas. This will allow us to understand whether nerves growing in disease are similar or different to nerves that grow during development.Lastly, we will use computational programs to compare developmental nerves to disease-nerves. This will allow us to decide how to target the disease-nerves.
Potential applications and benefits:
We will be the first group to perform single-cell sequencing on the developing nervous system in human. This will allow discovery of new cell-types, and create an atlas for them throughout the human body.
These findings will further our understanding of all painful conditions. In the case of osteoarthritis, it may allow us to identify targets that can be exploited to allow depletion of the pain-associated nerves described above. We aim to disseminate our findings to allow public access by the research community. This will lead to improved understanding of other diseases, such as in cancer, where nerves can also sprout during the disease process.
In the long term, our findings can also be applied to help improve models of nerves grown in the laboratory, and potentially also inform ways of promoting nerves to regenerate in the body.I aim to test the hypothesis that the process of neo-innervation of the adult osteoarthritic joint by pain-associated nerve afferents recapitulates transcriptional profiles that are active in the developing human fetal sensory nervous system, with a view to obtain mechanistic insight, and identify potential therapeutic targets for pain.
First, I will create the first human cell atlas (HCA) of the developing sensory nervous system. Secondly, I will identify the transcriptional profiles of adult osteoarthritic joint cartilage that is innervated by pathogenic nociceptive afferents (absent in the osteochondral junction in health). Finally, I will compare the transcriptional profiles in these states to test our hypothesis, and additionally prioritise potential treatment targets.
Single-cell RNA sequencing(scRNAseq) will be applied to human dorsal root ganglia samples between the fetal ages of 6 to 20 weeks, with 1-2 sample(s) each gestational week.
To create a spatial atlas, single-nuclei RNAseq and Visium RNAseq (10X genomics) will be applied to sequential slices of the same tissue sample at ages of 6-7 weeks and 18 weeks. In adult osteoarthritis tissue, multiplex in situ hybridization will be used to identify regions of interest by neuronal markers followed by the use of Nanostring GeoMx for targeted sequencing. Finally, computational integration will be applied to reveal reciprocal matches in cell states between development and disease. Potential treatment targets will be tested in further projects through in vitro and in vivo experiments.
The study will create the first HCA of the developing nervous system and transcriptional profiles of disease, the findings will provide new insights into normal human development as well as disease, with therapeutic implications. The developmental dataset can also be studied to understand nerve regeneration in adulthood, with implications in regenerative medicine, and in generating in vitro models of sensory nerves.2025-01-01C008C651-F5B0-4859-A334-5F574AB6B57CMRC2021-09-30INCOME_ACTUAL170338Wellcome Sanger InstituteUnited KingdomHuman Developmental Cell Atlas (HDCA)2AAD1935-9966-4117-AA24-5063C710F9DBCompleted first trimester human fetal brainstem multiomic atlas (single-cell resolution).
Completed first trimester human fetal skull multiomic atlas (single-cell resolution).640f3e4e29cd47.76253476-1Following completion and analysis of the human cell atlases i have generated as part of the fellowship, the data will be deposited to the HDCA and made publically available to other researchers.I have collaborated extensively with the HDCA through my current ongoing work in mapping the cells of the
1. Developing fetal brainstem, which contains sensory neurons projecting to the head and neck
2. Developing craniofacial skeleton, which receive neurons projecting from the brainstem (both sensory and motor)
I have contributed to these projects (which form part of my PhD thesis), through tissue sample acquisition, processing, data generation and data analysis and interpretation.Charity/Non Profit2021-01-01Human Cell AtlasHuman Developmental Cell Atlas (HDCA)F244D9E6-FC1D-4C1A-97AD-9A72456DD81CForthcoming submission of publication to a major journal.65f041d186ccf6.57492108-1Data generation, intellectual input into the analysisI have undertaken analysis of spatial transcriptomic data generated as part of the "whole embryo" project which involves single-cell multiomic profiling of all regions of human embryos from 5-6PCW.
For this analysis, I focused on understanding development of the Dorsal Root Ganglia in the spinal column, and limb/joint developmet, relevant to aims of my funded fellowship.Charity/Non Profit2023-01-01Patient group workshopA formal working group, expert panel or dialogueNational738DC9F9-B926-4544-9FC7-13C7F7FA931BThrough my research, which is focused on atlasing tissues associated with musculoskeletal disease and pain, I have engaged with other members of the research group in which i am situated, in order to deliver a focus group in liaison with Rare Autoinflammatory Conditions Community (RACC-UK) in order to goal-set for future studies of CRMO (chronic recurrent multi-focal osteomyelitis); a chronic, painful MSK condition in the paediatric population.640f4723a6cd76.35603229falsePatients, carers and/or patient groups20221000United KingdomGBPUnited Kingdomen_GBAcademic clnical fellowship2028-08-01National Institute for Health and Care ResearchDD600E87-1BE7-4F35-9666-6C955976283567ae11ed50c2b1.43579043Public2025-07-31I have applied single-cell atlasing technologies to construct a cell atlas of the human fetal skeletal system in the first trimester.
This encompassed use of single-nuclei RNA and ATAC sequencing; as well as 10X visium to generate a comprehensive atlas across > 50 samples.
The focus of the dataset is on the major synovial joints and the suture joints of the skull.05AE1CDF-9428-4AE0-81F3-A94382BA1CECthis dataset has revealed the cell states during development of the osteogenic mesenchymal lineages in the human; this has previously evaded our knowledge due to technical challenges and difficulty of tissue acquisition.640f492c747710.27293871falseA single-cell atlas of the first trimester human fetal skeletal systemDatabase/Collection of data2022In the age of single-cell RNA sequencing, several tissues remain under studied due to technical challenges associated with cell-dissociation and extraction.
One such tissue, which is of interest in my fellowship project are bone and joint tissues, for which the cell types are embedded in dense collagen matrices and in calcified bone.
Through optimisation of existing protocols to isolate single-nuclei suspensions, we have developed a way to isolate fetal synovial joint bone nuclei, and produced good quality datasets using single-cell technologies.4D8F34ED-7382-47EC-835C-D99C8F8EB134We will publish this methodology in a manuscript in an open access journal once the body of related work is completed.640f47e4a9e7a5.50800482falseIsolation of stromal nuclei from fetal tissue samplesBiological samples2021C58EC2C7-DA23-4614-A860-7E8D76CB1337A multi-omic atlas of human embryonic skeletal development.Nature52e13c784cd812c8971c88b9a7d418b5To K2024-01-010028-083667ae0e18c78f98.964313071BED23B9-572B-4D7B-BECA-6148A646331DSingle-cell integration reveals metaplasia in inflammatory gut diseases.Naturebfdba03a9e5f731cd4b941728904275cOliver AJ2024-01-010028-083667ae0e194d1da1.56271164FFEB1531-F593-42BF-BD3F-85F8AE5A0CBCA spatial human thymus cell atlas mapped to a continuous tissue axis.Nature2fa89500e56c76039723276215b8cbabYayon N2024-01-010028-083667ae0e192c8243.9330957018C2CA1F-C4DD-49A6-8890-F784AFC555CFA multiomic atlas of human early skeletal developmentNature (currently under revision after first review)b4fea4d855831a0cd9b6e3c5b07e4204Ken To65f040bfcb1709.44469741MR/W000830/16CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0799175D-EB70-4F8A-87FA-0054F2B2D7D5Grey Milk and Lost Kin: Re-sounding, Re-visioning, and Re-membering Trauma in the Scottish Gypsy Traveller ArchivesClosed2775728Studentship"We have no right to any form of writing, that is our curse," proclaimed a 1950s Gypsy Queen (Lecouteux 2016, p.6). This research transforms the curse of "internalised oppression" (Davis 1981) as my ancestors incite an uprising by way of the archives. My practice-based research aims to retrieve and revalue "subjugated knowledge" (Foucault 1980) through critical archival interventions, place-based approaches, experimental filmmaking and literary practices. I will interrogate the absence and rupture of 'knowing' caused by forced assimilation and cultural dispossession, exploring the sociocultural impacts of knowledge suppression and its far reaching mechanisms of denial. Grounded in lived experience, this study adds to urgent scholarly work seeking to transform the cultural ramifications of colonial legacies which actively erase Indigenous and Local knowledge systems, their cultural heritage, and collective identity. My family avoided persecution by keeping our genealogy secret and disavowing our Scottish Gypsy Traveller ancestry.From the mid twentieth century onwards, vast institutional archives were amassed in Scotland of the travelling peoples' oral traditions. Newly accessible online since the pandemic, I will subvert these archives to activate the affective, cultural and experiential injuries of "racial capitalism", drawing out the traumatic traces of invisibility and exclusion (Gordon 2008). I will then reframe and valorise the Gypsy Travellers' knowledge system, building power relations through "re-citation" with other subjugated cosmologies. Finally, I will undertake an intersectional exploration emphasising the feminist and decolonising interventions of re-sounding, re-visioning and re-remembering, mobilising solidarity and liberatory consciousness to counteract "epistemic violence" (Galván-Álvarez 2010).Thus, I will create a body of work, including film, art and audio works, that act as "a counter-archive of knowledge"-underpinned by Indigenous narrative and listening strategies (Horavoka 2017). In this way, my research will contribute to experimental sonic and cinematic techniques and methodologies, whilst generating critical pathways that pluralise knowledge systems more widely.2025-03-301291772D-DFCE-493A-AEE7-24F7EEAFE0E9AHRC2022-09-30INCOME_ACTUAL027757286CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified07BECE74-80E1-4CA9-9643-012F35B2F636Medical diagnosis through the application of Artificial IntelligenceClosed2642845StudentshipThis project will look at some aspect of medical diagnosis through the application of Artificial Intelligence which will be determined in more detail by the end of year one2025-09-29B71128B2-1767-4204-9D19-EEB1383C2D1EOther NPIF2021-09-30INCOME_ACTUAL026428456CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified07D6E9EA-F096-44BF-BAF6-01F2D3DE4489DNA methylation age acceleration: examining the role of socioeconomic position and dietClosed1907672StudentshipThis project proposes to investigate whether socioeconomic position is associated with DNA methylation in the MRC National Survey of Health and Development (1946 birth cohort), and whether indicators of diet might mediate any associations found.2025-09-294A6A6A2B-EA26-4C59-867B-B531CEFE8374ESRC2017-09-30INCOME_ACTUAL0The first stage of analysis found an association between individuals' life course socioeconomic position (that is, parental occupation, educational attainment, adult occupation and household income) and epigenetic markers of biological ageing at age 53 in a sample of individuals from the MRC National Survey of Health and Development, a British birth cohort of individuals born in 1946.
Epigenetic ageing biomarkers are one of a set of novel ageing biomarkers based on molecular biology. Other biomarkers in this group included telomere length and biomarkers based on transcriptomics, metabolomics and proteomics. Epigenetic ageing biomarkers have been found to be better at quantifying biological ageing than the other novel ageing biomarkers in this group. Greater epigenetic ageing has been associated with increased risk of mortality, increased risk of cancer and cardiovascular disease, and worse ageing outcomes such as poorer physical function and frailty. The analysis examined first and second generation epigenetic ageing biomarkers. The research makes use of second generation epigenetic ageing biomarkers which have not been examined in UK data to date.
The results show that early life disadvantage is associated with greater midlife biological ageing. There is also evidence that disadvantage across the life course is associated with greater biological ageing in midlife depending on the epigenetic ageing biomarker examined. The results indicate that social disadvantage is associated with worse biological ageing.Greater epigenetic biological ageing has been associated with increased mortality risk, increased risk of cancer and cardiovascular disease and worse physical functioning in old age. The results show the importance of preventative measure for later life health and ageing that focus on reducing societal inequalities, and also suggest that these measures should be applied from early childhood and beyond.8F5A0202-B472-45A6-B1DB-7A9C7F2114C45e5f9863ab6364.01330492Communities and Social Services/PolicyHealthcareA72B9CB1-8503-4BB8-A79A-1164687A81DBSocioeconomic position and body composition in childhood in high- and middle-income countries: a systematic review and narrative synthesis.International journal of obesity (2005)efb0009ac942206954268ce9341f9093Bridger Staatz C2021-01-010307-05656213685d898d33.163929044ED42792-6EBA-4500-88D5-B4EDD94EAD93Life course socioeconomic position and body composition in adulthood: a systematic review and narrative synthesis.International journal of obesity (2005)efb0009ac942206954268ce9341f9093Bridger Staatz C2021-01-010307-05656213685d5315c4.37496201ACEB7C6A-A6C2-4B2E-96B4-9A3913862679Life course socioeconomic position and DNA methylation age acceleration in mid-life.Journal of epidemiology and community healthcf4482a475dc1df134493fab62407a61George A2021-01-010143-005X6213685d1b6cf4.7104483519076726CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified00985EBB-E6BE-41BC-BF76-003FE42B0869Exploiting natural product assembly line genomics and synthetic biology for discovery and optimisation of novel agrochemicalsClosedBB/K002341/1Research GrantMicroorganisms including bacteria and fungi are everywhere in the environment. Although a few microorganisms have roles in causing disease, most microorganisms are harmless, and many of them actually produce medicines and chemicals useful to man. A good example is penicillin which is produced by a fungus and used as an effective antibiotic in human and animal medicine. Other compounds include anticancer drugs, drugs which allow organ transplants by suppressing the immune system and anticholesterol drugs. Many microbes also produce compounds of huge importance in agriculture which can be used as insecticides, herbicides and fungicides. It is estimated that around 40% of current world food productivity would be lost without these. As the world population grows and as climate change takes hold efficient food production and food security will become more important and the roles of these naturally occurring compounds will increase yet further.
Penicillins came into use during the 1940s, and for around half a century research provided a steady stream of newly discovered natural products. However, traditional approaches began to fail as more and more compounds were discovered because the available methods kept finding the same known compounds. This led companies to try other avenues to provide new compounds for use as medicines and agrochemicals - however fully synthetic compounds have not proven as successful as natural products.
Over the past decade academic research, much funded in the UK by BBSRC, but also an international effort, has led to the understanding that most microbes have the capacity to produce very many more compounds than observed - perhaps only 10% of a given organism's potential has been collected to-date. Genome sequencing has revealed that the biosynthetic potential of known organisms is huge - and new organisms are continually being found. If the 90% of unused genes in just the known organisms could be activated there could be a strong flow of new compounds for testing as medicines and agrochemicals - this flow could be increased to a flood if a generic technology could exploit all the as-yet undiscovered microbes.
In parallel with the genome sequencing efforts huge progress has also been made in understanding the genes, enzymes and chemistry involved in the microbial synthesis of secondary metabolites. This now allows the pathways responsible for the synthesis of secondary metabolites in microbes to be engineered to produce yet more compounds. The confluence of cheap whole genome sequencing and the ability to engineer microbial pathways underpins this research proposal.
The project will be a collaboration between 6 partners: the Challis group at Warwick, expert in microbial genome analysis; the Leadlay group at Cambridge, expert in bacterial polyketide biosynthesis; the Micklefield group in Manchester, expert in bacterial peptide production; the Cox group in Bristol expert in fungal biosynthesis; and Syngenta and Biotica, UK companies with major interest in secondary metabolites. We will obtain the genome sequences of bacteria and fungi known to produce agrochemically useful compounds. We will find the genes responsible for their production and recombine and engineer them to make higher amounts of these compounds, and then libraries of related compounds for testing. We will work with partners in the international agrochemical company Syngenta to develop these as new herbicides, insecticides and fungicides, while partners at the Biotechnology company Biotica will focus on compounds with use in human medicine. Overall we aim to develop a platform technology which can exploit the potential of microbes for the production of useful compounds for use in agriculture and medicine. We will also disseminate our results widely and undertake outreach activities to increase public awareness of industrial biotechnology and the role of genetic engineering and microbiology in ensuring future food security.This project will exploit a major opportunity which has arisen due to three factors: the dramatic lowering in cost of microbial full genome sequencing; the recent advances in rational engineering of microbial metabolic pathways; and the re-emergence of interest in natural products as new agrochemicals and drugs by international companies. The project will bring together 6 partners: the Challis group at Warwick, expert in genomics-based natural product discovery; the Leadlay group at Cambridge, expert in bacterial polyketide biosynthesis; the Micklefield group in Manchester, expert in bacterial nonribosomal peptide bioengineering; the Cox group in Bristol expert in fungal biosynthesis; and Syngenta and Biotica, UK companies with major interest in secondary metabolites. The collaboration will allow the 6 partners to embark on an ambitious programme to rapidly sequence the genomes of 40 microorganisms with the known ability to produce compounds with potential in the agrochemical arena. New bioinformatic methods will be used to rapidly identify biosynthetic gene clusters and link them to the synthesis of particular compounds. Engineering will then be employed to increase titres and activate 'silent' gene clusters with potential to produce bioactive compounds. Focussed libraries of target compounds will be made by biosynthetic engineering and the libraries used for SAR by Syngenta. Compound activity will then be maximised by a combination of biosynthetic engineering and synthetic chemistry. The partners will also engage in dissemination, training and outreach activities designed to maximise the impact of the project in the academic, industrial and public communities.Short term: The project will have high impact with the directly involved partners. For the companies involved it will allow them to gain access to and exploit the significant pool of knowledge and experience within the UK academic community in the area of biosynthetic engineering and synthetic biology. In particular this will help give Syngenta a competitive advantage and maintain their significant research and employment base in the UK. It will have a significant impact for the 4 academic groups involved because it will allow them to collaborate and disseminate best practice in complementary areas of research - this is likely to lead to more publications and publications of higher impact and thus help maintain the UK's competitivity in this area. It will help the academic groups focus their efforts on the development of new products and bring knowledge and experience from commerce into the academic arena. This in turn will enable the academic groups to form new and effective collaborations.
Medium term: The research has a good likelihood of leading to the development of new products with utility in the agrochemicals sphere which will underpin improvements in food security internationally. The project will train at least 8 PDRAs and up to 4 students in the area of synthetic biology as applied to industrial biotechnology. These people will form a core of expertise which will benefit both academia and industry.
Long term: The development of a platform technology for the systematic exploitation of microbes for the development of new medicines and agrochemicals will form the basis for the development of new technologies using synthetic biology. For example it is likely that similar methodology will underpin the development of new materials, new fine chemicals and processes, new methods to access biofuels and new methods to access foodstuffs.2018-07-30198E4A3D-B2DC-45D4-8351-7CCEC4061876BBSRC2013-07-31INCOME_ACTUAL3552006Syngenta International AGUnited KingdomSyngenta Ltd (Bracknell)Syngenta screening collaborationF291FD3E-0E2B-4021-A208-8F11A9ADC357none yet!
yes, this multidisciplinary - combines natural products chemical biology and crop scinece.622b27368bc167.02189879-1Tested compounds supplied in herbicidal, insecticidal and fungicidal assaysSupplied novel natural products for biological testingPrivate2022-01-01Syngenta International AGUnited KingdomSyngenta Ltd (Bracknell)Syngenta matched funding838F475D-DA34-49D5-96D4-C21DEF046C0CThe pesticidal activity has been determined of several natural products and derivatives that have hitherto never been tested by Syngenta. In some cases potent agrochemically-relevant biological activity has been observed. Discussions with Syngenta about how to further develop these compounds are ongoing. In addition, Syngenta have increased their activity in the area of natural product discovery and development, in particular through recruiting to specialist in this field who received postdoctoral and or PhD training in our group at the University of Warwick.5aa69d5b758843.58753452-1Our collaborators have have investigated the pesticidal activity of the natural products we have isolated.We have isolated and structurally characterized several tens of natural products from Actinobacteria and filamentous fungi.Private2013-01-01Schools mini-projectParticipation in an open day or visit at my research institutionRegionalCE1BDDE2-CBBB-4A1F-AB3F-D02E7305DC52"Discovery of Agrochemical Natural Products" practical science projects were run with groups of GCSE and A-level students from local schools in economically disadvantaged areas. This involved the students in a series of visits to our laboratories on Wednesday afternoons to carry out practical laboratory tasks and data interpretation exercises, which guided them through the steps from isolating and characterizing a new microbial strain, through assessing its potential to produce novel bioactive metabolites, to elucidating the structures of the metabolites. At the end of one of the projects, the students were accompanied by the PI/researchers/school teachers on a visit to Syngenta where the students gave a presentation on their project to colleagues in the company. The participants were also given a tour of the company's facilities. Postgraduate students from the lab were involved in the preparation and delivery of the project, in addition to the researchers employed on the project. At our grant partner Manchester, several groups of year 12 students visited for a day. Their studies and interests, as well as their future plans, were discussed. They were provided with an introduction to Streptomyces and biosynthesis of secondary metabolites with a particular focus on the wide variety of antimicrobials and agrochemicals that are of Streptomyces origin. The process of how early stage drug discovery has changed from screening to the development of genome sequencing and synthetic biology and how modern techniques are used in the lab to create bespoke compounds of interest was discussed. The students had plenty of opportunity to ask questions in an informal setting and engage with a variety of researchers from at different levels (masters students, PhD students and postdoctoral research fellows). The overall goal was to develop understanding of how life in a research lab actually operates and the exciting technologies that are driving innovation.5aa69989083ab7.69062616falseSchools2013,2015,2016113573United KingdomGBPUnited Kingdomen_GBNewton International Links2019-09-01British Council261846416324FE796-BA4D-4DD4-8C36-C4409B6374695aa691b05c2820.12029360Charity/Non Profit2017-03-31198477United KingdomGBPUnited Kingdomen_GBGEN2NCE - a synthetic biology platform for natural product discovery2022-03-02Biotechnology and Biological Sciences Research Council (BBSRC)BB/T017163/1DC84B509-23AD-44E6-9F75-4EF28DF93881622af61f7cbea6.67227175Public2020-07-3145508212AustraliaAUDAustraliaen_AUCentre of Excellence for Innovations in Peptide and Protein Science2028-01-02Australian Research CouncilCE2001000129A0531CF-94A1-4596-A416-16560B6CE271622afa9d7b8ec0.19961364Public2021-01-01121493United StatesGBPUnited Kingdomen_GBIndustrial Contract2018-09-01AchaogenEC04DDF5-01C5-47FC-A019-1D2C71D2DBC95aa6923aead1a2.48027304Private2017-09-3051903United KingdomGBPUnited Kingdomen_GBWarwick Impact Fund2019-04-01University of Warwick0E25C235-ABFE-466B-AD10-AD593C7E7FD85aa69407a881c1.88667621Academic/University2018-07-31209834United KingdomGBPUnited Kingdomen_GBICURe Follow on Funding Grant2023-08-01Innovate UK4493034FE3E03-E170-4D83-AC77-BE01F917124E622af7b81247f8.20269082Public2021-08-3110521613United KingdomGBPUnited Kingdomen_GBBBSRC/EPSRC Multidisciplinary Research Centres in Synthetic Biology2020-05-01Biotechnology and Biological Sciences Research Council (BBSRC)BB/M017982/1B6E2B2BF-9B98-4E90-8F44-AA54F3CCC20B5aa690f060f0e2.00651157Public2015-05-311000United KingdomGBPUnited Kingdomen_GBBBSRC-IAA2016-07-01Biotechnology and Biological Sciences Research Council (BBSRC)BB/IAA/Warwick/15BA54ED38-3639-4FD1-A277-FA2EF651218458c81399368945.85465284Public2016-01-01Our findings are being used by Syngenta in agrochemical discovery programs. To date we have supplied them with more than 70 natural products for pesticidal screening, of which 24% showed activity.
We have also received financial support from the Warwick Impact Fund to further develop some of the methods we established during the course of the project and explore their commercial potential. We have participated in ICURe, leading to the award of Innovate UK funding to establish a spin out company.2014CA6B721E-40DB-4E97-BC50-51CB53978AC1Economic5464cc32244496.60457391Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical BiotechnologyThis project has allowed us to build on earlier work to develop what appears to be a widely applicable strategy for the activation of silent biosynthetic gene clusters.BB/K002341/1F465EC18-499D-4701-994E-74A52F20C4F8In December 2017 we received funding form the Warwick Impact Fund to explore the commercial prospects for this strategy with a view to establishing a spin-out company. In 2019, Dr Douglas Roberts, who worked as a postdoctoral research fellow on the project, successfully completed the midlands Innovation to Commercialisation of University Research (ICURe) program and in 2020 we were awarded Innovate UK funding to set up a spin out company (Erebagen). We are currently in the process of securing matchin Venture Capital investment to enable us to set up the company.No5aa69aed03b3b0.91238917Protection not requiredA genomics-driven platform for novel bioactive natural product discovery44 Streptomyces and 10 fungal genomes have been sequenced. Numerous novel specialised metabolite biosynthetic pathways have been discovered by analysing the genome sequences. The metabolic products of numerous pathways have been isolated and sent to Syngenta for biological testing. Several pathways of interest have been experimentally elucidated. Examples include: thaxtomin A, TMC-86A, malonomycin, cycloaspeptide, strobilurin and marginolactones. The thaxtomin and cycloaspeptide pathways have also been manipulated, providing access to novel derivatives of the natural products. A wide range of methods for activating biosynthetic gene clusters in Actinobacteria that are poorly expressed in laboratory cultures have been explored, leading to the identification of a method that appears to have general applicability. This method has been applied to the discovery of a range of novel metabolites, the structures and biological activities of which are being elucidated through follow-on funding.Syngenta will take our findings forward to help develop novel crop protection chemicals. Our results also have potential to be used by the pharmaceutical and animal health industries. The novel insights into molecular mechanisms of natural product biosynthesis we have generated can be exploited to develop new biocatalysts with a range of potential applications. They can also be harnessed to develop new biosynthetic engineering strategies able to create novel natural product analogues with improved application potential. The broadly applicable method we have developed for activation of "silent" biosynthetic gene clusters offers significant potential for the generation of novel natural product libraries. We have explored the possibility of commercializing this with support from the Warwick Impact Fund and through a BBSRC Pathfinder Award. Following successful completion of ICURe we have secured funding from Innovate UK to set up a spinout company.48C7BFA3-91C6-47F8-B538-5659EE731B655464d0044715b7.65894921Agriculture Food and DrinkChemicalsEducationManufacturing including Industrial BiotechologyPharmaceuticals and Medical BiotechnologyRelated Article: Kate M. J. de Mattos-Shipley, Catherine E. Spencer, Claudio Greco, David M. Heard, Daniel E. O'Flynn, Trong T. Dao, Zhongshu Song, Nicholas P. Mulholland, Jason L. Vincent, Thomas J. Simpson, Russell J. Cox, Andrew M. Bailey, Christine L. Willis|2020|Chemical Science|11|11570|doi:10.1039/D0SC04309EB879615A-A27F-4A36-913D-3A4BDAAA1B8B65ddf4fbd4bd24.62298274trueCCDC 2011264: Experimental Crystal Structure DeterminationDatabase/Collection of datahttp://www.ccdc.cam.ac.uk/services/structure_request?id=doi:10.5517/ccdc.csd.cc25hwh2&sid=DataCite2020Related Article: Kate M. J. de Mattos-Shipley, Catherine E. Spencer, Claudio Greco, David M. Heard, Daniel E. O'Flynn, Trong T. Dao, Zhongshu Song, Nicholas P. Mulholland, Jason L. Vincent, Thomas J. Simpson, Russell J. Cox, Andrew M. Bailey, Christine L. Willis|2020|Chemical Science|11|11570|doi:10.1039/D0SC04309E34ECE41C-6A0A-4796-BB8A-F4ED06941D3D65ddf626871635.31203389trueCCDC 2011262: Experimental Crystal Structure DeterminationDatabase/Collection of datahttp://www.ccdc.cam.ac.uk/services/structure_request?id=doi:10.5517/ccdc.csd.cc25hwf0&sid=DataCite2020Related Article: Kate M. J. de Mattos-Shipley, Catherine E. Spencer, Claudio Greco, David M. Heard, Daniel E. O'Flynn, Trong T. Dao, Zhongshu Song, Nicholas P. Mulholland, Jason L. Vincent, Thomas J. Simpson, Russell J. Cox, Andrew M. Bailey, Christine L. Willis|2020|Chemical Science|11|11570|doi:10.1039/D0SC04309E29369052-2D71-4D29-8214-F99F2BE9FF2165ddf8dcf0e7b5.25827124trueCCDC 2011263: Experimental Crystal Structure DeterminationDatabase/Collection of datahttp://www.ccdc.cam.ac.uk/services/structure_request?id=doi:10.5517/ccdc.csd.cc25hwg1&sid=DataCite2020ErebagenErebagen develops software that uses bioinformatics to discover compounds for pharmaceuticals development.A75AB364-C86F-43F3-81C5-9D20DCD060E12 FTE scientific post currently in the company.622b0002732d18.848488941773203198https://erebagen.com/20207CE4B921-B3FB-4CEB-988A-3C36518BC8C2A dual transacylation mechanism for polyketide synthase chain release in enacyloxin antibiotic biosynthesis.dd992b9cd11a41174e3e501cdc3a7b21Masschelein J2019-01-0165e885c46df807.1091247446586A0E-A3F6-4482-BF5A-A0F5A730CC1CWatasemycin biosynthesis in Streptomyces venezuelae: thiazoline C-methylation by a type B radical-SAM methylase homologue.Chemical sciencebb81dad617a4110bfd4afe8a50fb1b19Inahashi Y2017-01-012041-65205aa68d7f229df3.23067879F33DA1C9-AC20-4666-AC0A-DEC766BF138BHarnessing and engineering amide bond forming ligases for the synthesis of amides.Current opinion in chemical biology54dcab1088db15fe632408a63baab337Winn M2020-01-011367-59315f80a77c132624.534853449E22B0DE-E975-40AB-BCC5-4F71124C29F2Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity.mBio6a234e45e5f6e33f898094e9d0f41645Mullins AJ2021-01-0161f707148fef15.247888491AEEB2BF-ACDF-489D-B75A-B81FF6826223Heterologe Produktion pilzlicher Maleidride enthüllt die kryptische Cyclisierung in ihrer BiosyntheseAngewandte Chemiec06da4926bbf05c100ed251f0d7ec1faWilliams K2016-01-0165bb7ad10ba816.13165708E37899BC-8CCF-4AE2-8B9B-35CB8822F0C9Parallelized gene cluster editing illuminates mechanisms of epoxyketone proteasome inhibitor biosynthesis.Nucleic acids researchc5b4ef969040b66fb3a85f89c05a4178Huang C2023-01-010305-104863ee91a0b81db9.07786107E7303127-F477-4182-A535-CC5777B879CADiscovery and Biosynthesis of Gladiolin: A Burkholderia gladioli Antibiotic with Promising Activity against Mycobacterium tuberculosis.fe0c303eb11e18ccfbeebde200a22b90Song L2017-01-0165e8698c07ae23.376361549E8E5DEB-D450-40CB-81B6-65CA2D9A2AD0Bovistol B, bovistol D and strossmayerin: Sesquiterpene metabolites from the culture filtrate of the basidiomycete Coprinopsis strossmayeri.PloS one43e87eac6e1838b948a58356ea5ac353Banks AM2020-01-011932-62036030769689ff6B353319A-6745-4626-B4D3-50DECDB8E7C2An Amidinohydrolase Provides the Missing Link in the Biosynthesis of Amino Marginolactone AntibioticsAngewandte Chemie4864445b19a3f452037b2b692cb0926cHong H2015-01-01585d321363cae5.67486541F39267E5-12C5-4819-962C-E9F98094BA86The cycloaspeptides: uncovering a new model for methylated nonribosomal peptide biosynthesis.Chemical sciencea065d2a3a0ca48fafa1e6dc8a89f998fde Mattos-Shipley KMJ2018-01-012041-65205b633129244bf3.15104161828FC1BA-0188-410B-BE36-955C428DF0A0The cycloaspeptides: Uncovering a new model for methylated nonribosomal peptide biosynthesisee910d8e75e3adaa24139924b5d3c5bfDe Mattos-Shipley K2018-01-0167520d54ba17d3.17961550ED450E9F-DC0F-448E-8005-F03800B38D81Heterologous Production of Fungal Maleidrides Reveals the Cryptic Cyclization Involved in their Biosynthesisc06da4926bbf05c100ed251f0d7ec1faWilliams K2016-01-0165e866b906be69.078645249CD99D06-6847-4346-B6EB-FE2E0276DD85A dual transacylation mechanism for polyketide synthase chain release in enacyloxin antibiotic biosynthesis.Nature chemistrydd992b9cd11a41174e3e501cdc3a7b21Masschelein J2019-01-011755-43305d91d815ed2f06.390297957A988870-6065-4236-B454-E8F828D89D75Pentamycin Biosynthesis in Philippine Streptomyces sp. 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biotechnologyc06da4926bbf05c100ed251f0d7ec1faWilliams K2022-01-012054-308562763048156042.1494992240D55A93-BE8C-402B-ACF8-ABEBC85BACCDGenomics-Driven Discovery of a Novel Glutarimide Antibiotic from Burkholderia gladioli Reveals an Unusual Polyketide Synthase Chain Release MechanismAngewandte Chemieb7715f91ed30555ad08314c9c7795ecbNakou I2020-01-015fb8b3ac263cb7.175076391D309CB4-2835-4481-AECD-0001CE7C8C07MmfL catalyses formation of a phosphorylated butenolide intermediate in methylenomycin furan biosynthesis.Chemical communications (Cambridge, England)bf718ff7d1450b2d6d791149cba67dccZhou S2020-01-011359-73455fb8b7514885d5.779014582CBF319E-4D26-44B4-9B6F-5EC0B5A973F3Recent advances in engineering nonribosomal peptide assembly lines.Natural product reports54dcab1088db15fe632408a63baab337Winn M2016-01-010265-056856e172f18ebc64.960703592D2BA68B-BC48-4584-AEAE-9383DF643CF4Discovery and Biosynthesis of Gladiolin: A Burkholderia gladioli Antibiotic with Promising Activity against Mycobacterium tuberculosis.Journal of the American Chemical Societyfe0c303eb11e18ccfbeebde200a22b90Song L2017-01-010002-78635aa6739f290a93.4060514859259A89-781E-4725-B820-6196F42E40FBIn silico analyses of maleidride biosynthetic gene clustersc06da4926bbf05c100ed251f0d7ec1faWilliams K2021-01-01675212d358e407.17726153FAF78322-F879-4FE8-8A2F-B5EBCC1D69CBEvidence for an iterative module in chain elongation on the azalomycin polyketide synthase.Beilstein journal of organic chemistry4864445b19a3f452037b2b692cb0926cHong H2016-01-011860-53975f2002281dd1e2.090939020BAD5837-23CA-4FA8-AC6A-DB069FA2A75FAdditional file 1 of In silico analyses of maleidride biosynthetic gene clustersc06da4926bbf05c100ed251f0d7ec1faWilliams K2022-01-0165e873146ecbf9.6365431346F8F0DE-B725-4793-9BAF-A74F874DA572C-Nucleoside Formation in the Biosynthesis of the Antifungal Malayamycin A.Cell chemical biology4864445b19a3f452037b2b692cb0926cHong H2019-01-012451-94485f1ff90c2f6028.9314076430C28F4F-D2F2-411B-AA4E-A83AD0E6BD9FThioester 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S816: Cytochrome P450-catalysed installation of the C-14 hydroxyl groupbf718ff7d1450b2d6d791149cba67dccZhou S2019-01-016112904b640c8CD3D9100-9359-4AB4-972F-F928FCD45AD5Antibiotic skeletal diversification via differential enoylreductase recruitment and module iteration in trans -acyltransferase polyketide synthases8a4aae6c6d55bed2162309db037d0147Jian X2023-01-0166450464c2d52FE568418-FF90-4938-87A0-0AB4EB5FEBD4An unusual Burkholderia gladioli double chain-initiating nonribosomal peptide synthetase assembles 'fungal' icosalide antibiotics.Chemical sciencefebd0f2c18e989c5205c193f9de5a8e6Jenner M2019-01-012041-65205d91d8162df310.57474032CAD97F10-0F58-463E-9611-95AB53C4D083Discovery of microbial natural products by activation of silent biosynthetic gene clusters.Nature reviews. Microbiology06e370ead6e106f84b21ade1d9cbe8a9Rutledge PJ2015-01-011740-15265675e7792bb09AF3D81BE-7AA4-4811-9F4D-5E012AB48017Heterologous reconstitution of the biosynthesis pathway for 4-demethyl-premithramycinone, the aglycon of antitumor polyketide mithramycin.Microbial cell factories22846bfd2bfb90dd03356d8184e85ae0Zabala D2020-01-011475-28596030769d7f0cc21B2283F-F7D4-4CE4-B3EE-ED7D8D8862A8Discovery, characterization and engineering of ligases for amide synthesis.Nature54dcab1088db15fe632408a63baab337Winn M2021-01-010028-083665a6f9016279c9.785439900CE257AD-01BB-4262-9614-01C77DED2AC0Heterologous Production of Fungal Maleidrides Reveals the Cryptic Cyclization Involved in their Biosynthesis.Angewandte Chemie (International ed. in English)c06da4926bbf05c100ed251f0d7ec1faWilliams K2016-01-011433-785165bb7ae901edb2.4367621563810581-9E5C-4A2D-9B07-29594667F934The good, the bad and the tasty: The many roles of mushrooms.Studies in mycology50ed6688112f052ae5c18f1eaab9ce4fde Mattos-Shipley KM2016-01-010166-061658c7fbc04191f6.64911302D2A69E30-FF58-4FB5-A97A-066F8F923505Heterologe Produktion pilzlicher Maleidride enthüllt die kryptische Cyclisierung in ihrer Biosynthesec06da4926bbf05c100ed251f0d7ec1faWilliams K2016-01-0167520daa8bc469.082628187823BB6E-B8F2-439D-8E2E-FE28DE9CB017Modern Biocatalysis - Advances Towards Synthetic Biological Systems8b1691ccbba8d85e8e4e149b4cc32467de Mattos-Shipley K2018-01-0117576733 1757672567ce5a68c1abd9.352602434C0F9271-19F0-4092-9FC7-4F7DD2E4D43BStructural basis for chain release from the enacyloxin polyketide synthase.Nature chemistryc707e3035af2c42c4107fa1fe19b5d98Kosol S2019-01-011755-43305d91d8165a1174.40214075F3AA15F5-59D5-42D7-8666-41F8E5A08E87Anti-microfouling Activity of Glycomyces sediminimaris UTMC 2460 on Dominant Fouling Bacteria of Iran Marine Habitats.Frontiers in microbiology6c108ca8e93a720c4dff5ebd3c498f07Heidarian S2018-01-011664-302X5c87b90851db76.0544137597A9D817-4D53-41DC-A76C-2BD0C1464FE7Diene incorporation by a dehydratase domain variant in modular polyketide synthases.Nature chemical biology7d0da7c719661bbb1c10d204bae4a2d7Hobson C2022-01-011552-4450632e2f6945a536.18649930BB/K002341/12D9083F0-05FA-4726-9EB2-3FCC293CAAF960Biomolecules & biochemistry4CCA4C04-0C28-41BE-8869-FA6391A7F00540Microbial sciences6997E843-AD07-4064-B67D-D4A928309DB440Biochemistry & physiology6D0F40FF-D03E-4429-A764-185BC521A84060Catalysis & enzymology00A9E48C-4629-44EF-B21A-00C8EFB2709CEGOR: Environmental Guidelines: Opportunities and RisksClosedAH/G015198/1Research GrantThis research cluster will bring together a team of key professionals, academic researchers representing AHRC/EPSRC disciplines as well as heritage practitioners to appraise the costs and risks of current environmental guidelines for cultural heritage in response to a changing climate. This theme has a national and international dimension since climate change, energy consumption, visitation and pressures for greater access to collections will continue to make considerable demand on cultural heritage in the 21st century globally. The scale and pace of these changes are posing unique challenges to managing the long-term preservation of material culture and are the focus of discussion amongst professional communities both nationally and internationally.This research cluster will inform this debate.\n\nCurrent environmental parameters and tolerances set out in national and international guidelines and standards as well as Governmental Sustainable Development Targets play a critical role in shaping practices in the cultural heritage sector such as building construction, and environmental management. This includes the control of temperature, moisture, light and pollution - the main factors affecting the conservation of material culture. Environmental guidelines impact significantly on how collections are stored, accessed, loaned and displayed. \n\nEqually, the cultural heritage sector is not immune from the challenges posed by global responsibility: reducing reliance on fossil fuels, changing behaviours in favour of re-use and alternative energy sources, for example. It is within this context the appropriateness of current environmental guidelines designed to meet an agreed standard for managing material culture change, enable visitors to access and experience collections to a seasonal standard of comfort, and provide access to collections both locally and internationally is being questioned as the 'costs' of this are being realised. Unfortunately, there are no easy or headline-grabbing answers to this problem: the risks need to be identified, the costs understood, the options appraised. \n\nEGOR will provide the necessary framework to develop thinking in this area in order to realise an intellectual step change in understanding the risks and uncertainties of current environmental guidelines, standards and targets in a changing climate. Consideration will be largely focused on indoor environments, collections and the people who engage with and work in the cultural heritage arena, and will build on foundations established by other research projects e.g. Noah's Ark (EU), Engineering our Futures (EPSRC), Living with Environmental Change (NERC) largely focused on climate impacts outdoors. This will be achieved through 5 sequential activities: \n1. An inaugural meeting of the steering group which includes professional leaders, and named investigators to shape thinking and initiate cross fertilisation of ideas and perspectives;\n2. 3 working group meetings comprising specialists in art history, engineering, material science and conservation for coherent discussion, and lively debate to understand the implication for current environmental guidelines in a changing climate for people, their values and history, buildings housing collections (often historic structures themselves) and collections. The implications will be considered against a background of global responsibility.\n3. A two-day residential event will conclude this investigative process; the three working groups will present their findings, areas of convergence and divergence will be further debated to determine the risks and uncertainties surrounding environmental guidelines and standards in a changing climate, and the outstanding research needed to fully inform this debate.\n\nA summary of the challenges and user-led research emerging within this theme will be reached at the end of the meeting and presented at the Programme conference in July 2009.2009-12-311291772D-DFCE-493A-AEE7-24F7EEAFE0E9AHRC2009-01-01INCOME_ACTUAL24367The findings of this award led to the publication:
British Standard Publically Available Specification: 198 Specification for Managing Environmental Conditions for Cultural Collections2012C664E230-CDFD-46B7-AB74-E6BE3B5D45EACulturalEconomicPolicy & public services56e006140e5968.17907723Education,Energy,Culture, Heritage, Museums and CollectionsThis project identified what was needed to deliver improved environmental standards for the movable heritage sector.The findings of this research network led to the development of a British Standards published Publically Available Specification for Environmental Management of Cultural Heritage Collections. This standard has been recognised internationally as a ground breaking.8476BBE3-F930-4276-918D-0D8C83B6DD3F54635a41d58dc5.45769760EnergyEnvironmentGovernment Democracy and JusticeCulture Heritage Museums and CollectionsOtherhttp://www.nationalarchives.gov.uk/archives-sector/assessing-environmental-impact.htmDD28B571-2487-42FF-8252-7711CAC125DAVolatile aldehydes in libraries and archivesAtmospheric Environment64a7586467e5c699a5202ec20c2b2efaFenech A2010-01-01doi_53cfe5fe569b88ddAH/G015198/12693EEB1-BEF5-45C6-999E-D56488EFFAD7100Cultural & museum studies77E870DC-ED98-44DF-A0C8-06A874EB34A2100Cultural Studies & Pop Culture03E282E3-DFF0-4794-ADE0-00B1A7BA0ED8Wittos - Mobile Internet Analytics & Predictive Content Over WiFiClosed710397GRD Proof of ConceptThe increasing availability and uptake of smart mobile devices offering broadband
connectivity has raised demand for a smarter in-store experience, specifically a means for
bricks and mortar retailers to connect to and engage with their customers. Whilst analytics of
traditional Internet user behaviour has matured, and a myriad of solutions offering insight and
engagement have evolved, no comparable solutions exist to offer retailers insight into a
customer's online behaviour whilst within their premises.
Wittos has developed a breakthrough new solution that offers real-time actionable intelligence
and awareness of the customer's in-store intentions. This technology forms the core of the
Wittos platform which builds upon a traditional Wireless hotspot offering Internet
connectivity. Wittos combines data gathered from the user's online activity, their physical
location and path through a venue and uses this to match their actions to a behavioural profile
(companion or shopper). This profile can then be matched with products of interest (their
online focus) and acted upon to serve the most relevant content to user or improving their instore
experience by providing real-time intelligence to staff on the floor. This reactive
intelligence offers the retailer a means to increase the customer’s dwell time and increase the
chance that an in-store customer transacts.
This technology will offer traditional retailers a competitive advantage as relevant alternatives
to their purely electronic competitors, a greatly improved in-store customer experience and the
ability to match demand and supply in real-time.2015-03-3012E03F45-B517-4D83-A182-3D142D1A471AInnovate UK2014-01-01INCOME_ACTUAL904617103976CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified03E55638-AD33-4353-BE3E-00A85A5C6DF8Post-Translational Modifications Orchestrate Organ SymmetryClosed2444772StudentshipA major challenge during morphogenesis includes the establishment of symmetry types, such as radial and bilateral symmetry: a developmental commitment which greatly impacts on organ function. In humans, defects in organ-symmetry establishment leads to malformation and diseases, but despite its importance, our knowledge about symmetry foundation in multicellular organisms is very limited. Less intuitively, organ symmetry establishment is fundamental for plant survival too.
Therefore, the aim of this project is to shed light on a new mechanism regulating radial and bilateral symmetry establishment during plant organogenesis, using A.thaliana as a model; investigating how a specific post-translational modifications underpins direct protein interactions between key regulators of plant organ symmetry, which in turn switches on and off gene expression, precisely and quickly, during organ development.2024-09-29198E4A3D-B2DC-45D4-8351-7CCEC4061876BBSRC2020-09-30INCOME_ACTUAL024447726CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified040C2814-53E6-488F-BDA9-01B1A0F63777Random metrics on the CLE carpetClosed2434402StudentshipConformal loop ensembles (CLE) are random collections of loops defined in simply connected domains. They exhibit a fractal structure and arise as conjectured and proved scaling limits of a number of lattice models from Statistical Physics.
Since their introduction, connections between CLE, Schramm-Loewner evolution (SLE) curves, and the Gaussian Free Field (GFF) have been shown and categorized. In this project we consider natural random metrics defined on the set of points not surrounded by CLE loops (the CLE carpet) and investigate their properties. A first goal is to build on the relationship between CLE, SLE, and the GFF to show that geodesics in a natural CLE metric are singular with respect to SLE. This disproves a conjecture from 2014 that was based on empirical results.2023-09-29798CB33D-C79E-4578-83F2-72606407192CEPSRC2020-09-30INCOME_ACTUAL024344026CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0C552636-8921-4940-9DAB-01530F14011ASafe and Sound - secure and sustainable Cloud3D servicesClosed750553VouchersSafe and Sound will enable Hao2.eu to research and develop good practise standards and approaches to deliver secure and sustainable Cloud3D services which proactively anticipate and support the needs of vulnerable groups such as people with autism and learning disabilities.2014-01-3112E03F45-B517-4D83-A182-3D142D1A471AInnovate UK2013-07-31INCOME_ACTUAL50007505536CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0C7B57E9-2B50-4E12-863B-01EFA021D066Undestanding microbial communities through in situ environmental 'omic data synthesisClosedNE/L011956/1FellowshipThe purpose of this research is to integrate different sources of 'omics data in environmental science for microbial community analysis. The computational based comparative analysis of DNA sequences may provide information about genome structure, gene function, metabolic and regulatory pathways and how microbial genomes evolve. However, to fully delineate microbial activity and its response to environmental factors, it is necessary to include all levels of gene products, mRNA, protein, metabolites, as well as their interactions. I propose to use large-scale whole genome metagenomic sequencing for assessment of taxonomic and functional diversity of microbial communities. The data generated by metagenomic experiments are both enormous and inherently noisy, containing fragmented DNA sequences representing as many as thousands of microbial species. After using pre-filtering steps, including removal of redundant, low quality sequences, the short DNA sequences are assembled together into longer contigs of overlapping reads, and these contigs may then be scaffolded into full genomes in a bottom-up approach. Having obtained the assembled contigs, the obvious next step is to use publically available databases to annotate the coding regions in these contigs. This will tell us WHAT functionality is available and provide information on WHO is there, the metagenomic sequences are binned, i.e., by associating a particular sequence with an organism. This can be done by either searching for phylogenetic markers or by looking for similar sequences in existing public databases. The end result is the community profile of different samples in terms of organismal abundances within each sample. Whilst metagenomic analysis gives a profile of the microbial community at a specific place or time, and their potential functional, it does not reveal which genes are actually being transcribed. I thus propose to integrate sequencing-based metatranscriptomics in which total RNA (a proxy for gene activity) is extracted from microbial community, converted to cDNA and sequenced without the need for cloning. This will provide information on the regulation and expression profiles of complex communities by enabling quantitative measurements of dynamic expression of RNA molecules and their variation between different states reflecting the genes that are being actively expressed at any given time. However, the story is still far from complete, as we do not have direct evidence of the metabolism within a cell. To give a more complete picture of living organisms, I will integrate metabolomics which will provide unique chemical fingerprints that are a function of specific cellular activity. In particular, the focus will be on identifying habitat-specific endogenous and exogenous metabolites along distinct geochemical conditions. These metabolites will be detected using two-dimensional gas chromatography coupled with mass spectrometry. They will be related to the expression levels from transcriptomes using information on metabolic pathways readily available from annotating metagenomic sequences. In this way we will integrate all three sources of information, mapping the metatranscriptome onto the assembled annotated metagenomes and reconciling the reconstructed metabolic pathways with observations on metabolite concentrations and fluxes. From this we will be able to predict the metabolic function of the entire community not simply who is there.The removal of complex organic contaminants from soils will be one of the major environmental challenges facing the United Kingdom over the coming decades and recommendations based on this proposal will be of use to stakeholders especially, the remediation consultants, industry regulators i.e. SEPA and local councils. Brownfield development is an important part of the societal shift towards sustainability. Many contaminated brownfield sites sit unused for decades because the cost of cleaning them is more than the land would be worth after redevelopment. This research will impact on our ability to achieve sustainable reclaim of environmental capital and will allow adaptive re-usability.
The Earth Microbiome Project has generated an enormous collection of data with the intention of producing a global Gene Atlas describing protein space, environmental metabolic models, and characterizing a global environmental parameter space for microbial communities. This global environmental sample database is an ambitious initiative that is community-driven. The tools developed in this fellowship will exploit this vast amount of information to provide useful insights on the Earth's microbiome and to catalogue all the microbes that live on earth. This will be of great benefit to mankind as whole, these microbes are performing vital functions, and to environmental researchers.
Methanogenesis is a key process in the carbon cycle, methane is a more potent greenhouse gas than carbon dioxide, therefore understanding its metabolism at a community level is of fundamental importance if we are to incorporate microbial processes into models of climate change. Methane is an important greenhouse gas yet its production could play a part in the transition to a low carbon economy. Water treatment is the fourth most energy intensive sector in the UK and consumes approximately 1% of the UK's electricity. Reducing the energy required to treat wastewater would therefore have major benefits both by reducing costs and carbon dioxide emissions. Anaerobic digestion (AD) reactors have the potential to provide these benefits. They do not require the same energetically costly aeration as aerobic methods and through the action of methanogens produce biogas. Better understanding of methanogenesis could lead to more efficient AD reactors.2019-10-318A03ED41-E67D-4F4A-B5DD-AAFB272B6471NERC2014-11-01INCOME_ACTUAL425506The analytical tools led to the exploration and in turn development of a CD-TREAT diet for treatment of Crohn's Disease https://www.medpagetoday.com/gastroenterology/inflammatoryboweldisease/76931and was published in Gastroenterology 2019291AA87F-7DB9-448F-BA15-C158EA426C85SocietalEconomic56db53d617c9b4.68617352Agriculture, Food and Drink,Education,Environment,Healthcare,Pharmaceuticals and Medical BiotechnologyI established my Environmental'Omics lab in School of Engineering, University of Glasgow in November 2014 which specialises in developing novel pipelines for analysing genomic data in an environmental context. My lab is centered around my fellowship and focuses on microbial ecology at both mesoscopic and macroscopic scales by integrating 'omics data (metagenomics, metatranscriptomics, metabolomics, and metaproteomics) for microbial community analysis.
Software (http://userweb.eng.gla.ac.uk/umer.ijaz/#bioinformatics): Under this grant I am developing software tools and methodologies to integrate different sources of omics data, namely, metagenomics, metatranscriptomics, metabolomics, and metaproteomics. Here are the list of major software I have contributed to during my fellowship:
RvLab (R virtual Laboratory for ecological community analysis)
Software:https://portal.lifewatchgreece.eu/
Reference: A. Oulas et al. Biodiversity Data Journal, 4, e8357, 2016.(doi:10.3897/BDJ.4.e8357)
CONCOCT (A software for binning metagenomic contigs with coverage and composition)
Software: https://github.com/BinPro/CONCOCT
Reference:J. Alneberg et al. Nature Methods, 11(11):144-1146, 2014. (doi:10.1038/NMETH.3103) (PMID:25218180)
TAXAassign (A bash based pipeline for generating taxonomic profiles using NCBI's Taxonomy)
Software: http://www.github.com/umerijaz/taxaassign
Reference: J. Alneberg et al. Nature Methods, 11(11):144-1146, 2014. (doi:10.1038/NMETH.3103) (PMID:25218180)
NMGS (A software for fitting the Unified Neutral Theory of Biodiversity with Hierarchical Dirichlet Proces)
Software: https://github.com/microbiome/NMGS
Reference: K. Harris et al. Proceedings of the IEEE, 105(3):516-529, 2017 (doi:10.1109/JPROC.2015.2428213)
seqenv (A pipeline capable of annotating genetic sequences with Environmental Ontology)
Software: https://bitbucket.org/seqenv/seqenv/src
Reference: L. Sinclair & U. Z. Ijaz et al. PeerJ, e2690, 2016. (doi: 10.7717/peerj.2690)
microbiomeSeq (An R package for microbial community analysis in an environmental context)
Software: https://github.com/umerijaz/microbiomeSeq
Tutorial/Demo: http://userweb.eng.gla.ac.uk/umer.ijaz/projects/microbiomeSeq_Tutorial.html
SeqEnv-Ext (A taxa-centric extension to seqenv pipeline, which consisted of two parts, each providing environmental annotations under different context, with first part providing taxon abundance on a per term basis while the second part lists environmental term abundance under a per taxon context. A separately developed program that required the use of the original seqenv pipeline, this enabled two different methods of viewing environmental annotations, which significantly augments the analysis capability of the pipeline.
Software: http://hie-pub.westernsydney.edu.au/0610b020-39fb-11e7-b55d-525400daae48/
Reference: A. Z. Ijaz, T. Jeffries, U. Z. Ijaz et al. PeerJ, 5:e3827, 2017. (doi:10.7717/peerj.3827)
pyTag (A tool for identification and analyses of ontological terms in application area specific literature surveys)
Software: https://github.com/KociOrges/pytag
NanoAmpli-Seq (A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform)
Code: https://github.com/umerijaz/nanopore
Reference:
S. T. Calus, U. Z. Ijaz, and A. Pinto. bioRxiv 244517, 2018 (doi: 10.1101/244517)
Orion Cluster: Without any institutional or dedicated technical support, I have single-handedly built and managed an HPC facility in Engineering called Orion Cluster (http://userweb.eng.gla.ac.uk/umer.ijaz/#orion). I bought first server in 2012 through the Unilever grant and since then I have religiously pursued my collaborators for in-kind contributions, as well as allocating small equipment budget on every grant I am applying. Five years later, I have spent ~£114K on 13 servers with more equipment to be purchased in two months time through recently allocated £22K (on SAIC) grant. Orion Cluster stands at an operational capacity of 368 cores, ~450TB disk space, and will serve >70 PGR/T and staff (60 existing and regular users and hence the reason why I have an increasing supervision workload). This facility now sits at the heart of all major research groups I am involved with and is envy of many others. One of the reason why I have managed to attract funding and collaborators is through development of bespoke workflows (originating from my research) that I regularly updates and share on my website (http://userweb.eng.gla.ac.uk/umer.ijaz/#bioinformatics; http://www.tinyurl.com/JCBioinformatics; and http://www.tinyurl.com/JCBioinformatics2) as well as providing a single place for >400 bioinformatics tools. My cluster and bioinformatics tutorials are of strategic importance
Expansion to other technologies/hardware and award generation (http://userweb.eng.gla.ac.uk/umer.ijaz/#research_Grants): The developed tools/software methodologies and the research being conducted under my NERC fellowship was instrumental in getting further funding from numerous research councils. This includes recent expansion to population genomics and epidemiology (Scottish Infection Research Network/Chief Scientist Office Project entitled "Molecular epidemiology of Clostridium difficile in Scotland: developing novel, clinically applicable research methods to combine genomic analysis with health informatics"). For the past one year, I am trying to put my engineering experience to good use, by expanding my research to include: Raman spectroscopy enabled microfluidics (NERC NE/P003826/1 grant entitled "Stable Isotope Probing with Resonance Raman Cell Sorting to profile influence of ocean acidification on microbial carbon fixation"); hardware system integrating liquid handling, incubation and sensing with an embodied genetic algorithm, which directs evolutionary optimisation of microbial growth (with Professor William T Sloan, University of Glasgow; EPSRC Global Challenges Research Fund EP/P029329/1); and development of artificial intestinal Salmon gut system through bioreactors (BBSRC BB/P001203/1 grant entitled "A microbial basis for Atlantic Salmon energetics").
Supervision (http://userweb.eng.gla.ac.uk/umer.ijaz/#supervisions): I have been directly involved with the supervision of 13 PhD students and 2 PDRAs (with more to be recruited). Two PGR students (Caitlin Jukes, and Asha Rani) have recently defended their viva successfully. All of my supervisions involve utilisation of tools developed under my NERC grant.
Repute: I have gained considerable repute at both national and international levels. I am collaborating widely with academics located in Manchester, Warwick, Dundee, Aberdeen, Liverpool, Norwich, Reading, London, Belgium, Finland, Greece, Norway, Ireland, Austria, Thailand, Czech republic, Australia, Germany, France, and Netherlands. As a consequence I have been invited to visit/speak at numerous institutes including: Faculty of Science, Ceské Budejovice; Helenic Centre for Marine Research, Greece; Centre for Microbial Ecology and Technology, Ghent, Belgium; Edinburgh Amplicon Sequencing Group; Earhlam Institute (formerly TGAC); Unilever R&D laboratories (Colworth/Port Sunlight); London School of Hygiene and Tropical Medicine; and Health Informatics Centre Dundee. My research leadership potential was recognized by NERC who funded me to attend a £23,100 advanced leadership course in Cambridge.Please see the section on "What have you discovered or developed through the research funded on this grant"B0C9E924-423A-498C-8D8C-B8779E08088A56db4f3db020b5.66717896Agriculture Food and DrinkDigital/Communication/Information Technologies (including Software)EducationHealthcarehttp://userweb.eng.gla.ac.uk/umer.ijazThis article presents metagenomic-assembled genomes (MAGs) of prokaryotic organisms originating from chicken caeca. The samples originate from broiler chickens, one group was infected with Newcastle Disease Virus (NDV) and one uninfected control group. There were four birds per group. Both groups were raised on commercially available antibiotic free feed under a semi-controlled setup. The binning step of the samples identified 130 MAGs with50% completion, and10% contamination. The data presented includes sequences in FASTA format, tables of functional annotation of genes, and data from two different approaches for phylogenetic tree construction using these MAGs. Major geochemical cycles at community level including carbon, sulfur, and nitrogen cycles are also presented.08E7A941-2D56-4AA9-9015-13E7DDCABC0365a5a993843e80.18637899true<b>Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan</b>Database/Collection of datahttps://figshare.com/articles/dataset/_b_Dataset_of_130_metagenome-assembled_genomes_of_healthy_and_diseased_broiler_chicken_ceca_from_Pakistan_b_/249018782024Amplicon sequencing on Illumina sequencing platforms leverages their deep sequencing and multiplexing capacity, but is limited in genetic resolution due to short read lengths. While Oxford Nanopore or Pacific Biosciences platforms overcome this limitation, their application has been limited due to higher error rates or smaller data output. In this study, we introduce an amplicon sequencing workflow, i.e., NanoAmpli-Seq, that builds on Intramolecular-ligated Nanopore Consensus Sequencing (INC-Seq) approach and demonstrate its application for full-length 16S rRNA gene sequencing. NanoAmpli-Seq includes vital improvements to the aforementioned protocol that reduces sample-processing time while significantly improving sequence accuracy. The developed protocol includes chopSeq software for fragmentation and read orientation correction of INC-Seq consensus reads while nanoClust algorithm was designed for read partitioning-based de novo clustering and within cluster consensus calling to obtain full-length 16S rRNA gene sequences. The datafiles and protocols provided here represent the intermediate files during data processing and associated detailed workflow.D7E6EF02-FF6B-4FB3-98CB-1FE6B6B7E67FB0282B32CAAtrueSupporting data for "NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform."Database/Collection of data201845146765-34D8-4C12-B53E-81C19B4DBDFBDietary Triggers of Gut Inflammation Following Exclusive Enteral Nutrition in Children with Crohn's Disease: A Pilot Study7d782475214c1e77b1f4c44845973befGkikas K2021-01-0160fecb64cbf18794A9475-1FBC-4606-A90C-83C8ACC3EA59Binning metagenomic contigs by coverage and composition.Nature methodsde8d1caf81e365c3e9ff09579de0a6e2Alneberg J2014-01-011548-70915536c93bf386f3.6336115031A09631-E395-4B7C-B3CA-654B2527D181Carboxylic acids production and electrosynthetic microbial community evolution under different CO2 feeding regimens.Bioelectrochemistry (Amsterdam, Netherlands)1651a8c8389e19c3747e331370f69a76Dessì P2021-01-011567-5394602717ddc10780AC111FF-060D-4FC7-80FC-094FDA9E9206Additional file 2 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526b0aa52a76.777670891EE66F0E-757E-4946-841F-08E986C0F42ATerminal restriction fragment length polymorphism is an "old school" reliable technique for swift microbial community screening in anaerobic digestion.Scientific reports39207eeeb3e0ec22ec112980ea9a6788De Vrieze J2018-01-012045-23225c5aba21094629.971870372030AE6B-D420-4823-920F-1963CF3E9FB7Exploration of marine bacterioplankton community assembly mechanisms during chemical dispersant and surfactant-assisted oil biodegradation.Ecology and evolution61ac1dc6db0e8a5735887de507ea5c31Nikolova C2021-01-012045-7758613fdc5364162E4ABFE6F-2603-4246-AC99-D6AEC9733977The Effects of Smoking on Human Pharynx Microbiota Composition and Stability.Microbiology 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synthetic surfactants61ac1dc6db0e8a5735887de507ea5c31Nikolova C2021-01-0165e8e684c02465.947487293DB2D05F-4DA2-4583-BA2D-0ECB7F74870DAdditional file 12 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526c3b4a4bf7.82874084775B0FA6-E343-4AB7-B51B-9E4512DCB9F9Stratification of alopecia areata reveals involvement of CD4 T cell populations and altered faecal microbiota.Clinical and experimental immunologybd2f8d880574decf9f03188847bde989Bain KA2022-01-010009-9104634447f4375578D3F749E-1B6E-403D-AC83-EEA7D4CD57E3Autotrophic denitrification of nitrate rich wastewater in fluidized bed reactors using pyrite and elemental sulfur as electron donorsEnvironmental Technology & Innovation16e22ff86c1e7a58715f7a6a9c9ac73fCarboni M2022-01-01630824beefd24E14C0E55-8F84-46D7-A4D9-CF888C48C0EDCommunity recovery dynamics in yellow perch microbiome after gradual and constant metallic 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Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7e002ff86.653416967C6502F9-A2C6-4980-A7AA-90C3D7BDD66C16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus.Scientific reports53b66e3fe5923aa8e9a27654748caecbReich I2018-01-012045-23225c5aba19c52272.62585242EA1E13D8-BDC9-4962-997F-800B1917ACE9Additional file 10 of Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants61ac1dc6db0e8a5735887de507ea5c31Nikolova C2021-01-0165e8e693566d36.7397576138F31B27-1A0A-409A-B6B3-E549E2930BEACold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage.FEMS microbiology ecology17af8dd4a59a944e9d8515761540a353Keating C2018-01-010168-64965c5aba304aabd0.3786823257D893E3-E6B1-4BA3-A4E5-E03EA9371D1FO-05: Metagenomic analysis of the gut microbiome during a course of Exclusive Enteral Nutrition (EEN) provides novel insights on mechanism of EEN actionJournal of Crohn's and Colitis41592addbe7ed7bd4bb66e0747bf25b4Gerasimidis K2014-01-015536c93c4d8038.83847990B0D6073A-2284-48DC-BDE2-C67C3DE7FF0DA comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.BMC genomicse90ec32912b02872478bb9b712f90b59D'Amore R2016-01-011471-216456db4d97da70a3.60422067C216F28C-740E-4E15-A690-A8545C99899AP380 Changes in faecal microbiome and metabolome are more pronounced in Crohn's disease patients who adhered to the CD-TREAT diet and responded by calprotectin.Journal of Crohn's and Colitisd7345234614416bb9bd579b4d96b81e4Svolos V2023-01-0163dc07a5a370fF1C78C9A-57C7-4320-B098-09DD03DFC4CANanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform.GigaScienceaa355ef57171cdd24102ce23d9d70ee4Calus ST2018-01-012047-217X5c65634a1cb966.941822128142B4B2-2915-402F-B1D7-ACCAE4F07892Additional file 1 of Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbationsebf4406f047e3e8937b4f5853015c88dCheaib B2020-01-0165e8e89361f5d4.462614727A80B8DF-91EE-4203-A7F4-F908CEC7EED7Additional file 5 of Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants61ac1dc6db0e8a5735887de507ea5c31Nikolova C2021-01-0165e8e68628fd61.34340211EB8EB359-EA69-4F81-BBE8-131446C11EF5Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition.The American journal of gastroenterology17620d321d3b329acfee3c0bd6e3632cQuince C2015-01-010002-9270563c7295ee0b11.498435769B9526AD-4346-48E6-9608-C784B67BC681Additional file 8 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526c44a62817.40966070D1FEFE65-EEE8-4561-A994-E35521031239Additional file 9 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7a56ee648.90176462BB79F297-28EF-408F-8BDA-AAED7BEF66B2SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communitiesbd8899b572ba2cff70a3204d25097102Kazlauskaite R2021-01-01602ae84ba620a4C23F34F-6DAF-4411-A996-A7FBAD9E4AD0The reduction of faecal calprotectin during exclusive enteral nutrition is lost rapidly after food re-introduction.Alimentary pharmacology & therapeutics4146c13ab42c36eb8f95381540ba3073Logan M2019-01-010269-28135dae5e46b11c40.833439549F9ABD2C-66F5-44CC-BDDB-D648E88840F8Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori -induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor useee380db2dd0572ff1f27c88b0e07f243Parsons B2017-01-01602718da27d476C7CB76B-A908-43F3-95BD-E8D25681C047Disease Resistance correlates with Core Microbiome Diversity in Cottonbc32f3a8cc40351683169581b006a88dAqueel R2023-01-0164eae7d69667fE6E0A3B7-43CC-48FA-B6F8-D82D3A0BF95BTerminal restriction fragment length polymorphism is an "old school" reliable technique for swift microbial community screening in anaerobic digestion39207eeeb3e0ec22ec112980ea9a6788De Vrieze J2018-01-0165e8eb2524d5e6.39333812E1AF01E0-52F4-41B7-B794-CF501489D881Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn's disease.The American journal of clinical nutrition5ca7b1bb586940a4e6b03c3eb9275dbaNichols B2024-01-010002-9165662262e4ea55a0.77127777E3EA9BBD-9A78-4BB4-BCD8-4F8B8E2F2449Additional file 1 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526b0586b757.36545527DCF5297D-BC5A-4D8E-B0C3-8488BA7F6BDFTemporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae.Animal microbiome17af8dd4a59a944e9d8515761540a353Keating C2021-01-012524-4671602717af47e718A4ADDDD-323E-4732-A650-DB0F90B754BCAnalysis of 61 exclusive enteral nutrition formulas used in the management of active Crohn's disease-new insights into dietary disease triggers.Alimentary pharmacology & therapeutics4146c13ab42c36eb8f95381540ba3073Logan M2020-01-010269-28136023de9f43a1e5.7385288299AA2FA6-BA4C-45C4-9504-2F6213E7F2B6Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use.PLoS pathogens3c4e16cbb7c88f019e8c81e723a76c35Parsons BN2017-01-011553-73665a2fc818ce9a19.46096306F7BC3888-9472-43C8-A6D6-9A74D1C6A4AEA Distinct, Flocculent, Acidogenic Microbial Community Accompanies Methanogenic Granules in Anaerobic Digesters.Microbiology spectrumebcb32334e2f74144f1d0934387a51abMills S2021-01-012165-0497618e19c7866c4E77BABC9-4AA5-479D-B004-7F2C6677173CCotton Microbiome Profiling and Cotton Leaf Curl Disease (CLCuD) Suppression through Microbial Consortia associated with Gossypium arboreumbc32f3a8cc40351683169581b006a88dAqueel R2023-01-0164aff45b5b26043280197-382A-4360-BC50-3BA72E0B3075A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome.Scientific reports7f2f30a3b1d435bc063bb9a7cfd90b75Aziz I2023-01-012045-232264490f2ecaad4BF16F523-7FC5-443F-8ADA-2ADC3F0FE49BLinking microbial community structure and function during the acidified anaerobic digestion of grassf0daad434060fd5eb8027acc38087e5dJoyce A2018-01-0167526bf8671ab8.12239143259D98CD-EA1C-4169-A071-52E15B64E5F2Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-01602717e100d2f64E9A372-202D-4B94-8182-E23D1D484BF1Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar.Applied and environmental microbiology04325d9feab8d669c8595336fc064408Heys C2020-01-010099-22406023de96cd0869.9259913580400AF8-5265-44F6-90A0-30C600A088CFEmerging investigators series: microbial communities in full-scale drinking water distribution systems - a meta-analysisEnvironmental Science: Water Research & Technology3bf3bace9d94ea130939e341c0f5b065Bautista-de los Santos Q2016-01-01589482acd19003.33207167C1B0D273-750A-425F-80C1-885CCE03B9A3Linking microbial community structure and function during the acidified anaerobic digestion of grassf0daad434060fd5eb8027acc38087e5dJoyce A2018-01-0167526bc84797c7.50369928BD4944F6-01FC-42A0-AB4F-053058BBDD3AAdditional file 12 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526bebaab2e8.8349225983EC3227-D8D3-4758-8EDD-AB2FC450D39DFecal Enterobacteriales enrichment is associated with increased in vivo intestinal permeability in humans.Physiological reports687a9ee4731147702ef3139511110ff0Pedersen C2018-01-012051-817X5b6591c4e6eca4.14868861C210EAD2-8FA8-40E9-8EE5-3FECFB280A40Additional file 3 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7b56c5da7.49970909D694E6E2-9DA5-4D75-ADE4-DC5F5F01B00BAdditional file 10 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7dc04b709.63263041F5FA34EA-AA04-4727-B032-4CFFDB1A831AAdditional file 6 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526be6b5c1e5.575729746ED02182-696E-4D46-B54E-079E5A9E96DBThe effect of DNA extraction methodology on gut microbiota research applications.BMC research notes41592addbe7ed7bd4bb66e0747bf25b4Gerasimidis K2016-01-011756-0500589482ac630306.24314046NE/L011956/1F673FD2B-013B-47E5-9E62-03BAB1E7348E10Environmental engineering4CCA4C04-0C28-41BE-8869-FA6391A7F00520Microbial sciences29F3DF16-3094-4F79-BC69-8D05FB55182670Omic sciences & technologies513702B4-7C48-41F2-A1A0-8B4E8BEDCABC10Assess/Remediate ContaminationC6A85141-ED79-4266-86E5-F6D25217C97F40Environmental GenomicsAF3F5E7C-7FB6-4588-9174-6018BA2A231B20Environmental Microbiology7E61B40B-93E5-4D69-8C89-426ED7E0D2B420Metabolomics / Metabonomics937A9F23-021A-4604-8979-A28E0E04F82510Transcriptomics0C8BB41D-B4B5-4A91-B6AA-00D48582C5AEReal-time prediction of cellular states in 3D lattice light sheet microscopyClosed2430216StudentshipProgramme overview:
This MRC-funded doctoral training partnership (DTP) brings together cutting-edge molecular and analytical sciences with innovative computational approaches in data analysis to enable students to address hypothesis-led biomedical research questions. This is a 4-year programme whose first year involves a series of taught modules and two laboratory-based research projects that lead to an MSc in Interdisciplinary Biomedical Research. The first two terms consist of a selection of taught modules that allow students to gain a solid grounding in multidisciplinary science. Students also attend a series of masterclasses led by academic and industry experts in areas of molecular, cellular and tissue dynamics, microbiology and infection, applied biomedical technologies and artificial intelligence and data science. During the third and summer terms students conduct two eleven-week research projects in labs of their choice.
Project overview:
Lattice light sheet microscopy (LLSM) is a new technology to visualise fast cellular processes at the time scale of 1 second, in 3D. LLSM is very low through-put however, limiting its use for studying rare events, such as cell divisions. In close collaboration with industrial partner Intelligent Imaging Innovations Ltd. (3i), suppliers of LLSM, we will develop an integrated imaging pipeline to classify and anticipate physiologically meaningful events during the cell cycle using state of the art machine learning.
The main goal is to 1) enable automated control of the image acquisition and increase its throughput, and 2) make it possible to analyse statistically significant numbers of well-defined cellular events and their progression from an early stage, which often go unnoticed by even the most expert human experimenter. Enabling detailed spatio-temporal analysis of the 3D imaging data will help to better understand the timing and control of different stages of cell division and recognise more subtle defects in cell division which can affect development or diseases such as cancer where divisions occur uncontrolled.
This is an interdisciplinary project at the interface of cell biology, computer science and engineering, enabling fundamental science to improve human health through world-class biomedical research. Health focus is enabling biological research into genetic risk and disease mechanisms, aiming at new strategies for early diagnosis and treatment.
The specific training the student will receive is geared towards quantitative and interdisciplinary skills and understanding of whole organism physiology in addition to that of single cells in the main project. The training in advanced machine learning and computing addresses the demand for team scientists and technology specialists and will help to build new software technologies and imaging instruments that will become available to the biomedical community in the future.2024-12-30C008C651-F5B0-4859-A334-5F574AB6B57CMRC2020-10-04INCOME_ACTUAL024302166CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0CABBA18-5FC8-4B1F-BE98-00848D0342B4ERDERA - EUROPEAN RARE DISEASES RESEARCH ALLIANCEActive10159543EU-FundedThe European Rare Diseases Research Alliance (ERDERA) aims to improve the health and well-being of the 30 million people living with a rare disease in Europe, by making Europe a world leader in Rare Disease (RD) research and innovation, to support concrete health benefits to rare disease patients, through better prevention, diagnosis and treatment. This Partnership will deliver a RD ecosystem that builds on the successes of previous programmes by supporting robust patient need-led research, developing new diagnostic methods and pathways, spearheading the digital transformational change connecting the dots between care, patient data and research, while ensuring strong alignment of strategies in RD research across countries and regions. Structuring goal-oriented public-private collaborations targeted at interventions all along the R&D value chain will ensure that the journey from knowledge to patient impact is expedited, thereby optimising EU innovation potential in RD. To support its ambition and missions ERDERA has been designed as a comprehensive and integrated ecosystem of which structure can be compared to an institute encompassing three main parts: (i) funding, (ii) internal (in house) Clinical Research Network that implements research activities targeting clinical trial readiness of RDs and accelerating diagnosis and translation of research discovery into improved patient care, and (iii) related supporting services (Data, Expertise, Education and Training) as well as an acceleration hub that serve external and internal RD community, all supported by all-embracing coordination and strategy and foundational (inter)national alignment.2027-08-30240CEBFD-1052-4EAC-88DF-D88A163D61C8Horizon Europe Guarantee2024-08-31INCOME_ACTUAL265671101595436CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0CB9A4A7-4DC8-45F0-9A0C-01AC782A2E0EUsing Artificial Intelligence to Understand Zeolite CatalystsClosed2594586StudentshipElectron microscopy provides a unique tool for studying the local structure of materials at the atomic scale. However, a major challenge lies in correlating bulk measurements of properties with highly selective structural data. One approach is to take advantage of fast electron detectors to acquire large data sets of millions of images and to develop automated analysis tools based on deep learning to analyse these. The overall aim of this project is to study defect structures in zeolites involved in heterogeneous catalysis. This project will use recent developments in fast direct electron detectors for transmission electron microscopy for low dose imaging and neural networks trained for pattern recognition of specific defect structures. The potential impact of these studies is a better understanding of catalytic processes of interest to the industrial sponsor and an improved understanding of the relationships between catalytic performance and local structure.
Initially the project will use new detectors operating at kHz frame rates to record large datasets containing many TEM images of defect structures. In parallel the project will develop the use of machine learning based on convolution neural networks to build image analysis tools suitable for analysing large data sets containing millions of images. A convolutional neural network will be trained using simulated data of known defect structures for various electron dose budgets and other imaging conditions. This will then be used to analyse the experimental data to gain meaningful statistics on defect types. The research proposed relies heavily on unique instrumentation available at the electron Physical Sciences Imaging Centre. Specifically, a new high speed direct electron detector operating at a frame rate in excess of 2KHz in 12 bit counting mode will be used to acquire low dose data. Within all of the above aims and objectives it will be necessary to ensure that the methods developed are robust to low dose data acquisition as zeolites are known to be radiation sensitive and to ensure that electron beam induced effects are minimised. Initially pure zeolites will be studied but the project will also be extended to study metal loaded zeolites and comparisons between defects in these systems and the pure materials will provide insights into the mechanisms and structural consequences of metal loading. Finally catalytic data will be measured at the industrial sponsors laboratories to attempt to correlate catalytic performance with the nature and densities of defects present across a range of loaded and unloaded samples
The project falls within the EPSRC energy, Artificial Intelligence and Robotics and physical sciences research areas
The project is funded by Johnson Matthey plc through the iCase initiative.2025-09-29798CB33D-C79E-4578-83F2-72606407192CEPSRC2021-09-30INCOME_ACTUAL025945866CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0CF15F24-E99E-4496-83E0-0191A65E11DBPredicting Biological Carbon in the Ocean Globally (PRECOG)ActiveMR/Y016629/1FellowshipEmissions of carbon dioxide (CO2) from our society are rapidly warming our climate to currently 1.1 degrees C warmer than in preindustrial times. Global governments have pledged to reduce emissions to stabilise our warming climate at 1.5 degrees requiring us to reduce emissions of CO2 to a point where they no longer accumulate in the atmosphere: Net Zero. A crucial consideration in this effort are natural reservoirs of carbon on the Earth's surface such as permafrost and soils that store large amounts of carbon away from the atmosphere, but which are vulnerable to environmental change. The destabilisation of these reservoirs over time, releasing more CO2 into the atmosphere, presents a challenge to stabilising climate upon reaching Net Zero. Therefore, predicting how these natural carbon reservoirs will change in the future is a crucially important task.
The Biological Carbon Pump is one of these natural reservoirs of carbon in our Earth System. It stores carbon in the ocean by plankton (microscopic plants) taking up CO2 as they grow in the surface ocean. The sinking remains of these plankton carry the carbon into the deep ocean locking it away for hundreds to thousands of years. This carbon pool is equivalent in size to the anthropogenically-driven increase in atmospheric CO2 over the 20th century. The Biological Carbon Pump is widely expected to be sensitive to environmental change and could therefore release CO2 in the future. However, we have limited knowledge of what those changes might be and why because we don't have the necessary outputs from the state-of-the-art future projections by Earth System Models that underpin the Intergovernmental Panel on Climate Change (IPCC) reports that inform social, economic and political decisions about Climate Change.
PREdicting biological Carbon in the Ocean Globally (PRECOG) will build a team of experts at the University of Liverpool to comprehensively explore the future of the Biological Carbon Pump using state-of-the-art Earth System Model projections. PRECOG will strategically align with an international network of researchers and industry partners to build a new knowledge framework that will inform future IPCC reports and mitigation strategies.
PRECOG will:
1) Derive new standard quantitative measures of the Biological Carbon Pump in a future changing ocean.
2) Quantify how and why the Biological Carbon Pump changes in state-of-the-art future projections that underpin the IPCC reports.
3) Determine the long-term impact of the Biological Carbon Pump beyond the year 2100 using new Earth System Model simulations.
4) Predict which future projections of the Biological Carbon Pump are most likely and how this might impact schemes to artificially enhance carbon storage by combining future projections with new compilations of observations.
PRECOG has a strong focus on connecting scientific outcomes to societally relevant outcomes. The research team will maintain a strong and active link with IPCC activities through its international network with the aim of raising the profile of Biological Carbon Pump research. PRECOG will also work with industry partners interested in techniques that will enhance the carbon storage of the Biological Carbon Pump to help mitigate rising CO2 such as kelp farming and seeding the ocean with iron. PRECOG will provide the state-of-the-art estimates for the best locations to undertake these activities and disseminate these findings through its industrial partners.
In summary, the Biological Carbon Pump is a vulnerable natural carbon pool in the ocean that can influence atmospheric CO2 in response to environmental change. The future of this carbon pool is however poorly known. This Future Leaders Fellowship, PRECOG, will establish a team of experts to explore the Biological Carbon Pump in state-of-the-art IPCC projections to find out what the likely future changes are and translate this is into a societally relevant agenda.2028-10-3150B4BB1A-2D10-4C8C-A35D-1ED2DB0ABB51UKRI FLF2024-11-01INCOME_ACTUAL1346258Italian National Institute of Oceanography and Experimental Geophysics (OGS)ItalyAtlantECOA3FC397F-9850-49C5-B5F6-EA83CECB0134A manuscript titled "Carbon sequestration service in the Atlantic Ocean: an assessment from coastal to ocean ecosystems" currently being revised for Earth-Science Reviews. This collaboration is multi-disciplinary combining ocean sciences with policy-based blue carbon ecosystems research69aea6af661171.89904241-1Provided intellectual framework that integrated the Biological Carbon Pump within a Blue Carbon Ecosystems framework.I provided analysis detailing the Biological Carbon Pump in the Atlantic from IPCC model projectionsPublic2025-01-01National Oceanography CentreUnited KingdomAtlantECOAC682B76-E5C5-4D14-9E11-498667AFEBAEA manuscript titled "Carbon sequestration service in the Atlantic Ocean: an assessment from coastal to ocean ecosystems" currently being revised for Earth-Science Reviews. This collaboration is multi-disciplinary combining ocean sciences with policy-based blue carbon ecosystems research69aea6af661171.89904241-2Provided intellectual framework that integrated the Biological Carbon Pump within a Blue Carbon Ecosystems framework.I provided analysis detailing the Biological Carbon Pump in the Atlantic from IPCC model projectionsAcademic/University2025-01-01World Climate Research ProgrammeSwitzerlandCMIP7 Earth System Data Request96273E30-9E1C-49AC-ACC5-C165C7A418A1Manuscript in revision at Geoscientific Model Development ("CMIP7 Data Request: Earth System Priorities and Opportunities") within the special issue on CMIP7 scientific objectives, experimental design, and organization69aea7b86b7d43.42730510-1Provided the data request frameworkEngaged with the broader ocean biogeochemistry scientific community to develop a list of desired model outputs that can be integrated into the next phase of the Coupled Model Intercomparison Project (CMIP7)Academic/University2025-01-01The research has influenced the next round of international climate model projections that underpin the Intergovernmental Panel on Climate Change (IPCC) reports. Specifically, we have engaged with the wider scientific community to develop specific model outputs required to quantify the future changes in biological carbon storage from the Biological Carbon Pump.We have specified new climate model outputs that will enable future researchers to quantify future changes in the Biological Carbon Pump in more detail than previously possible.596E181B-211F-4638-AF81-45D3B91BD14669aeab2dab9e25.95798995EnvironmentThis *.rar file contains the model output from seasonal variability experiments using the NPZD-DOP GEOMAR biogeochemical model (Kriest et al., 2010) coupled with the MITgcm 2.8deg ocean circulation via the transport matrix method (Khatiwala et al., 2005; Khatiwala, 2007, 2018).
These model outputs are presented and discussed in the Preprint "Seasonality in carbon flux attenuation explains spatial variability in transfer efficiency", available on EarthArXiv (de Melo Viríssimo et al., 2023). The manuscript describes the experiments performed, the parameter values used and the modifications done to the original model. For this matter, we also refer you to de Melo Viríssimo et al. (2022).
All files uploaded were generated from simulations run by the authors, except: the grid file, the salinity field, and the temperature field, which came with the model; and the density fields, who were computed from the MITgcm 2.8deg transport matrix by Rafaelle Bernadello, using a TEOS-10 matlab routine (http://www.teos-10.org/).
For specific information about each file uploaded, please refer to the README file. If you have any questions, please feel free to contact me.
References:
Kriest et al. (2010): https://doi.org/10.1016/j.pocean.2010.05.002
Khatiwala et al. (2005): https://doi.org/10.1016/j.ocemod.2004.04.002
Khatiwala (2007): https://doi.org/10.1029/2007GB002923
Khatiwala (2018): https://doi.org/10.5281/zenodo.1246300
de Melo Viríssimo et al. (2022): https://doi.org/10.1029/2021GB007101
de Melo Viríssimo et al. (2023): https://doi.org/10.31223/X5966J64FD948D-0BA2-49D5-B683-9C0BBD1EDF4667c7b0eeaf3017.59908161trueModel output used in the manuscript "Seasonality in carbon flux attenuation explains spatial variability in transfer efficiency"Database/Collection of datahttps://zenodo.org/doi/10.5281/zenodo.75141292023Marine dissolved organic carbon (DOC) is a significant carbon reservoir that impacts climate but remains poorly quantified. The absence of a comprehensive DOC climatology impedes model validation, estimation of the current DOC inventory, and comprehension of DOC's role in the carbon cycle and climate. To tackle this issue, we employed boosted regression trees to link a compilation of DOC observations with various environmental climatologies, extrapolating these relationships across the entire ocean to generate annual layer-wise DOC climatologies with associated uncertainties. The prediction performance was satisfactory, with R² values ranging from 0.6 to 0.8 across all layers. In the bathypelagic layer, DOC was primarily predicted by dissolved oxygen, while nutrients were the main predictors in other layers. We estimate the total oceanic DOC inventory to be approximately 690 PgC. Our findings demonstrate that machine learning is a powerful tool for developing climatologies from limited observations.
Files description
annual_climatologies.csv - lon: longitude - lat: latitude - surf_doc_avg: average DOC prediction in the surface layer (0 - 10 m) - surf_doc_sd: standard deviation of DOC prediction in the surface layer (0 - 10 m) - epi_doc_avg: average DOC prediction in the epipelagic layer (10 - 200 m) - epi_doc_sd: standard deviation of DOC prediction in the epipelagic layer (10 - 200 m) - meso_doc_avg: average DOC prediction in the mesopelagic layer (200 - 1000 m) - meso_doc_sd: standard deviation of DOC prediction in the mesopelagic layer (200 - 1000 m) - bathy_doc_avg: average DOC prediction in the bathypelagic layer (> 1000 m) - bathy_doc_sd: standard deviation of DOC prediction in the bathypelagic layer (> 1000 m)
seasonal_climatologies.csv - lon: longitude - lat: latitude - season: meteorological season in the northern hemisphere as 1 = DJF, 2 = MAM, 3 = JJA, 4 = SON - surf_doc_avg: average DOC prediction in the surface layer (0 - 10 m) - surf_doc_sd: standard deviation of DOC prediction in the surface layer (0 - 10 m)9CA16334-3ADA-41E4-97B4-21F8CC6B1F4B67c7b0ee0bf596.49347898trueA machine learning-based dissolved organic carbon climatologyDatabase/Collection of datahttps://www.seanoe.org/data/00900/101170/20246F2427C5-BA23-4C7F-9C6C-DA00394E9548NutGEnIE 1.0: nutrient cycle extensions to the cGEnIE Earth system model to examine the long-term influence of nutrients on oceanic primary productionGeoscientific Model Development7be910bddebfbcf0c05c3db0b46ac7cfStappard D2025-01-0168de7973cebe3A6CE7FD1-7D83-4FE4-838F-C253F94B417ECMIP7 Data Request: Earth System Priorities and Opportunitiesda5365aed0ddcc31e07ef751b6d45ce2McPartland M2025-01-016877ad65c3add3E1B409A-1C8D-409E-97EC-D95081785623A Machine Learning-Based Dissolved Organic Carbon ClimatologyGeophysical Research Lettersb222e5dd6a4f4cc88181f499dde1de8dPanaïotis T2025-01-0167ecc1be9260eB2E46A31-E395-4C6C-A08F-77EAE2262ADBLong-term impacts of mixotrophy on ocean carbon storage: insights from a 10 000 year global model simulationBiogeosciencesbbfa41b334d859bb7d8deae24529cd30Puglia M2026-01-016969d8fb2edeaMR/Y016629/16CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified