Developments in Global Food Prices

Global food prices have increased significantly since the early 2000s, reversing the long-run trend decline in relative food prices over previous decades. A range of supply disruptions in key food-producing countries have contributed to higher food prices, along with strong demand from developing countries as per capita incomes rise and consumption patterns change. Rising commodity prices are leading to higher headline consumer price inflation in many countries though, at this stage, core measures of inflation remain relatively contained.food prices; food demand; food supply; biofuels; crop yields; food price inflation

Functional analysis of POLE exonuclease domain mutations in cancer

POLE encodes the polymerase and exonuclease domains of the leading strand replicase, DNA polymerase ε. Somatic and germline POLE exonuclease domain mutations (EDMs) occur in colorectal and endometrial cancer and are associated with tumour ultramutation, a distinct mutation signature and an excellent prognosis. However, the mechanism by which POLE EDMs cause mutagenesis and the molecular consequences of this are unclear. Previous functional studies in several POLE EDM knock-in cell and mouse models have been performed, however they all have limitations regarding their clinical relevance. In addition, the timing of POLE EDMs in tumour development is based purely on genomic data from advanced POLE EDM tumours with no direct evidence of their occurrence in pre-cancers. The aim of this thesis was to study the function of POLE EDMs in clinically relevant human cell-line and mouse models and determine their timing in cancer development. Corrected somatic POLEP286R EDM isogenic colorectal cancer cell lines were generated using CRISPR-Cas9. Correction of the POLE mutation resulted in a striking reduction in the HPRT1 mutation rate (11-75-fold), consistent with a causal role in tumour ultramutation. Furthermore, the POLE EDM cell line somatic mutation spectra exhibited a significant bias towards POLE signature mutations: TCT>TAT, TCG>TTG and TTT>TGT (P<0.0001). Analysis of uterine and intestinal-specific tissue and constitutive germline PoleL424V EDM knock-in mice revealed no gross morphological or histopathological phenotype, however constitutive models demonstrated elevated Cleaved-Caspase-3 expression in the small intestine (P<0.05). Germline PoleL424V expression increased the colonic polyp burden in ApcMin mice (P<0.05), although there was no significant difference in the small intestinal polyp burden. Finally, a somatic POLEV411L EDM was identified in a colorectal pre-cancer with an elevated T-cell infiltrate, increased somatic mutation burden and a bias of POLE EDM-associated amino acid substitutions. Overall, this work provides strong evidence that POLE exonuclease domain mutations cause tumour ultramutation, a distinct mutation signature and are an early event in cancer. POLE EDM mice only developed a gross morphological phenotype when crossed with ApcMin mice, raising interesting questions regarding the mechanism of tumour initiation in cancers with POLE exonuclease domain mutations

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

Noncoding regulatory variants play a central role in the genetics of human diseases and in evolution. Here we measure allele-specific transcription factor binding occupancy of three liver-specific transcription factors between crosses of two inbred mouse strains to elucidate the regulatory mechanisms underlying transcription factor binding variations in mammals. Our results highlight the pre-eminence of cis-acting variants on transcription factor occupancy divergence. Transcription factor binding differences linked to cis-acting variants generally exhibit additive inheritance, while those linked to trans-acting variants are most often dominantly inherited. Cis-acting variants lead to local coordination of transcription factor occupancies that decay with distance; distal coordination is also observed and may be modulated by long-range chromatin contacts. Our results reveal the regulatory mechanisms that interplay to drive transcription factor occupancy, chromatin state, and gene expression in complex mammalian cell states.We thank the CRUK—CI Genomics, BRU, and Bioinformatics Cores for technical assistance and the EMBL-EBI systems team for management of computational resources. This research was supported by the European Molecular Biology Laboratory (E.S.W., D.T., J.C.M., P.F.), Cancer Research UK (B.M.S., T.F.R., F.C., C.F., A.R., D.T.O.), the BOLD ITN (B.M.S.), Darwin Fellowship (A.K.), the Wellcome Trust (WT202878/B/16/Z, WT108749/Z/15/Z) (P.F.), (WT202878/A/16/Z) (D.T.O), (WT095606) (A.C.F.-S) and (WT098051) (P.F., D.T.O.), EMBO Long-term (ALTF1518-2012) and Advanced Fellowships (aALTF1672-2014) (E.S.W.), and by the European Research Council (award 615584) and EMBO Young Investigator Programme (D.T.O.)

Transforming the Landscape: Gawthorpe, Harewood and the creation of the modern landscape 1500-1750

This thesis focuses on landscape change at Harewood House, Yorkshire, during the period 1500 to 1750. The main themes explored throughout this research are: the establishment of the nature of landscape change during the stated period; the effects of these changes on the lives of the people living and working in the landscape; and finally understanding the developments at Harewood within the broader context of changing agrarian landscapes during a period which has been widely described as an ‘age of transition’. Landscape change is explored here using a combination of archival and archaeological material, viewed from a landscape archaeology perspective. This research begins by examining the influence of theoretical debates surrounding the use of different sources of data by Landscape Archaeology and Historical Archaeology to examine this post-medieval period. A key theoretical concern to this endeavour has been the scales of interpretation which are used to examine this period, and the creation of this localised example to add to our understanding of broader national trends. In doing so, this perspective has focused on people living and working within the landscape, rather than the individuals, such as the land owners, which have dominated previous interpretations. One of the main findings of this research is that although significant landowners such as the Gascoigne family, Thomas Wentworth and the Lascelles family undoubtedly impacted upon the Harewood landscape, people living and working within the estate retained a degree of control over their own daily lives. Significant features such as Harewood Castle, All Saints Church and Gawthorpe Hall were displays of power and control over the landscape, which to some degree shaped movement through and interaction with the landscape, but archaeological data have here been shown to suggest that power relations in the day-to-day lives of the community were more nuanced than these large-scale interpretations might suggest. An additional element of this research is an exploration of the potential of public engagement with relatively under-studied and under-represented perspectives on country houses. This research has made some initial attempts to challenge current understanding of the public history of Harewood estate and examines the potential for future developments within this setting.

CRISPR-Cas9 Causes Chromosomal Instability and Rearrangements in Cancer Cell Lines, Detectable by Cytogenetic Methods

CRISPR-Cas9 has quickly become the method of choice for genome editing, with multiple publications describing technical advances and novel applications. It has been widely adopted as a tool for basic research and has significant translational and clinical potential. However, its usage has outpaced the establishment of essential and rigorous controls for unwanted off-target effects, manifested as small mutations, large deletions of target loci, or large-scale chromosomal rearrangements. A common application of CRISPR-Cas9 is as a tool for creating isogenic cell-line models to study the effects of precise mutations, or variants, on disease traits. Here, we describe the effect of standard CRISPR-Cas9 mutagenesis protocols on well characterized cancer cell lines. We demonstrate that commonly used methods for detecting correctly mutated clones fail to uncover large-scale rearrangements. We show that simple cytogenetic methods can be used to identify clones carrying chromosomal abnormalities and large mutations at target loci. These methods are quick and cost-efficient, and we suggest that such controls should be performed prior to publication of studies based on novel CRISPR-Cas9 mutated cancer cell lines

Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. METHODS: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource-Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of <1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. RESULTS: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (Kco; 33% [interquartile range, 30%-35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23-38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. CONCLUSIONS: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low Kco and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation

Adjuvant treatment for POLE proofreading domain-mutant cancers: sensitivity to radiotherapy, chemotherapy, and nucleoside analogues

Purpose: Pathogenic POLE proofreading domain mutations are found in many malignancies where they are associated with ultramutation and favorable prognosis. The extent to which this prognosis depends on their sensitivity to adjuvant treatment is unknown, as is the optimal therapy for advanced-staged or recurrent POLE-mutant cancers. Experimental design: We examined the recurrence-free survival of women with POLE-mutant and POLE-wild-type endometrial cancers (ECs) in the observation arm of the randomized PORTEC-1 EC trial (N=245 patients with stage I EC for analysis). Sensitivity to radiotherapy and selected chemotherapeutics was compared between Pole-mutant mouse embryonic stem (mES) cells, generated using CRISPR-Cas9 (Pole mutations D275A/E275A, and cancer-associated P286R, S297F, V411L) and isogenic wild-type cell lines. Results: In the observation arm of the PORTEC-1 trial (N=245), women with POLE-mutant ECs (N=16) had an improved recurrence-free survival (10yr RFS 100% vs 80.1% for POLE-wild-type; HR=0.143, 95% CI=0.001-0.996, P=0.049). Pole mutations did not increase sensitivity to radiotherapy nor to chemotherapeutics in mES cells. In contrast, Pole-mutant cells displayed significantly increased sensitivity to cytarabine and fludarabine (IC50 Pole P286R-mutant vs wild-type: 0.05 vs 0.17 μM for cytarabine, 4.62 vs 11.1 μM for fludarabine; P <0.001 for both comparisons). Conclusions: The favorable prognosis of POLE-mutant cancers cannot be explained by increased sensitivity to currently used adjuvant treatments. These results support studies exploring minimization of adjuvant therapy for early-stage POLE-mutant cancers, including endometrial and colorectal cancers. Conversely, POLE mutations result in hypersensitivity to nucleoside analogs, suggesting the use of these compounds as a potentially effective targeted treatment for advanced-stage POLE-mutant cancers

Long Covid active case finding study protocol: A co-produced community-based pilot within the STIMULATE-ICP study (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways)

BACKGROUND AND AIM: Long Covid is a significant public health concern with potentially negative implications for health inequalities. We know that those who are already socially disadvantaged in society are more exposed to COVID-19, experience the worst health outcomes and are more likely to suffer economically. We also know that these groups are more likely to experience stigma and have negative healthcare experiences even before the pandemic. However, little is known about disadvantaged groups' experiences of Long Covid, and preliminary evidence suggests they may be under-represented in those who access formal care. We will conduct a pilot study in a defined geographical area in London, United Kingdom to test the feasibility of a community-based approach of identifying Long Covid cases that have not been clinically diagnosed and have not been referred to Long Covid specialist services. We will explore the barriers to accessing recognition, care, and support, as well as experiences of stigma and perceived discrimination. METHODS: This protocol and study materials were co-produced with a Community Advisory Board (CAB) made up primarily of people living with Long Covid. Working with voluntary organisations, a study leaflet will be distributed in the local community to highlight Long Covid symptoms and invite those experiencing them to participate in the study if they are not formally diagnosed. Potential participants will be assessed according to the study's inclusion criteria and offered the opportunity to participate if they fit them. Awareness of Long Covid and associated symptoms, experiences of trying to access care, as well as stigma and discrimination will be explored through qualitative interviews with participants. Upon completion of the interviews, participants will be offered a referral to the local social prescribing team to receive support that is personalised to them potentially including, but not restricted to, liaising with their primary care provider and the regional Long Covid clinic

Barriers to healthcare access and experiences of stigma: Findings from a coproduced Long Covid case-finding study

BACKGROUND AND AIM: Long Covid is often stigmatised, particularly in people who are disadvantaged within society. This may prevent them from seeking help and could lead to widening health inequalities. This coproduced study with a Community Advisory Board (CAB) of people with Long Covid aimed to understand healthcare and wider barriers and stigma experienced by people with probable Long Covid. METHODS: An active case finding approach was employed to find adults with probable, but not yet clinically diagnosed, Long Covid in two localities in London (Camden and Merton) and Derbyshire, England. Interviews explored the barriers to care and the stigma faced by participants and were analysed thematically. This study forms part of the STIMULATE-ICP Collaboration. FINDINGS: Twenty-three interviews were completed. Participants reported limited awareness of what Long Covid is and the available pathways to management. There was considerable self-doubt among participants, sometimes reinforced by interactions with healthcare professionals (HCPs). Participants questioned their deservedness in seeking healthcare support for their symptoms. Hesitancy to engage with healthcare services was motivated by fear of needing more investigation and concerns regarding judgement about the ability to carry out caregiving responsibilities. It was also motivated by the complexity of the clinical presentation and fear of all symptoms being attributed to poor mental health. Participants also reported trying to avoid overburdening the health system. These difficulties were compounded by experiences of stigma and discrimination. The emerging themes reaffirmed a framework of epistemic injustice in relation to Long Covid, where creating, interpreting and conveying knowledge has varied credibility based on the teller's identity characteristics and/or the level of their interpretive resources. CONCLUSION: We have codeveloped recommendations based on the findings. These include early signposting to services, dedicating protected time to listening to people with Long Covid, providing a holistic approach in care pathways, and working to mitigate stigma. Regardless of the diagnosis, people experiencing new symptoms must be encouraged to seek timely medical help. Clear public health messaging is needed among communities already disadvantaged by epistemic injustice to raise awareness of Long Covid, and to share stories that encourage seeking care and to illustrate the adverse effects of stigma. PATIENT OR PUBLIC CONTRIBUTION: This study was coproduced with a CAB made up of 23 members including HCPs, people with lived experience of Long Covid and other stakeholders

Towards a process of translational palaeoecology: a practical guide to research co-production

1. Palaeoecology has the potential to support practical conservation, offering a long-term perspective to issues such as biodiversity loss, environmental restoration and peatland carbon storage. However, achieving a widespread and effective application of palaeoecology within conservation practice requires greater and more efficient collaboration between academics, practitioners and policymakers.2. Translational palaeoecology offers a methodological approach to achieve collaboration between academia and conservation and produce palaeoecological research that can support and inform conservation action.3. This paper reports the results of a workshop involving academics undertaking palaeoenvironmental research and conservation practitioners concerning the barriers and practical recommendations for effective research-practice collaboration. The experiences of the participants highlight the benefits of a collaborative approach for producing palaeoecological research that is enriched with experiential and contextual knowledge. Key themes emerging from the workshop include the importance of mutual learning and knowledge exchange, and supporting practitioners to be co-researchers.4. Practical implication. The workshop outcomes are presented as a framework of practical guidelines for implementing translational palaeoecology. Key recommendations for academics include engaging with practitioner activities as relationship-building opportunities, utilising field visits for knowledge exchange, adopting a knowledge facilitation role or involving a facilitator to support practitioner understanding, using workshops to explore the practical relevance of palaeoecological data and enabling practitioners to communicate palaeo-research findings in their sphere. Key recommendations for practitioners include inviting academics to practitioner meetings, providing tacit and experiential knowledge throughout the process, exploring practitioner- or land-owner-led funding opportunities for translational research and partaking in communication roles for wider dissemination of research<br/