9,698 research outputs found

    An investigation of the relationship between perioperative characteristics and perioperative anaesthesia on the postoperative systemic inflammatory response and clinical outcome in patients undergoing surgery for colorectal cancer

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    In UK, colorectal cancer (CRC) is the fourth most common cancer and the second most common cause of cancer death. Until now, surgical resection remains the cornerstone for the management of CRC in all stages, however, stress response elicit from surgery may cause different changes through multiple systems in human body including neural, endocrine, metabolic, inflammatory, and immunological changes. In addition, other perioperative factors such as volatile anaesthetic and opioids may induce the immunosuppression. There is a proportional correlation between the stress response and the magnitude of the inflammatory immune response, invasiveness, and duration of surgery. The pre-operative and post-operative status of patients are important when considering the prognosis. The systemic inflammatory response (SIR) has been recognised to correlate with tumour progression and the prognosis of CRC. An exaggerated postoperative SIR is associated with postoperative infective complications and poor survival. Several predictive markers of the SIR have been used, such as the neutrophil to lymphocyte ratio (NLR), serum C-reactive protein (CRP) level, and Glasgow prognostic score (GPS). Some evidence reported that general anaesthesia (GA) combined with regional anaesthesia (RA) are better than the single use of general anaesthesia in reducing the post-operative immuno-suppression in some degrees. Furthermore, the peri-operative inflammatory process may be affected by the choice of anaesthetic technique, with propofol reported to have anti-inflammatory effect by targeting neutrophil activity. Up to now, there is insufficient evidence to recommend any specific anaesthetic or analgesic technique for patients undergoing surgery for tumour resection based on inflammatory response, recurrence, and metastasis. The work presented in this thesis further examines the relationship between the perioperative characteristics, perioperative anaesthesia, and the postoperative systemic inflammatory response following surgery for colorectal cancer. Several preoperative medications along with anaesthesia might influence the postoperative systemic inflammatory response but the question is whether the post-operative systemic inflammatory response affected by the administration of different types of anaesthesia or not following surgery for colorectal cancer. Chapter 1 discusses the epidemiology, aetiology, carcinogenesis, risk factors of colorectal cancer, pro-carcinogenic factors, anti-carcinogenic agents, inflammation and cancer, the post-operative systemic inflammatory response, tumour staging, screening, and diagnosis of colorectal cancer. Chapter 2 discusses the treatment of colorectal cancer. Chapter 3 discusses different anaesthetic techniques and agents. Chapter 4 provides summary and aims of the thesis. Chapter 5 represents findings from a systematic review and meta-analysis about the effect of anaesthesia on the postoperative systemic inflammatory response in patients undergoing surgery. The results conclude that there was some evidence that anaesthetic regimens may reduce the magnitude of the post-operative SIR. However, the studies identified in this systematic review were heterogeneous and generally of low quality. Chapter 6 represents a retrospective cohort study about the relationship between anaesthetic technique, clinicopathological characteristics and the magnitude of the postoperative systemic inflammatory response in patients undergoing elective surgery for colon cancer. The results show that the type of anaesthesia varied over time and appears to influence the magnitude of the postoperative SIR on post-operative day 2 for those patients who underwent for open surgery but not laparoscopic surgery. Chapter 7 represents a prospective cohort study about the effect of anaesthesia on the magnitude of the postoperative systemic inflammatory response in patients undergoing elective surgery for colorectal cancer in the context of an enhanced recovery pathway. The results show that there was a modest but an independent association between regional anaesthesia (RA) and a lower magnitude of the postoperative SIR. Chapter 8 represents the relationship between pre-operative medications, the type of anaesthesia and post-operative sequelae in patients undergoing surgery for colorectal cancer. The results show that there was no association between the preoperative administration of aspirin, statins and ACE inhibitors and anaesthesia. Chapter 9 represents the relationship between nutritional status, anaesthetic approach, and peri-operative characteristics of patients undergoing surgery for colorectal cancer. The results show that there was no significant association between measures of nutritional status and anaesthetic approach. Chapter 10 represents the relationship between opioid administration, type of anaesthesia and clinicopathological characteristics in patients undergoing surgery for colorectal cancer. The results show that opioid administration was independently associated with both anaesthetic and operative factors. Chapter 11 represents the main findings of the thesis and some recommendation for a future work

    Modelling and Solving the Single-Airport Slot Allocation Problem

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    Currently, there are about 200 overly congested airports where airport capacity does not suffice to accommodate airline demand. These airports play a critical role in the global air transport system since they concern 40% of global passenger demand and act as a bottleneck for the entire air transport system. This imbalance between airport capacity and airline demand leads to excessive delays, as well as multi-billion economic, and huge environmental and societal costs. Concurrently, the implementation of airport capacity expansion projects requires time, space and is subject to significant resistance from local communities. As a short to medium-term response, Airport Slot Allocation (ASA) has been used as the main demand management mechanism. The main goal of this thesis is to improve ASA decision-making through the proposition of models and algorithms that provide enhanced ASA decision support. In doing so, this thesis is organised into three distinct chapters that shed light on the following questions (I–V), which remain untapped by the existing literature. In parentheses, we identify the chapters of this thesis that relate to each research question. I. How to improve the modelling of airline demand flexibility and the utility that each airline assigns to each available airport slot? (Chapters 2 and 4) II. How can one model the dynamic and endogenous adaptation of the airport’s landside and airside infrastructure to the characteristics of airline demand? (Chapter 2) III. How to consider operational delays in strategic ASA decision-making? (Chapter 3) IV. How to involve the pertinent stakeholders into the ASA decision-making process to select a commonly agreed schedule; and how can one reduce the inherent decision-complexity without compromising the quality and diversity of the schedules presented to the decision-makers? (Chapter 3) V. Given that the ASA process involves airlines (submitting requests for slots) and coordinators (assigning slots to requests based on a set of rules and priorities), how can one jointly consider the interactions between these two sides to improve ASA decision-making? (Chapter 4) With regards to research questions (I) and (II), the thesis proposes a Mixed Integer Programming (MIP) model that considers airlines’ timing flexibility (research question I) and constraints that enable the dynamic and endogenous allocation of the airport’s resources (research question II). The proposed modelling variant addresses several additional problem characteristics and policy rules, and considers multiple efficiency objectives, while integrating all constraints that may affect airport slot scheduling decisions, including the asynchronous use of the different airport resources (runway, aprons, passenger terminal) and the endogenous consideration of the capabilities of the airport’s infrastructure to adapt to the airline demand’s characteristics and the aircraft/flight type associated with each request. The proposed model is integrated into a two-stage solution approach that considers all primary and several secondary policy rules of ASA. New combinatorial results and valid tightening inequalities that facilitate the solution of the problem are proposed and implemented. An extension of the above MIP model that considers the trade-offs among schedule displacement, maximum displacement, and the number of displaced requests, is integrated into a multi-objective solution framework. The proposed framework holistically considers the preferences of all ASA stakeholder groups (research question IV) concerning multiple performance metrics and models the operational delays associated with each airport schedule (research question III). The delays of each schedule/solution are macroscopically estimated, and a subtractive clustering algorithm and a parameter tuning routine reduce the inherent decision complexity by pruning non-dominated solutions without compromising the representativeness of the alternatives offered to the decision-makers (research question IV). Following the determination of the representative set, the expected delay estimates of each schedule are further refined by considering the whole airfield’s operations, the landside, and the airside infrastructure. The representative schedules are ranked based on the preferences of all ASA stakeholder groups concerning each schedule’s displacement-related and operational-delay performance. Finally, in considering the interactions between airlines’ timing flexibility and utility, and the policy-based priorities assigned by the coordinator to each request (research question V), the thesis models the ASA problem as a two-sided matching game and provides guarantees on the stability of the proposed schedules. A Stable Airport Slot Allocation Model (SASAM) capitalises on the flexibility considerations introduced for addressing research question (I) through the exploitation of data submitted by the airlines during the ASA process and provides functions that proxy each request’s value considering both the airlines’ timing flexibility for each submitted request and the requests’ prioritisation by the coordinators when considering the policy rules defining the ASA process. The thesis argues on the compliance of the proposed functions with the primary regulatory requirements of the ASA process and demonstrates their applicability for different types of slot requests. SASAM guarantees stability through sets of inequalities that prune allocations blocking the formation of stable schedules. A multi-objective Deferred-Acceptance (DA) algorithm guaranteeing the stability of each generated schedule is developed. The algorithm can generate all stable non-dominated points by considering the trade-off between the spilled airline and passenger demand and maximum displacement. The work conducted in this thesis addresses several problem characteristics and sheds light on their implications for ASA decision-making, hence having the potential to improve ASA decision-making. Our findings suggest that the consideration of airlines’ timing flexibility (research question I) results in improved capacity utilisation and scheduling efficiency. The endogenous consideration of the ability of the airport’s infrastructure to adapt to the characteristics of airline demand (research question II) enables a more efficient representation of airport declared capacity that results in the scheduling of additional requests. The concurrent consideration of airlines’ timing flexibility and the endogenous adaptation of airport resources to airline demand achieves an improved alignment between the airport infrastructure and the characteristics of airline demand, ergo proposing schedules of improved efficiency. The modelling and evaluation of the peak operational delays associated with the different airport schedules (research question III) provides allows the study of the implications of strategic ASA decision-making for operations and quantifies the impact of the airport’s declared capacity on each schedule’s operational performance. In considering the preferences of the relevant ASA stakeholders (airlines, coordinators, airport, and air traffic authorities) concerning multiple operational and strategic ASA efficiency metrics (research question IV) the thesis assesses the impact of alternative preference considerations and indicates a commonly preferred schedule that balances the stakeholders’ preferences. The proposition of representative subsets of alternative schedules reduces decision-complexity without significantly compromising the quality of the alternatives offered to the decision-making process (research question IV). The modelling of the ASA as a two-sided matching game (research question V), results in stable schedules consisting of request-to-slot assignments that provide no incentive to airlines and coordinators to reject or alter the proposed timings. Furthermore, the proposition of stable schedules results in more intensive use of airport capacity, while simultaneously improving scheduling efficiency. The models and algorithms developed as part of this thesis are tested using airline requests and airport capacity data from coordinated airports. Computational results that are relevant to the context of the considered airport instances provide evidence on the potential improvements for the current ASA process and facilitate data-driven policy and decision-making. In particular, with regards to the alignment of airline demand with the capabilities of the airport’s infrastructure (questions I and II), computational results report improved slot allocation efficiency and airport capacity utilisation, which for the considered airport instance translate to improvements ranging between 5-24% for various schedule performance metrics. In reducing the difficulty associated with the assessment of multiple ASA solutions by the stakeholders (question IV), instance-specific results suggest reductions to the number of alternative schedules by 87%, while maintaining the quality of the solutions presented to the stakeholders above 70% (expressed in relation to the initially considered set of schedules). Meanwhile, computational results suggest that the concurrent consideration of ASA stakeholders’ preferences (research question IV) with regards to both operational (research question III) and strategic performance metrics leads to alternative airport slot scheduling solutions that inform on the trade-offs between the schedules’ operational and strategic performance and the stakeholders’ preferences. Concerning research question (V), the application of SASAM and the DA algorithm suggest improvements to the number of unaccommodated flights and passengers (13 and 40% improvements) at the expense of requests concerning fewer passengers and days of operations (increasing the number of rejected requests by 1.2% in relation to the total number of submitted requests). The research conducted in this thesis aids in the identification of limitations that should be addressed by future studies to further improve ASA decision-making. First, the thesis focuses on exact solution approaches that consider the landside and airside infrastructure of the airport and generate multiple schedules. The proposition of pre-processing techniques that identify the bottleneck of the airport’s capacity, i.e., landside and/or airside, can be used to reduce the size of the proposed formulations and improve the required computational times. Meanwhile, the development of multi-objective heuristic algorithms that consider several problem characteristics and generate multiple efficient schedules in reasonable computational times, could extend the capabilities of the models propositioned in this thesis and provide decision support for some of the world’s most congested airports. Furthermore, the thesis models and evaluates the operational implications of strategic airport slot scheduling decisions. The explicit consideration of operational delays as an objective in ASA optimisation models and algorithms is an issue that merits investigation since it may further improve the operational performance of the generated schedules. In accordance with current practice, the models proposed in this work have considered deterministic capacity parameters. Perhaps, future research could propose formulations that consider stochastic representations of airport declared capacity and improve strategic ASA decision-making through the anticipation of operational uncertainty and weather-induced capacity reductions. Finally, in modelling airlines’ utility for each submitted request and available time slot the thesis proposes time-dependent functions that utilise available data to approximate airlines’ scheduling preferences. Future studies wishing to improve the accuracy of the proposed functions could utilise commercial data sources that provide route-specific information; or in cases that such data is unavailable, employ data mining and machine learning methodologies to extract airlines’ time-dependent utility and preferences

    The Adirondack Chronology

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    The Adirondack Chronology is intended to be a useful resource for researchers and others interested in the Adirondacks and Adirondack history.https://digitalworks.union.edu/arlpublications/1000/thumbnail.jp

    Socio-endocrinology revisited: New tools to tackle old questions

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    Animals’ social environments impact their health and survival, but the proximate links between sociality and fitness are still not fully understood. In this thesis, I develop and apply new approaches to address an outstanding question within this sociality-fitness link: does grooming (a widely studied, positive social interaction) directly affect glucocorticoid concentrations (GCs; a group of steroid hormones indicating physiological stress) in a wild primate? To date, negative, long-term correlations between grooming and GCs have been found, but the logistical difficulties of studying proximate mechanisms in the wild leave knowledge gaps regarding the short-term, causal mechanisms that underpin this relationship. New technologies, such as collar-mounted tri-axial accelerometers, can provide the continuous behavioural data required to match grooming to non-invasive GC measures (Chapter 1). Using Chacma baboons (Papio ursinus) living on the Cape Peninsula, South Africa as a model system, I identify giving and receiving grooming using tri-axial accelerometers and supervised machine learning methods, with high overall accuracy (~80%) (Chapter 2). I then test what socio-ecological variables predict variation in faecal and urinary GCs (fGCs and uGCs) (Chapter 3). Shorter and rainy days are associated with higher fGCs and uGCs, respectively, suggesting that environmental conditions may impose stressors in the form of temporal bottlenecks. Indeed, I find that short days and days with more rain-hours are associated with reduced giving grooming (Chapter 4), and that this reduction is characterised by fewer and shorter grooming bouts. Finally, I test whether grooming predicts GCs, and find that while there is a long-term negative correlation between grooming and GCs, grooming in the short-term, in particular giving grooming, is associated with higher fGCs and uGCs (Chapter 5). I end with a discussion on how the new tools I applied have enabled me to advance our understanding of sociality and stress in primate social systems (Chapter 6)

    Cis-Regulation of Gremlin1 Expression during Mouse Limb Bud Development and its Diversification during Vertebrate Evolution

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    Embryonic development and organogenesis rely on tightly controlled gene expression, which is achieved by cis-regulatory modules (CRMs) interacting with distinct transcription factors (TFs) that control spatio-temporal and tissue-specific gene expression. During organogenesis, gene regulatory networks (GRNs) with selfregulatory feedback properties coordinately control growth and patterning and provide systemic robustness against genetic and/or environmental perturbations. During limb bud development, various interlinked GRNs control outgrowth and patterning along all three limb axes. A paradigm network is the epithelial-mesenchymal (e-m) SHH/GREM1/AER-FGF feedback signaling system which controls limb bud outgrowth and digit patterning. The BMP antagonist GREMLIN1 (GREM1) is central to this e-m interactions as its antagonism of BMP activity is essential to maintain both AER-Fgf and Shh expression. In turn, SHH signaling upregulates Grem1 expression, which results in establishment of a self-regulatory signaling network. One previous study provided evidence that several CRMs could regulate Grem1 expression during limb bud development. However, the cis-regulatory logics underlying the spatio-temporal regulation of the Grem1 expression dynamics remained obscure. From an evolutionary point of view, diversification of CRMs can result in diversification of gene regulation which can drive the establishment of morphological novelties and adaptions. This was evidenced by the observed differences in Grem1 expression in different species that correlates with the evolutionary plasticity of tetrapod digit patterning. Hence, a better understanding of spatio-temporal regulation of the Grem1 expression dynamics and underlying cis-regulatory logic is of interest from both adevelopmental and an evolutionary perspective. Recently, multiple candidate CRMs have been identified that might be functionally relevant for Grem1 expression during mouse limb bud development. For my PhD project, I genetically analyzed which of these CRMs are involved in the regulation of the spatial-temporal Grem1 expression dynamics in limb buds. Therefore, we generated various single and compound CRM mutant alleles using CRISPR/Cas9. Our CRMs allelic series revealed a complex Grem1 cis-regulation among a minimum of six CRMs, where a subset of CRMs regulates Grem1 transcript levels in an additive manner. Surprisingly, phenotypic robustness depends not on threshold transcript levels but the spatial integrity of the Grem1 expression domain. In particular, interactions among five CRMs control the characteristic asymmetrical and posteriorly biased Grem1 expression in mouse limb buds. Our results provide an example of how multiple seemingly redundant limb-specific CRMs provide phenotypical robustness by cooperative/synergistic regulation of the spatial Grem1 expression dynamics. Three CRMs are conserved along the phylogeny of extant vertebrates with paired appendages. Of those, the activities of two CRMs recapitulate the major spatiotemporal aspects of Grem1 expression in mouse limb buds. In order to study their functions in species-specific regulation of Grem1 expression and their functional diversification in tetrapods, I tested the orthologous of both CRMs from representative species using LacZ reporter assays in transgenic mice, in comparison to the endogenous Grem1 expression in limb buds of the species of origin. Surprisingly, the activities of CRM orthologues display high evolutionary plasticity, which correlates better with the Grem1 expression pattern in limb buds of the species of origin than its mouse orthologue. This differential responsiveness to the GRNs in mouse suggests that TF binding site alterations in CRMs could underlie the spatial diversification of Grem1 in limb buds during tetrapod evolution. While the fish fin and tetrapod limb share some homologies of proximal bones, the autopod is a neomorphic feature of tetrapods. The Grem1 requirement for digit patterning and conserved expression in fin buds prompted us to assess the enhancer activity of fish CRM orthologues in transgenic mice. Surprisingly, all tested fish CRMs are active in the mouse autopod primordia providing strong evidence that Grem1 CRMs are active in fin buds and that they predate the fin-to-limb transition. Our results corroborate increasing evidence that CRMs governing autopodial gene expression have been co-opted during the emergence of tetrapod autopod. Furthermore, as part of a collaboration with Dr. S. Jhanwar, I contributed to the study of shared and species-specific epigenomic and genomic variations during mouse and chicken limb bud development. In this analysis, Dr. S. Jhanwar identified putative enhancers that show higher chicken-specific sequence turnover rates in comparison to their mouse orthologues, which defines them as so-called chicken accelerated regions (CARs). Here, I analyzed the CAR activities in comparison to their mouse orthologues by transgenic LacZ reporter assays, which was complemented by analysis of the endogenous gene expression in limb buds of both species. This analysis indicates that diversified activity of CARs and their mouse orthologues could be linked to the differential gene expression patterns in limb buds of both species

    Investigating the role of R2TP-like co-chaperone complexes during axonemal dynein assembly

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    Motile cilia are specialised cell-types which in humans have important roles in the linings of the airways, the reproductive system and the brain. The movement, required for this type of cilia to function, is facilitated by structures called axonemal dynein motor complexes. These are large, multi-subunit structures, and so it is crucial that they are assembled correctly. In humans, if the motility of these is defective, it can lead to a disorder called Primary Ciliary Dyskinesia, or PCD. This is a heterogeneous, autosomal recessive disorder – symptoms of which include abnormally positioned organs, chronic respiratory infections and infertility. Therefore, the development and structure of the motile cilia is tightly regulated by multiple proteins including chaperones, dynein axonemal assembly factors (DNAAFs), microtubule inner proteins (MIPs), the outer arm docking complex (ODA-DC) and the nexin-dynein regulatory complex (N-DRC). Chaperones work with co-chaperones to regulate their many functions within the cell. One of these co-chaperones is the R2TP complex, which was originally discovered in yeast but is conserved in higher organisms. This multi-protein co-chaperone is involved in the assembly of multi-subunit complexes such as the axonemal dynein motors. Two of the R2TP subunits, Pontin and Reptin, are involved in many cellular functions both in this co-chaperone complex and independently. It is thought that as some DNAAFs share similar protein domains to the components of the R2TP complex, they may form R2TP-like complexes. However, the specific details surrounding the roles of these complexes during the assembly process remains unclear. The structure of motile cilia is highly conserved throughout evolution and Drosophila melanogaster has been shown previously to be an excellent model for furthering understanding into the development and function of these structures as only two cell types in the fly contain axonemal dynein motor complexes. These are the chordotonal neuron, which has a motile ciliated dendrite essential for its mechanosensory function, and the sperm flagellum. In this thesis, I use the Drosophila model to further characterise putative ciliary genes (Wdr16 and Dpcd) identified by a transcriptome analysis previously carried out in the lab. RNAi knockdown experiments as well as expression analysis supported motile cilia functions. The diversity which has been identified regarding the roles of these two putative ciliary genes highlights how proteins can be involved in motile cilia in different ways. I also use this genetically tractable model to further understand the roles of the individual proteins of a previously identified R2TP-like complex (R2DP3). Electron microscopy, proteomics and investigation into how the localisation of dynein subsets was affected in null mutants (generated using CRISPR/Cas9) allowed for the role of this R2TP-like complex in the dynein assembly process to be further specified. Using co-immunoprecipitation and affinity purification, we identified an additional protein complex featuring Pontin and Reptin of the R2TP complex, alongside the DNAAF Heatr2 and the putative DNAAF Dpcd. As well as a role in dynein assembly, both DNAAFs are additionally expressed in the neuroblasts of the CNS, and disruption to their function results in a late larval lethality. Therefore, we have found these genes to not be specific to the dynein assembly process and hypothesise that Dpcd may have an additional function (working with Pontin, Reptin and potentially Heatr2) in the regulation of AKT signalling and therefore impact cell proliferation

    Qunity: A Unified Language for Quantum and Classical Computing (Extended Version)

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    We introduce Qunity, a new quantum programming language designed to treat quantum computing as a natural generalization of classical computing. Qunity presents a unified syntax where familiar programming constructs can have both quantum and classical effects. For example, one can use sum types to implement the direct sum of linear operators, exception handling syntax to implement projective measurements, and aliasing to induce entanglement. Further, Qunity takes advantage of the overlooked BQP subroutine theorem, allowing one to construct reversible subroutines from irreversible quantum algorithms through the uncomputation of "garbage" outputs. Unlike existing languages that enable quantum aspects with separate add-ons (like a classical language with quantum gates bolted on), Qunity provides a unified syntax along with a novel denotational semantics that guarantees that programs are quantum mechanically valid. We present Qunity's syntax, type system, and denotational semantics, showing how it can cleanly express several quantum algorithms. We also detail how Qunity can be compiled to a low-level qubit circuit language like OpenQASM, proving the realizability of our design.Comment: 60 pages, presented at QPL 202

    Structural basis of translational recycling and bacterial ribosome rescue

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    In the last step of gene expression, a messenger RNA (mRNA) sequence is translated into a polypeptide. This highly regulated and dynamic process is carried out by the ribosome, a ribonucleoprotein complex composed of two unequal subunits. The translation cycle is initiated when the small ribosomal subunit (SSU) binds to an mRNA and recognizes the start codon of the open reading frame (ORF). Then the large ribosomal subunit (LSU) joins and the ribosome starts moving along the mRNA. A protein is synthesized until the ribosome reaches a stop codon. A cell needs thousands (prokaryotes) or millions (eukaryotes) of ribosomes for protein production and spends enormous amounts of energy on the assembly of this macromolecular machinery. Therefore, it is crucial to recycle the machinery after each successful round of translation. The recycling step allows release of mRNA, transfer RNA (tRNA) and the synthesized polypeptide from ribosomal subunits and subsequent binding of the next mRNA for protein synthesis. The first part of this dissertation includes studies of the highly conserved and essential ribosome recycling factor ATP binding cassette (ABC) Subfamily E Member 1 (ABCE1). In eukaryotes and archaea, ABCE1 binds the ribosome and in concert with an A-site factor and splits the ribosome into large and small subunits. ABCE1 harbors two nucleotide binding sites (NBSs), which are formed at the interface of two nucleotide binding domains (NBDs). Prior to this work, the ABCE1-bound pre-splitting complex, as well as the ABCE1-bound post-splitting complex, had been visualized by cryo-electron microscopy (cryo-EM) at medium resolution. This structural analysis combined with functional studies led to a model for the mechanism of the splitting event. ATP-binding and the closure of the NBSs lead to repositioning of the iron-sulfur cluster domain, which results in collision with the A-site factor and ribosome splitting. Yet, how conformational changes during the splitting event are triggered and communicated to the NBSs of ABCE1, was not understood. To gain molecular insights into this process, a structure of a fully nucleotide-occluded (closed) state of ABCE1 bound to the archaeal 30S post-splitting complex was solved by cryo-EM. At a resolution of 2.8 Å a detailed molecular analysis of ABCE1 was performed and confirmed by a combination of mutational and functional studies. This allowed to propose a refined model of how the ATPase cycle is linked to ribosome splitting and which role the different domains of ABCE1 play. In eukaryotes, the recycling phase is directly linked to translation initiation via the SSU. After being released from the mRNA 3’ end, the SSU can engage with another or even the same mRNA at the 5’ end. The recycling factor ABCE1 was found to be associated with initiation complexes, but whether it plays a role in initiation was not clear. Using cryo-EM, structures of native ABCE1-containing initiation complexes were solved and intensive 3D classification allowed to distinguish different stages of initiation, during which ABCE1 may play a role. Surprisingly, ABCE1 adopted a previously unknown state for ABC-type ATPases that was termed “hybrid state”. Here, the NBSI is in a half open state with ADP bound and the NBSII is in a closed state with ATP bound. Further, eukaryotic initiation factor 3j (eIF3j) was found to stabilize this hybrid conformation via its N-terminus. Since eIF3j had already been described to assist ABCE1 in ribosome dissociation, in vitro splitting assays were performed demonstrating that eiF3j indeed actively enhances the splitting reaction. On top of this, the high-resolution structure allowed to describe the interaction network of eIF3j with the ribosome, initiation factors (IFs), and ABCE1. Independent of ABCE1, the structures presented here allowed to provide an improved molecular model of the human 43S pre-initiation complex (PIC) and to analyze its sophisticated interaction network. In particular, new molecular insights into the large eIF3 complex encircling the 43S PIC, and the eIF2 ternary complex delivering the initiator tRNA are provided. Equally important as canonical recycling is the recognition and recycling of ribosomes that result from translational failure. Aberrant translation elongation and ribosome stalling can be caused by a plethora of different stresses. In bacterial cells, multiple rescue systems are known such as trans-translation or alternative ribosome rescue factor-mediated termination, which act on ribosome nascent chain complexes with an empty A-site (non-stop complexes). It has been a long standing question how ribosomes that are stalled in the middle of an ORF (no-go complexes) are recognized and recycled. The second part of this dissertation reports a new bacterial rescue system that acts on no-go complexes. In eukaryotes, the concept of ribosome collisions as a trigger for ribosome rescue has been studied extensively. Here, it was found that a similar mechanism exists in bacteria and thus a structural analysis of collided disomes in E. coli and B. subtilis was conducted. In a genetic screen, the endonuclease SmrB was identified as one candidate for a collision sensor. Structural analysis of SmrB-bound disomes elucidated how this rescue factor is recruited to collided ribosomes. Its SMR domain binds to the disome interface between the stalled and the collided ribosome in close proximity to the mRNA and in a position ideal to perform endonucleolytic cleavage. Such cleavage then results in non-stop complexes that can be recycled by the pathways mentioned above. In conclusion, this work provides mechanistic insights into how a cell distinguishes stalled ribosomes from actively translating ribosomes and characterizes a novel ribosome rescue pathway

    Essays on Indian Futures Markets

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    Exchange derivatives trading for national level commodity futures and equity index futures in India started in 2003 and 2001 respectively. Despite of the institutional ecosystem being put in place for nearly two decades, the participation of farmers and Farmer Producer Organizations' (FPOs) in agricultural futures trade is extremely low in India; and unlike most global Exchanges, the decision for contract sizes, margins and open position limits on the equity or equity index derivatives still remains a part of the regulator's mandate. This doctoral thesis by identifying two regulatory reforms from the Indian market concerning outright suspension of wheat futures contracts and increase in the market lot size of the index futures contracts, focuses on three essays relating to relative market efficiency, price discovery performance and market quality measures. The first essay examines the impact of wheat trading suspension on the degree of market efficiency in the pre-ban and post-ban phases. The second essay using data from the analogous wheat contract analyses if the trading ban have consequences on the market leadership and information flow between the spot and futures prices, under different trading periods. Lastly, the third essay examines whether the increase in the minimum lot sizes of index futures contracts can affect the trading activity variables, market liquidity and price volatility. Analysis from the first essay show that interventions like abrupt trading bans had negative effects on both the long-run market efficiency and short-run efficiency measure. Further results from the second essay reveal that trading suspensions have negative consequences on the short-run price discovery dynamics. Therefore from a viewpoint of attracting more hedgers (farmers' or FPOs) into the market for increasing liquidity and depth, regulators must provide stable policy environment for future trade to flourish. Finally, findings from the third essay suggest that increase in the contract size had positive impact only for the open interest, but the trading volume and liquidity variables were negatively affected. Therefore, the Securities market regulator's interventions in the Exchange's commercial decisions may discourage interest in the equity futures products at large in the long-term
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