3,227 research outputs found

    Genome editing of candidate genes related to disease resistance to Piscirickettsia salmonis in Atlantic salmon (Salmo salar)

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    Salmon Rickettsial Syndrome (SRS), caused by the bacterium Piscirickettsia salmonis, is one of the most severe infectious diseases threatening the Chilean Atlantic salmon industry. Among the leading causes of mortality and morbidity, SRS significantly affect the seawater production stage, where biomass losses account for a major economic impact. One potential avenue to tackle SRS is the improvement of host resistance using selective breeding. To accomplish this, insight into the genetic basis of host response, identifying specific genes and pathways involved in this response, and comprehending the potential function these genes have in infection overcome, is valuable. Consequently, this study aims to identify functional genes and pathways that contribute to genetic host resistance to SRS and investigate the effect of CRISPR/Cas9 knockout on these genes during P.salmonis infection. Candidate genes were identified from a previous in vivo large-scale infection study of 2,265 Atlantic salmon smolts injected with P.salmonis and genotyped. These data were used to estimate SRS resistance breeding values. Head-kidney and liver samples for RNA-Seq were obtained from 48 individuals at pre-infection, 3 and 9 days post-infection, and tests of differential expression between pre- and post-infection, and between high and low resistance breeding values were performed. From the thousands of differentially expressed genes, enrichment of several KEGG pathways related to immune response such as bacterial internalisation, intracellular trafficking, apoptosis, and inflammasome was observed in both tissues in fish relatively more resistant to infection. A literature review of the biological function of genes in these pathways highlighted the most suitable candidates for functional studies. Subsequently, five genes related to SRS resistance were successfully edited using a CRISPR/Cas9 Ribonucleoprotein (RNP) transfection to knockout these genes in an Atlantic salmon cell line (SHK-1). An in vitro infection challenge model of the knockout and control cell lines with P.salmonis was performed to elucidate the impact on cytopathic damage, cell viability and bacterial load during infection. These findings suggest a promising avenue of research into the genetic architecture of host resistance to SRS

    An agent-based approach for energy-efficient sensor networks in logistics

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    As part of the fourth industrial revolution, logistics processes are augmented with connected information systems to improve their reliability and sustainability. Above all, customers can analyse process data obtained from the networked logistics operations to reduce costs and increase margins. The logistics of managing liquid goods is particularly challenging due to the strict transport temperature requirements involving monitoring via sensors attached to containers. However, these sensors transmit much redundant information that, at times, does not provide additional value to the customer, while consuming the limited energy stored in the sensor batteries. This paper aims to explore and study alternative approaches for location tracking and state monitoring in the context of liquid goods logistics. This problem is addressed by using a combination of data-driven sensing and agent-based modelling techniques. The simulation results show that the longest life span of batteries is achieved when most sensors are put into sleep mode yielding an increase of ×21.7 and ×3.7 for two typical routing scenarios. However, to allow for situations in which high quality sensor data is required to make decisions, agents need to be made aware of the life cycle phase of individual containers. Key contributions include (1) an agent-based approach for modelling the dynamics of liquid goods logistics to enable monitoring and detect inefficiencies (2) the development and analysis of three sensor usage strategies for reducing the energy consumption, and (3) an evaluation of the trade-offs between energy consumption and location tracking precision for timely decision making in resource constrained monitoring systems

    Elucidating How MLH1 Loss Regulates a Metabolic Phenotype in Endometrial Cancer

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    Endometrial cancer is the fourth most common cancer in women and the most common gynaecological malignancy in the developed world. No new systemic treatments for endometrial cancer have been developed in recent years and its incidence is expected to double over the next decade. As such, there is a need to better understand key molecular pathways that are altered in the disease and could be targeted by novel treatments. The DNA MMR pathway is lost in approximately 30% of endometrial cancers. A small proportion of these are caused by germline mutations in one of the four MMR genes, however, the majority result from the epigenetic silencing of MLH1. Recently, our lab has shown that MLH1-deficient cells demonstrate a mitochondrial phenotype characterised by reduced OXPHOS, reduced mtDNA copy number and Complex I inhibition. OXPHOS-deficient cells must adapt their metabolism to compensate for energy defects and the inability to efficiently use the tricarboxylic acid cycle to generate energy. We hypothesise that this altered metabolism is driving tumourigenesis by increasing the tumour cells' metastatic potential. In this PhD we aimed to further investigate the influence MLH1 loss has on cellular metabolism using MLH1 positive and negative paired endometrial cell lines. Ultimately, we aim to understand whether altered metabolism in MLH1-deficient endometrial cancer may be therapeutically targeted

    Metabolic pathways and therapeutic opportunities in the chronic lymphocytic leukemia microenvironment

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    This study delves into the intricate metabolic dynamics of chronic lymphocytic leukaemia (CLL) within the tumour microenvironment (TME) of lymphoid tissues. Unlike the traditional focus on quiescent CLL cells in peripheral blood, this study aims to unravel complex metabolic behaviour of CLL cells in the lymph node compartment, where CLL cells divide and become activated.Utilizing state-of-the-art methods, such as metabolomics, transcriptomics, and fluxomics, we found that interaction of CLL cells with adjacent cells within the TME results in significant metabolic alterations. Particularly, we discovered a shift towards glutamine dependency of CLL cells upon TME-related stimulation. Such metabolic alterations impact sensitivity of these leukaemia cells to treatments, especially to specific apoptosis inducing agents, such as venetoclax, which has become the cornerstone of CLL treatment. The study demonstrates that by targeting specific metabolic pathways, such as the electron transport chain, CLL cells can be sensitized to venetoclax treatment. This finding can be exploited for the development of innovative strategies in order to overcome drug resistance.Additionally, the thesis explores the effects of mitochondrial glutamine transporters and the broader implications of lipid metabolism alterations in CLL. It also probes into the role of key genetic factors, such as p53, in the metabolic regulation of CLL and other B cell malignancies, unveiling new insights into potential therapeutic vulnerabilities.Conclusively, this research not only fills critical gaps in our understanding of CLL metabolism within the TME but also paves the way for novel, targeted therapeutic interventions. By linking metabolic alterations to treatment responses, it sets the stage for more effective, personalized approaches in the management of CLL

    Developing great teachers through professional development: a comparative international case study in England, Israel, South Korea, and Turkey

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    This comparative international case study explores teacher quality, that is, how teachers, who are regarded as great, train and develop. In particular, the thesis investigates ways in which participation in professional development programmes contributes to teachers’ professional knowledge and the personal virtues involved in teaching chemistry at secondary school level in England, Israel, South Korea, and Turkey as case study nations. The study employs a comparative case study approach. Empirical data collection was preceded by a document analysis and a comprehensive literature review which revealed three themes, namely community of practice, pedagogical content knowledge, and professional beliefs and virtues as impacting teachers in becoming great teachers. These themes were explored in practice utilising qualitative data collection methods, namely semi structured interviews with science teachers (mainly chemistry) who participated in professional development programmes and through observing lessons and professional development activities of teachers teaching science to 14-18-year-olds. Data was collected in South Korea, Israel, Turkey, and the United Kingdom (England) over a 1-year period. A volunteer sample of 40 science teachers (10 teachers for each country) were interviewed. Ten professional development activities were observed. The total length of observed PD activities was 1500 minutes. Nine science teachers were observed in four countries. The total length of observed lessons was 525 minutes. Four focus group interviews with the participation of 18 teachers were conducted. Thematic analysis was used to analyse the data. The data shows that great teacher appears differently in the four nations. A great teacher is identified variously as an amalgamation of a lifelong learner (South Korea), a moral exemplar (Turkey), a reflective practitioner (England), and an educator (Israel). Great teachers as lifelong learners promote students’ practical wisdom and wise decision-making ability, skills which are required to live a good life. Moral exemplars transmit their personal moral values to their students. Reflective practitioner teachers demonstrate intellectual and performance virtues in practice. As educators, great teachers motivate their students to be good human beings. The results of the study reveal that practical wisdom is an essential lens for making teachers educationally wise people. Great teacher is perceived to empower practical wisdom, which helps teachers establish mutual understanding and let them have more space to draw ii upon intellectual, social, moral and performance virtues through collaboration, mutual engagement and sharing in community of practice. The teachers in the study who participated in community-based professional development programmes enhanced the intellectual, moral, performance, and social virtues, pedagogical content knowledge associated with being a great teacher. The study finds that nations whose educational systems build strong connections between teachers through development and application of learning communities tend to generate a higher proportion of great teachers and that those teachers have positive and extensive influences on each other’s intellectual and personal development. This research also found that one of the most important dispositions that enable teachers to become responsible for students' learning is passion in science teaching. The teachers' passion, motivation, and love for teaching helped them to expand their professional knowledge and techniques of instruction in distinctive manners. The character traits that a great teacher must possess should receive a lot of consideration. Emphasise also should be on developing character strengths in the professional development. Community of practice has potential to achieve this through mutual engagement, shared repertoire and joint enterprise. The research emphasizes the vital role of teachers' passion for science teaching in enabling them to take responsibility for their students' learning. It advocates for the development of character strengths in teacher professional development, particularly through the cultivation of community of practice, characterized by mutual engagement, shared repertoire, and joint enterprise. This comparative study offers valuable insights into the dynamic interplay of teacher development, enhancing the quality of education across diverse contexts

    Identifying alterations in adipose tissue-derived islet GPCR peptide ligand mRNAs in obesity: implications for islet function

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    In addition to acting as an energy reservoir, white adipose tissue is a vital endocrine organ involved in the modulation of cellular function and the maintenance of metabolic homeostasis through the synthesis and secretion of peptides, known as adipokines. It is known that some of these secretory peptides play important regulatory roles in glycaemic control by acting directly on islet β-cells or on insulin-sensitive tissues. Excess adiposity causes alterations in the circulating levels of some adipokines which, depending on their mode of action, can have pro-inflammatory, pro-diabetic or anti-inflammatory, anti-diabetic properties. Some adipokines that are known to act at β-cells have actions that are transduced by binding to G protein- coupled receptors (GPCRs). This large family of receptors represents ~35% of all current drug targets for the treatment of a wide range of diseases, including type 2 diabetes (T2D). Islets express ~300 GPCRs, yet only one islet GPCR is currently directly targeted for T2D treatment. This deficit represents a therapeutic gap that could be filled by the identification of adipose tissue-derived islet GPCR peptide ligands that increase insulin secretion and overall β-cell function. Thus, by defining their mechanisms of action, there is potential for the development of new pharmacotherapies for T2D. Therefore, this thesis describes experiments which aimed to compare the expression profiles of adipose tissue-derived islet GPCR peptide ligand mRNAs under lean and obese conditions, and to characterise the functional effects of a selected candidate of interest on islet cells. Visceral fat depots were retrieved from high-fat diet-induced and genetically obese mouse models, and from human participants. Fat pads were either processed as whole tissue, or mature adipocyte cells were separated from the stromal vascular fraction (SVF) which contains several other cell populations, including preadipocytes and macrophages. The expression levels of 155 islet GPCR peptide ligand mRNAs in whole adipose tissue or in isolated mature adipocytes were quantified using optimised RNA extraction and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) protocols. Comparisons between lean and obese states in mice models and humans revealed significant modifications in the expression levels of several adipokine mRNAs. As expected, mRNAs encoding the positive control genes, Lep and AdipoQ were quantifiable, with the expression of Lep mRNA increasing and that of AdipoQ mRNA decreasing in obesity. Expression of Ccl4 mRNA, encoding chemokine (C-C motif) ligand 4, was significantly upregulated in whole adipose tissue across all models of obesity compared to their lean counterparts. This coincided with elevated circulating Ccl4 peptide levels. This increase was not replicated in isolated mature adipocytes, indicating that the source of upregulated Ccl4 expression in obesity was the SVF of adipose tissue. Based on this significant increase in Ccl4 mRNA expression within visceral fat and its undetermined effects on β-cell function, Ccl4 was selected for further investigation in MIN6 β-cells and mouse islets. PRESTO-Tango β-arrestin reporter assays were performed to determine which GPCRs were activated by exogenous Ccl4. Experiments using HTLA cells expressing a protease-tagged β- arrestin and transfected with GPCR plasmids of interest indicated that 100ng/mL Ccl4 significantly activated Cxcr1 and Cxcr5, but it was not an agonist at the previously identified Ccl4-target GPCRs Ccr1, Ccr2, Ccr5, Ccr9 and Ackr2. RNA extraction and RT-qPCR experiments using MIN6 β-cells and primary islets from lean mice revealed the expression of Cxcr5 mRNA in mouse islets, but it was absent in MIN6 β-cells. The remaining putative Ccl4 receptors (Ccr1, Ccr2, Ccr5, Ccr9, Cxcr1 and Ackr2) were either absent or present at trace levels in mouse islets and MIN6 β-cells. Recombinant mouse Ccl4 protein was used for functional experiments at concentrations of 5, 10, 50 and 100ng/mL, based on previous reports of biological activities at these concentrations. Trypan blue exclusion testing was initially performed to assess the effect of exogenous Ccl4 on MIN6 β-cell viability and these experiments indicated that all concentrations (5-100ng/mL) were well-tolerated. Since β-cells have a low basal rate of apoptosis, cell death was induced by exposure to the saturated free fatty acid, palmitate, or by a cocktail of pro-inflammatory cytokines (interleukin-1β, tumour necrosis factor-α and interferon-γ). In MIN6 β-cells, Ccl4 demonstrated concentration-dependent protective effects against palmitate-induced and cytokine-induced apoptosis. Conversely, while palmitate and cytokines also increased apoptosis of mouse islets, Ccl4 did not protect islets from either inducer. Quantification of bromodeoxyuridine (BrdU) incorporation into β-cell DNA indicated that Ccl4 caused a concentration-dependent reduction in proliferation of MIN6 β-cells in response to 10% fetal bovine serum (FBS). In contrast, immunohistochemical quantification of Ki67-positive mouse islet β-cells showed no differences in β-cell proliferation between control- and Ccl4-treated islets. Whilst the number of β-cells and δ-cells were unaffected, α- cells were significantly depleted by Ccl4 treatment. Exogenous Ccl4 had no effect on nutrient- stimulated insulin secretion from both MIN6 β-cells and primary mouse islets. The 3T3-L1 preadipocyte cell line was used to assess potential Ccl4-mediated paracrine and/or autocrine signalling within adipose tissue. Ccl4 did not alter the mRNA expression of Pparγ, a master regulator of adipocyte differentiation, but did significantly downregulate the mRNA expression of the crucial adipogenic gene, adiponectin. Oil Red O staining and Western blotting were performed to assess lipid accumulation, and insulin and lipolytic signalling, respectively, and these experiments indicated that the observed Ccl4-induced decrease in adiponectin expression failed to correlate with any changes in adipocyte function. In summary, these data demonstrated anti-apoptotic and anti-proliferative actions of the adipokine, Ccl4, on MIN6 β-cells that were not replicated in mouse islets. The absence of any anti-apoptotic, insulin secretory and/or pro-proliferative effects of Ccl4 in islet β-cells suggests that it is unlikely to play a role in regulating β-cell function via crosstalk between adipose tissue and islets. The divergent functional effects highlight that whilst MIN6 cells are a useful primary β-cell surrogate for some studies, primary islets should always be used to confirm physiological relevance. On the other hand, significant α-cell depletion following Ccl4 treatment suggests a cell-specific function within the islets. Furthermore, Ccl4 impaired adiponectin mRNA expression in adipocytes, although, how adipocyte function is affected as a result requires further investigation. Collectively, these data have contributed increased understanding of the role of obesity in modifying the expression of adipose tissue-derived islet GPCR peptide ligands

    Inverse Design of Metamaterials for Tailored Linear and Nonlinear Optical Responses Using Deep Learning

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    The conventional process for developing an optimal design for nonlinear optical responses is based on a trial-and-error approach that is largely inefficient and does not necessarily lead to an ideal result. Deep learning can automate this process and widen the realm of nonlinear geometries and devices. This research illustrates a deep learning framework used to create an optimal plasmonic design for metamaterials with specific desired optical responses, both linear and nonlinear. The algorithm can produce plasmonic patterns that can maximize second-harmonic nonlinear effects of a nonlinear metamaterial. A nanolaminate metamaterial is used as a nonlinear material, and a plasmonic patterns are fabricated on the prepared nanolaminate to demonstrate the validity and efficacy of the deep learning algorithm for second-harmonic generation. Photonic upconversion from the infrared regime to the visible spectrum can occur through sum-frequency generation. The deep learning algorithm was improved to optimize a nonlinear plasmonic metamaterial for sum-frequency generation. The framework was then further expanded using transfer learning to lessen computation resources required to optimize metamaterials for new design parameters. The deep learning architecture applied in this research can be expanded to other optical responses and drive the innovation of novel optical applications.Ph.D

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    Effects of municipal smoke-free ordinances on secondhand smoke exposure in the Republic of Korea

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    ObjectiveTo reduce premature deaths due to secondhand smoke (SHS) exposure among non-smokers, the Republic of Korea (ROK) adopted changes to the National Health Promotion Act, which allowed local governments to enact municipal ordinances to strengthen their authority to designate smoke-free areas and levy penalty fines. In this study, we examined national trends in SHS exposure after the introduction of these municipal ordinances at the city level in 2010.MethodsWe used interrupted time series analysis to assess whether the trends of SHS exposure in the workplace and at home, and the primary cigarette smoking rate changed following the policy adjustment in the national legislation in ROK. Population-standardized data for selected variables were retrieved from a nationally representative survey dataset and used to study the policy action’s effectiveness.ResultsFollowing the change in the legislation, SHS exposure in the workplace reversed course from an increasing (18% per year) trend prior to the introduction of these smoke-free ordinances to a decreasing (−10% per year) trend after adoption and enforcement of these laws (β2 = 0.18, p-value = 0.07; β3 = −0.10, p-value = 0.02). SHS exposure at home (β2 = 0.10, p-value = 0.09; β3 = −0.03, p-value = 0.14) and the primary cigarette smoking rate (β2 = 0.03, p-value = 0.10; β3 = 0.008, p-value = 0.15) showed no significant changes in the sampled period. Although analyses stratified by sex showed that the allowance of municipal ordinances resulted in reduced SHS exposure in the workplace for both males and females, they did not affect the primary cigarette smoking rate as much, especially among females.ConclusionStrengthening the role of local governments by giving them the authority to enact and enforce penalties on SHS exposure violation helped ROK to reduce SHS exposure in the workplace. However, smoking behaviors and related activities seemed to shift to less restrictive areas such as on the streets and in apartment hallways, negating some of the effects due to these ordinances. Future studies should investigate how smoke-free policies beyond public places can further reduce the SHS exposure in ROK

    Vital Sign Monitoring in Dynamic Environment via mmWave Radar and Camera Fusion

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    Contact-free vital sign monitoring, which uses wireless signals for recognizing human vital signs (i.e, breath and heartbeat), is an attractive solution to health and security. However, the subject's body movement and the change in actual environments can result in inaccurate frequency estimation of heartbeat and respiratory. In this paper, we propose a robust mmWave radar and camera fusion system for monitoring vital signs, which can perform consistently well in dynamic scenarios, e.g., when some people move around the subject to be tracked, or a subject waves his/her arms and marches on the spot. Three major processing modules are developed in the system, to enable robust sensing. Firstly, we utilize a camera to assist a mmWave radar to accurately localize the subjects of interest. Secondly, we exploit the calculated subject position to form transmitting and receiving beamformers, which can improve the reflected power from the targets and weaken the impact of dynamic interference. Thirdly, we propose a weighted multi-channel Variational Mode Decomposition (WMC-VMD) algorithm to separate the weak vital sign signals from the dynamic ones due to subject's body movement. Experimental results show that, the 90th{^{th}} percentile errors in respiration rate (RR) and heartbeat rate (HR) are less than 0.5 RPM (respirations per minute) and 6 BPM (beats per minute), respectively
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