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Investigation of the impact of elevated phosphorus concentrations on the different life phases of two species of Ephemeroptera
No full textFreshwaters are persistently threatened by anthropogenic activities that disrupt the chemistry and ecology of the ecosystem. In England, despite notable improvements in surface water quality since the 1990s, nutrient pollution -particularly elevated phosphorus concentrations - remains a significant obstacle to achieving the “good ecological status” outlined by the Water Framework Directive. Poor water quality has led to a decline in the abundance and diversity of pollution-sensitive aquatic insects such as the Ephemeroptera (mayflies) across many English rivers. As a bioindicator of aquatic environment health, mayflies provide critical insights into ecosystem change. However, while the link between phosphorus and freshwater eutrophication is well documented, declining mayfly populations have also been observed in river systems impacted by nutrient pollution but not classified as eutrophic.
Research on nutrient pollution in relation to mayflies has previously predominantly focused on the eutrophic effects on the nymph life phase. Therefore, there remains limited understanding of three critical aspects: (1) the specific effect of elevated phosphorus concentrations on the egg stage of mayflies which are particularly vulnerable due to their inability to evade polluted environments: (2) how phosphorus enrichment directly impacts mayflies across all life-stages in non-eutrophic conditions; and (3) how nutrient pollution affects aquatic fungal growth and the reciprocal interactions between fungal communities and mayflies from the moment their eggs are deposited.
The body of work presented here aimed to address these knowledge gaps through a series of mesocosm experiments and a year-long field study. For the mesocosm trials, a reductionist approach was taken to isolate the effects of elevated phosphorus concentrations on the fitness and hatching success of eggs from the mayfly species, Ecdyonurus venosus and Ephemera danica, captured from field sites in spring 2022 and 2023, respectively. Adult mayflies were encouraged to lay eggs in synthetic water in which all elements and pH were kept constant, apart from phosphorus. In addition, the direct effects of an elevated phosphorus concentration of 0.75 mg P L-1 on the nymph stages of the same species, while holding all other environmental factors constant, were evaluated.
For analysis of egg hatching, a Python programme was designed, written and implemented to aid in counting eggs. Egg and nymph survival data, and nymph growth and emergence values, showed that low concentrations of phosphorus (0.1 mg L-1) were required for physiological development and that elevated concentrations had no detrimental effect on either life stage of the species studied. Therefore, under controlled conditions, enhanced phosphorus concentrations did not detrimentally affect the eggs or nymphs of Ecdyonurus venosus and Ephemera danica when all other factors remained constant.
These data suggest that the observed (published and anecdotal) negative effects of phosphorus on mayflies under field conditions are likely to be more complicated than the negative effects of a single nutrient in isolation. To determine whether these findings would also be observed in the field, a river impacted by the treated discharge from a sewage outfall pipe was selected to evaluate mayfly populations and other invertebrates above, at, and below, the ingress point. The river was a chalk stream in Buckinghamshire – the River Chess. Biologically available phosphorus was consistently higher in the water near the outfall (> 2 mg L-1) relative to the upstream site (< 0.3 mg L-1) depending on season. Potassium and nitrogen concentrations were also higher at the outfall site; it was not possible to differentiate between the effects of phosphorus, other elements, or whether any effects were additive. However, pollution sensitive mayfly (e.g. Heptageniidae, Ephemeridae, Ephemerellidae) were absent from the outfall site, but were present elsewhere in the river. Other pollution-sensitive taxa in general were absent from samples taken from the outfall site across all seasons, whilst sensitive indicator species were observed in samples both above and below the outfall site in all seasons. More pollution-tolerant taxa were collected from the outfall site (e.g. Asellidae, Annelida, Sphaeriidae) than at other sites. There was evidence of ecological recovery by 830 m downstream of the outfall pipe although water nutrient concentrations were higher than at the site above the outfall pipe, although lower than at the outfall. During the laboratory-based mesocosms trials, an incidental observation of filamentous fungal hyphal entrapment of nymphs emerging from eggs and leading to their death, prompted further investigation into the effects of elevated nutrient concentrations on aquatic fungi and potential links between invertebrate and fungal populations. By subsequently analysing fungal taxa derived from DNA extracted from sediment at the three sites in the River Chess, differences in fungal community composition between sites were observed. Ascomycota and Basidiomycota abundance decreased significantly at the outfall site while Rozellomycota increased, relative to the upstream and downstream sites. Seasonal interactions complicated the overall picture, but multidimensional scaling ordinations showed that elevated nutrient concentrations, particularly phosphorus, were a key driver of the observed changes in fungal community composition. The fungal component of the river system is vital for ecosystem functions and any imbalance between ecosystem engineers (e.g. members of the Ascomycota and Basidiomycota) and potential parasites (e.g. Rozellomycota) could directly or indirectly affect invertebrate survival. Given that invertebrate health and population stability are closely tied to microbial communities, it is clear that the impacts of the outfall in the studied river were both widespread and significant.
The content and findings of this study provide valuable insights into the impact of nutrient pollution on freshwater ecosystems, particularly in relation to microbial and invertebrate communities. By identifying phosphorus as a key driver of community change, this research highlights the need for more nuanced water quality monitoring that includes microbial communities as indicators of ecosystem health. Incorporating these findings into policy could inform more targeted nutrient management strategies ensuring that even sub-eutrophic conditions are effectively addressed
An investigation into human perception highlights the automatic preference and prominence given to hands
Full text linkHand perception, akin to face perception, enables the discernment and communication of human intentions or emotions. Whilst face perception has been extensively investigated in terms of cognitive and neural processes, much less is known about the cognitive processes and neural activations associated with hand perception, which this PhD project aims to study. The project posits two primary questions: (1) Are viewed hands, particularly hands with distorted finger postures, such as those that may occur after an accident, exceptionally salient? Are hands with distorted finger postures quantitatively more salient than hands with natural finger postures? (2) Is there a particular cognitive process underlying this attention, such as the activation of the viewer's sensorimotor cortex as seen in automatic mental simulation, and are there distinct cognitive processes or brain activation patterns involved in processing distorted finger postures compared to natural finger postures? Despite the potential significance of hands in revealing intentions or emotions, as opposed to the potential of faces, this issue has received considerably less research attention, particularly regarding the perception of distorted finger postures, which remains a largely unexplored issue apart from a limited number of studies focusing on brain activation.
The aim of this thesis is to employ visual search and eye movement paradigms to investigate the processing of hands and, in particular, distorted finger postures. By examining how people visually search for and attend to these stimuli, we seek to gain insights into the underlying mechanisms involved in perceiving and processing distorted finger postures. A further aim is to address how salient information is processed by means of automatic mental simulation in the Simon task and motor cognition tasks. In addition to behavioural measures, previously acquired EEG were also analysed in this thesis to detect motor cortex activation as a correlate of automatic mental simulation in the perception of hands with distorted finger postures.
From the results of the visual search and eye movement tasks (Experiments 1, 3 and 5), the main findings of this research are that the hand images were more salient than the whole body images, both in active and passive vision. In addition, in the visual search and eye movement tasks (Experiments 2, 4 and 6), the distorted finger postures were found to be more salient than the natural finger postures, both in active and passive vision. From the control experiments (Control Experiments 1, 2 and 3), the findings are that the salience of hands was not caused by affective reaction and arousal, nor by limbs with similar anatomic structures. Results from the Simon task and the hand laterality judgement tasks (Experiments 7 to 10) both provide consistent evidence supporting the occurrence of automatic mental simulation. It is evident that automatic mental simulation for hands occurs in the Simon task. Additionally, evidence was found in the hand laterality judgement tasks supporting automatic mental simulation for both hands (together) and for a single hand. However, it was not evident that automatic mental simulation occurred for individual finger images when participants were instructed to respond with their corresponding fingers. The analysis of the EEG data revealed no interaction in mu oscillations between the factors of stimulus type (hand and chair, with the chair serving as the control stimulus) and configuration (distorted and natural/standard) and no difference in mu oscillations between the viewing of distorted and natural finger postures; however, a trend in differences in mu oscillations was found between the viewing of distorted and natural shapes (for the factor of configuration).
In conclusion, this PhD research demonstrates that viewed hands, particularly those with distorted finger postures, exhibit heightened salience in visual perception tasks, suggesting the involvement of automatic mental simulation processes. Thus, the PhD project explores the cognitive and neural mechanisms underlying hand perception, focusing specifically on distorted fingers. This study aims to elucidate why these distorted finger perceptions occur and what insights or conclusions can be drawn about neural processing and cognitive functions related to these distortions
Identification of an exosomal miRNA signature in newly diagnosed essential hypertensive adults
No full textBackground: Hypertension is a leading risk factor for cardiovascular disease (CVD) and premature death globally. Less than half of adults with hypertension are properly diagnosed and treated, highlighting a critical gap in current healthcare practices. The limitations of existing blood pressure measurement methods make it challenging to detect early cases of hypertension, which are often asymptomatic and, consequently, commonly undetected. This indicates the need for improved diagnostic and treatment strategies, particularly through precision medicine approaches. MicroRNAs (miRNAs) serve as master regulators of gene expression and are transported extracellularly by exosomes in various body fluids including plasma. Exosomal miRNAs have been implicated in hypertension development and have potential as non-invasive disease biomarkers. However, the profile of exosomal miRNA in a multi-ethnic population of essential hypertensives has yet to be elucidated.
Aim and objectives: This study aimed to investigate potential biomarkers of hypertension to enhance early detection. The objectives of this study were to screen and validate the differentially expressed exosomal miRNA profiles in essential hypertensive adults and identify their predicted targets and associated pathways.
Methods: Plasma exosomes were isolated and characterised. Total plasma exosomal RNA were extracted from ethnically Chinese and Malay stage 1 essential hypertensive and normotensive adults (30 to 55 years old). Samples were subjected to small RNA sequencing, differential expression analysis, target prediction, and pathway enrichment analysis. The differential expression profile was validated with real-time quantitative polymerase chain reaction (RTqPCR). The diagnostic value of the differentially expressed miRNAs were assessed. Enriched pathways and gene ontologies of predicted miRNA targets were compared against systemically dysregulated pathways to validate its biological function.
Results: Characterisation of plasma exosomes showed preferential release of medium- to large-vesicles with a significantly increased number of particles between 150 to 200 nm (P = 0.021) and an increased mean size (mean = 104.7 ± 19.3; P = 0.036) in hypertensives. Immunoblotting showed significantly xix reduced CD9 expression in hypertensives. The combination of hsa-miR-184, hsa-miR-432-5p, hsa-miR-1-3p, and hsa-miR-1246, along with BMI, efficiently identified hypertension risk with the highest area under the curve (AUC = 0.966, P < 0.0001) for the receiver’s operating characteristic (ROC) analysis. The miRNA signature together with systemically dysregulated pathways further highlighted the convergence of aberrant metabolic pathways in the development of hypertension.
Conclusions: This study provided the first comprehensive exosomal miRNAome in a multi-ethnic population of newly identified essential hypertensive adults. The differentially expressed miRNAs in essential hypertension provided leads for further validation and may provide unbiased insights into mechanisms involved in the early stages of hypertension, facilitating novel biomarker discovery or therapy development to alleviate the burden of CVDs
Applications of a high-throughput screen detecting CRISPR-Cas spacer acquisition
Full text linkThe arms race between prokaryotes and their foreign genetic elements has driven the evolution of a diverse and enigmatic array of immune systems. CRISPR-Cas systems uniquely provide adaptive immunity against these foreign elements. Immunity is achieved through the acquisition of DNA fragments derived from invaders’ genomes, catalysed by the Cas1-Cas2 integrase complex. These fragments are stored as spacers within CRISPR arrays and are transcribed to specifically direct the effector machinery against their complementary sequences.
Mutations in the Cas1 protein of the E. coli Type I-E CRISPR-Cas system have been identified that exhibit an increased rate of spacer acquisition. It has not been practical to perform systematic large-scale screening of mutagenic libraries using previous assays. I used a papillation reporter assay system to identify novel hyperactive mutations which exhibit up to five-fold increases in rates of spacer acquisition. These mutants also induce an elevated SOS response, suggesting increased integrase activity has the potential to confer a negative fitness cost to the host cell.
The screening of metagenomic libraries to identify anti-CRISPRs targeting the integrase machinery identified homologs of genes ancillary to the process of spacer acquisition as potential inhibitors. This suggests a mechanism whereby genetic elements may inhibit CRISPR systems without directly targeting the cas genes.
Finally, I constructed and tested several versions of a genetic circuit for the high-throughput detection of spacer acquisition, which may be universally applied to CRISPR systems
Computational analysis of the taxadiene synthase reaction pathway
No full textThe taxadiene synthase reaction pathway defines a complex carbocation cascade that offers multiple stable intermediates that, in turn, can lead to multiple relevant products in chemistry. Because of the promiscuity of the terpene chemistry, simple modifications to the natural taxadiene synthase protein can completely modify the potential energy landscape, leading to alternate major product distributions.
This research uses a variety of computational techniques including homology modelling, molecular dynamics, quantum mechanics, and hybrid quantum mechanics/molecular mechanics to better understand how terpene synthases control the distribution of the resultant products.
In this work, we present the first complete and active structure of the wildtype taxadiene synthase protein. Using this structure, we study the effect of truncating the protein, which is known experimentally to deactivate the enzyme. We also performed simulations of some of the key intermediates in the taxadiene synthase reaction pathway to investigate how the protein controls the conformation of each of the intermediates.
We also generated a mutant protein (V584M) of taxadiene, which is known to produce verticillene rather than taxadiene. Using this mutant protein, we studied the effect that the mutation had on the structure of the protein. We also performed simulations similar to those performed in the wildtype protein on key intermediates on the reaction pathway. This was to understand how the mutations interacted with the carbocation cascade
Lexical Bundles in Chinese Middle School English Language Teaching: Corpus and Pedagogical Insights
No full textThis study explores the use of lexical bundles (LBs) in the Chinese middle school English language teaching (ELT) context, focusing on ELT textbooks, high-stakes exams, and the influence of teachers’ attitudes on the application and challenges of using LBs in the classroom. Although LBs – high-frequency recurring fixed word sequences – have been shown to be crucial for learners of English as a second language (L2) in both spoken and written contexts, they are often overlooked in research as well as in the current curriculum and teaching practices in China. This study compares the highfrequency LBs found in Chinese middle school ELT textbooks with those in the British National Corpus (BNC) Sampler, which represents first language (L1) English contexts, as well as with the high-frequency LBs that appear in the Zhongkao (Hanzi: 中考, Middle School Scholastic Aptitude Examination). The results reveal that the LBs in the Chinese middle school textbooks not only fail to align with the high-frequency bundles in the L1 English corpus and the Zhongkao corpus, but also omit critical usage patterns evident in these contexts.
Through semi-structured interviews with Chinese middle school ELT teachers, the study highlights the strong influence of exam-oriented practices and native speakerism on teachers’ attitudes. Respondents tended to prioritise LBs that are aligned with exam requirements, particularly those that appear in the Zhongkao exam. In addition, they believed that introducing bundles from the output of L1 English users could help students to learn more authentic English and increase their interest in language learning. Furthermore, respondents expressed a willingness to incorporate LB lists into their teaching, but only if provided with more detailed guidance, such as example sentences and structured teaching materials. Respondents also reported a lack of formal training in the effective use of LBs, both in pre-service and in-service professional development programmes. As a result, they often tended to analyse LBs from a grammatical or lexical perspective rather than adopting the holistic teaching approaches recommended by researchers.
This study suggests that changes are needed in both teacher training and textbook design to better integrate LBs into ELT in China. Specifically, textbooks need to expand their coverage of high-frequency bundles and integrate them into context-rich communicative lessons. In addition, textbooks could use text enhancement techniques (e.g., bolding or highlighting) and include clear guidelines to increase both teacher and student awareness of LBs. Teacher training programmes could provide explicit strategies for incorporating LBs into classroom teaching and emphasise their role in facilitating authentic language use, rather than focusing solely on exam preparation. By addressing these gaps, it is hoped that LBs can be effectively integrated into ELT practice, ultimately helping students to improve both their test performance and their communicative competence in English
Induction of autophagy by non-structural protein 6 in important animal and human coronaviruses
No full textCoronaviruses (CoVs) are known to interfere and modulate host-cell processes to promote viral replication and evade immunity. A key role presented in available literature is that CoVs can modulate autophagy, a process critical to homeostatic maintenance. This thesis investigates the role of non-structural protein 6 (NSP6) of coronaviruses, including FCoV, the cause of feline infectious peritonitis virus (FIP), human CoV-OC43 (HCoV-OC43) and serve acute respiratory syndrome CoV 2 (SARS-CoV-2) in the manipulation of autophagy. Bioinformatic analysis, including Clustal Omega multiple sequence alignment and transmembrane prediction tools, showed that NSP6 has relatively few conserved domains and transmembrane regions across the viral species, potentially suggesting functional similarities may be preserved through structural adaptations, rather than sequence conservation.
Restriction digest cloning was employed to clone the NSP6 protein of the three viral species into a pCAGGS_mCherry vector, enabling protein expression analysis to investigate its effects on autophagy. Immunoblotting and indirect immunofluorescence showed an increase in production of autophagosomes when cells expressed NSP6, whilst also appearing to impair autophagic flux, observed by the accumulation of LC3-II and p62/SQSTM1, respectively. NSP6 appeared to have an effect mTOR signalling, which is a critical regulator of autophagy induction. Additionally, NSP6 was observed to co-localise with BST-2, indicating a potential interaction that could aid in the evasion of innate immunity by coronaviruses.
This study concludes that NSP6 may have a role in the modulation of autophagy, which could enhance viral survival and replication. In addition, co-localisation with BST-2 suggests that NSP6 may also play a role in evading host immunity and enhancing the viral survival in cells. Future studies could include analysis of NSP6 in autophagy knockout cell lines (e.g. ATG5 KO) and exploring the broader implications of potential interactions between NSP6, BST-2 and the autophagy pathway, providing an insight into host immune evasion
Understanding microenvironments and the potential of traditional farming systems in a changing climate in Mexico and Belize
Full text linkIn Latin America and the Caribbean, climate change impacts have been particularly strongly felt by small-scale farmers who still practice farming that is highly dependent on rainfall and on traditional management. In the Yucatan Peninsula (Southern Mexico, Belize, and Northern Guatemala), these effects have particularly impacted Maya indigenous communities (Maya Yucatec) that practice traditional rain-fed agriculture. One of the traditional farming systems that continues to be practiced by the Maya people for millennia but has also been changing from its ancient origin is the Maya milpa or Kool (as referred to in Maya language). The Maya milpa is a polyculture system planted with a wide variety of plants (mainly maize, beans, and squash), managed in many ways under a biocultural approach, and characterized for supporting local food systems, social structures and the use of indigenous knowledge.
Milpa has been of great scientific interest, not only because it has remained present in the livelihoods, culture, and local economy of Maya communities for centuries, providing income, food security, and cultural identity, but due to its vulnerability to extreme weather events such as droughts and hurricanes. Climatic variability, its impact on milpa, and how local societies adapt to climatic disturbances in this region has been explored by different authors. However, few studies have compared transnational adaptation responses within the same ethnic group practicing milpa and the role of indigenous knowledge in these adaptation strategies.
This thesis investigates what aspects Maya Yucatec farmers prioritise when building resilience to climate change and how they use and adapt indigenous and other knowledge systems to develop this resilience. The research uses a convergent mixed methods approach to document, assess and compare similarities and differences in views, experiences and capacities within the Maya Yucatec people to explore the adaptation processes in traditional milpa and describes and analyses changes in local environmental conditions impacting milpa management. This study was conducted by drawing on data collected from eight case studies and 35 surveys with Maya Yucatec farmers in six communities in Mexico and Belize and empirical data on local weather and soil conditions.
The results show that although sharing similar ethnicity, cultural background, environmental conditions, and livelihood patterns, Maya Yucatec farmers in the studied communities have remarkably different individual relationships with the milpa system. This farmer-milpa relationship has been shaped by historical processes and influenced by site-specific factors like social networks, interlinked with external factors. This has indirectly shaped milpa management and consequently their farming priorities, their adaptive capacity and their use of indigenous knowledge.
Although climate stressors have influenced changes in milpa, there are other factors that have driven changes in milpa and vary across countries. In Mexico, changes have been shaped by social and cultural elements and networks, while in Belize key drivers were market demands and business trends.
Within the past 30 years (1991-2021) different variable long-term monthly average precipitation and average temperature have been observed across three of the six communities studied. In terms of soil attributes, pH presented the lowest variability amongst the studied plots while phosphate, potassium, and particle size distribution showed the highest variability. Maya Yucatec farmers reported several, frequent, perceptible and situated changes in climate but variable precipitation and temperature appeared to be the most commonly perceived in both countries, which in most cases aligned with empirical data.
When adapting and building resilience to climate change, Maya Yucatec farmers in Mexico and Belize use a combination of indigenous and modern knowledge. The use of indigenous knowledge remains active but can vary significantly depending on farmer’s individual priorities and thus its capacity to be regenerated, renewed, and adapted is different and autonomous. Similarly, this research found that Maya Yucatec farmers are using epistemological pluralistic approaches and reshaping indigenous and modern knowledges into an indigenous adaptive knowledge as a coping mechanism.
The adaptation strategies implemented by Maya Yucatec farmers are heterogenous across both countries, but so is the knowledge embedded in these strategies. Changing or adjusting planting times, is perceived by farmers as the most reliable. Adaptation strategies are largely based on farmer’s individual knowledge and experiential learning in Mexico and on knowledge from external sources in Belize. Given that knowledge systems are a fundamental aspect of milpa management and of Maya Yucatec social identity, it can be inferred that climate change is also impacting social and cultural dynamics and driving cultural adaptation
Electric vehicle adoption behaviour in emerging markets: the case of Thailand’s consumer behaviour and preferences
No full textElectric vehicles (EVs) stand as an essential solution to fight climate change while reducing reliance on fossil fuels. Major challenges from structural barriers, like high costs and infrastructure deficiencies, restrict EV adoption in emerging markets such as Thailand. Prior research has focused on developed markets, leaving a knowledge gap regarding how consumers in resource-constrained contexts form intentions and make adoption-related choices in developing countries.
The research employs a quantitative multi-method framework based on a critical realist paradigm to investigate the psychological and contextual factors shaping EV adoption in Thailand. The first study combines the Theory of Planned Behaviour (TPB) with sustainability perceptions related to economic, environmental, and social factors to build a structural equation model (SEM) for understanding consumer intentions towards EV adoption. Study 2 applies utility theory alongside stated preference (SP) experiments through discrete choice modelling (DCM) and mixed multinomial logit (MMNL) models to assess consumer trade-offs between important vehicle attributes, such as price, range, charging infrastructure, and policy incentives.
Findings from Study 1 indicate economic sustainability perceptions dominate environmental concerns when forming intentions. This finding underscores economic feasibility as a vital factor for emerging markets. Study 2 identifies price and the availability of both public charging stations and home charging infrastructure as key determinants in vehicle selection while showing plug-in hybrid vehicles (PHEVs) as the top alternative choice because of their versatile nature. By synthesising the results from both studies, the research uncovers a perception–action gap in EV adoption: although consumers express favourable intentions, their stated choices remain constrained by structural limitations and practical trade-offs.
This thesis contributes to EV adoption by enhancing the TPB through sustainability perceptions in a developing market context and methodologically by integrating psychological intention models with stated choice frameworks. It offers targeted policy guidance for emerging markets, emphasising the importance of financial incentives, infrastructure investments, and communication strategies to close the gap between consumer motivation and market adoption
Technology-facilitated domestic abuse in the UK: the experiences of victim-survivors and their interactions with services
Full text linkThis thesis examines women’s experiences of technology-facilitated domestic abuse (TFDA) in the UK, a complex form of abuse at the intersection of historic manifestations of domestic abuse and modern-day digital society.
This research draws on three data sets: a survey with 141 women with lived experience of TFDA, in-depth interviews with six women with lived experience of TFDA, and interviews with 16 professionals working in the domestic abuse sector. Participants hail from all four countries across the UK, making this one of the most comprehensive UK-based studies of TFDA to date.
As well as documenting the types of TFDA women are experiencing during and post their relationship, this thesis also considers how TFDA shapes and disrupts women’s ability to interact with support services. Being under digital surveillance from an intimate partner limits, or sometimes prevents, women from accessing life-saving support, and consideration must be given to how services can continue to support women safely and effectively in the digital age. Once women are in touch with services, these services must also be equipped to support women in a way which accounts for the myriad dangers and harms caused by TFDA, especially during the delicate process of separation.
This thesis concludes with practical recommendations for victim-survivors, the domestic abuse sector, other services (including the police and social services), the tech sector, and policy makers. It is hoped that the outputs from this research will be informative for those working in the tech sector, and with women impacted by TFDA, so that women can be supported more appropriately in the future
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