Biogeochemical data from terrestrial and aquatic ecosystems in a periglacial catchment, West Greenland

Global warming is expected to be most pronounced in the Arctic where permafrost thaw and release of old carbon may provide an important feedback mechanism to the climate system. To better understand and predict climate effects and feedbacks on the cycling of elements within and between ecosystems in northern latitude landscapes, a thorough understanding of the processes related to transport and cycling of elements is required. A fundamental requirement to reach a better process understanding is to have access to high-quality empirical data on chemical concentrations and biotic properties for a wide range of ecosystem domains and functional units (abiotic and biotic pools). The aim of this study is therefore to make one of the most extensive field data sets from a periglacial catchment readily available that can be used both to describe present-day periglacial processes and to improve predictions of the future. Here we present the sampling and analytical methods, field and laboratory equipment and the resulting biogeochemical data from a state-of-the-art whole-ecosystem investigation of the terrestrial and aquatic parts of a lake catchment in the Kangerlussuaq region, West Greenland. This data set allows for the calculation of whole-ecosystem mass balance budgets for a long list of elements, including carbon, nutrients and major and trace metals.

Reference list of 265 sources used for the discovery of relationships between data clusters and metadata properties

Visual cluster analysis provides valuable tools that help analysts to understand large data sets in terms of representative clusters and relationships thereof. Often, the found clusters are to be understood in context of belonging categorical, numerical or textual metadata which are given for the data elements. While often not part of the clustering process, such metadata play an important role and need to be considered during the interactive cluster exploration process. Traditionally, linked-views allow to relate (or loosely speaking: correlate) clusters with metadata or other properties of the underlying cluster data. Manually inspecting the distribution of metadata for each cluster in a linked-view approach is tedious, specially for large data sets, where a large search problem arises. Fully interactive search for potentially useful or interesting cluster to metadata relationships may constitute a cumbersome and long process. To remedy this problem, we propose a novel approach for guiding users in discovering interesting relationships between clusters and associated metadata. Its goal is to guide the analyst through the potentially huge search space. We focus in our work on metadata of categorical type, which can be summarized for a cluster in form of a histogram. We start from a given visual cluster representation, and compute certain measures of interestingness defined on the distribution of metadata categories for the clusters. These measures are used to automatically score and rank the clusters for potential interestingness regarding the distribution of categorical metadata. Identified interesting relationships are highlighted in the visual cluster representation for easy inspection by the user. We present a system implementing an encompassing, yet extensible, set of interestingness scores for categorical metadata, which can also be extended to numerical metadata. Appropriate visual representations are provided for showing the visual correlations, as well as the calculated ranking scores. Focusing on clusters of time series data, we test our approach on a large real-world data set of time-oriented scientific research data, demonstrating how specific interesting views are automatically identified, supporting the analyst discovering interesting and visually understandable relationships.

Comprehensive Characterization of Measurement Data Gathered by the Pressure Tube to Calandria Tube Gap Probe

Multi-frequency eddy current measurements are employed in estimating pressure tube (PT) to calandria tube (CT) gap in CANDU fuel channels, a critical inspection activity required to ensure fitness for service of fuel channels. In this thesis, a comprehensive characterization of eddy current gap data is laid out, in order to extract further information on fuel channel condition, and to identify generalized applications for multi-frequency eddy current data. A surface profiling technique, generalizable to multiple probe and conductive material configurations has been developed. This technique has allowed for identification of various pressure tube artefacts, has been independently validated (using ultrasonic measurements), and has been deployed and commissioned at Ontario Power Generation. Dodd and Deeds solutions to the electromagnetic boundary value problem associated with the PT to CT gap probe configuration were experimentally validated for amplitude response to changes in gap. Using the validated Dodd and Deeds solutions, principal components analysis (PCA) has been employed to identify independence and redundancies in multi-frequency eddy current data. This has allowed for an enhanced visualization of factors affecting gap measurement. Results of the PCA of simulation data are consistent with the skin depth equation, and are validated against PCA of physical experiments. Finally, compressed data acquisition has been realized, allowing faster data acquisition for multi-frequency eddy current systems with hardware limitations, and is generalizable to other applications where real time acquisition of large data sets is prohibitive.

Maintaining legacy data: saving Belfast Harbour (UK) tide-gauge data (1902-2010)

Tide gauge data are identified as legacy data given the radical transition between observation method and required output format associated with tide gauges over the 20th-century. Observed water level variation through tide-gauge records is regarded as the only significant basis for determining recent historical variation (decade to century) in mean sea-level and storm surge. There are limited tide gauge records that cover the 20th century, such that the Belfast (UK) Harbour tide gauge would be a strategic long-term (110 years) record, if the full paper-based records (marigrams) were digitally restructured to allow for consistent data analysis. This paper presents the methodology of extracting a consistent time series of observed water levels from the 5 different Belfast Harbour tide gauges’ positions/machine types, starting late 1901. Tide-gauge data was digitally retrieved from the original analogue (daily) records by scanning the marigrams and then extracting the sequential tidal elevations with graph-line seeking software (Ungraph™). This automation of signal extraction allowed the full Belfast series to be retrieved quickly, relative to any manual x–y digitisation of the signal. Restructuring variably lengthed tidal data sets to a consistent daily, monthly and annual file format was undertaken by project-developed software: Merge&Convert and MergeHYD allow consistent water level sampling both at 60 min (past standard) and 10 min intervals, the latter enhancing surge measurement. Belfast tide-gauge data have been rectified, validated and quality controlled (IOC 2006 standards). The result is a consistent annual-based legacy data series for Belfast Harbour that includes over 2 million tidal-level data observations.

Machine learning and data decompositions for complex networked dynamical systems

Thesis (Ph.D.)--University of Washington, 2016-08

Multi-Disciplinary Applications of Oceanographic Geophysical Data Collection

Thesis (Ph.D.)--University of Washington, 2016-08

Identifying treatment effects and counterfactual distributions using data combination with unobserved heterogeneity

This paper considers identification of treatment effects when the outcome variables and covari-ates are not observed in the same data sets. Ecological inference models, where aggregate out-come information is combined with individual demographic information, are a common example of these situations. In this context, the counterfactual distributions and the treatment effects are not point identified. However, recent results provide bounds to partially identify causal effects. Unlike previous works, this paper adopts the selection on unobservables assumption, which means that randomization of treatment assignments is not achieved until time fixed unobserved heterogeneity is controlled for. Panel data models linear in the unobserved components are con-sidered to achieve identification. To assess the performance of these bounds, this paper provides a simulation exercise.

BUILDING EFFICIENT AND COST-EFFECTIVE CLOUD-BASED BIG DATA MANAGEMENT SYSTEMS

In today’s big data world, data is being produced in massive volumes, at great velocity and from a variety of different sources such as mobile devices, sensors, a plethora of small devices hooked to the internet (Internet of Things), social networks, communication networks and many others. Interactive querying and large-scale analytics are being increasingly used to derive value out of this big data. A large portion of this data is being stored and processed in the Cloud due the several advantages provided by the Cloud such as scalability, elasticity, availability, low cost of ownership and the overall economies of scale. There is thus, a growing need for large-scale cloud-based data management systems that can support real-time ingest, storage and processing of large volumes of heterogeneous data. However, in the pay-as-you-go Cloud environment, the cost of analytics can grow linearly with the time and resources required. Reducing the cost of data analytics in the Cloud thus remains a primary challenge. In my dissertation research, I have focused on building efficient and cost-effective cloud-based data management systems for different application domains that are predominant in cloud computing environments. In the first part of my dissertation, I address the problem of reducing the cost of transactional workloads on relational databases to support database-as-a-service in the Cloud. The primary challenges in supporting such workloads include choosing how to partition the data across a large number of machines, minimizing the number of distributed transactions, providing high data availability, and tolerating failures gracefully. I have designed, built and evaluated SWORD, an end-to-end scalable online transaction processing system, that utilizes workload-aware data placement and replication to minimize the number of distributed transactions that incorporates a suite of novel techniques to significantly reduce the overheads incurred both during the initial placement of data, and during query execution at runtime. In the second part of my dissertation, I focus on sampling-based progressive analytics as a means to reduce the cost of data analytics in the relational domain. Sampling has been traditionally used by data scientists to get progressive answers to complex analytical tasks over large volumes of data. Typically, this involves manually extracting samples of increasing data size (progressive samples) for exploratory querying. This provides the data scientists with user control, repeatable semantics, and result provenance. However, such solutions result in tedious workflows that preclude the reuse of work across samples. On the other hand, existing approximate query processing systems report early results, but do not offer the above benefits for complex ad-hoc queries. I propose a new progressive data-parallel computation framework, NOW!, that provides support for progressive analytics over big data. In particular, NOW! enables progressive relational (SQL) query support in the Cloud using unique progress semantics that allow efficient and deterministic query processing over samples providing meaningful early results and provenance to data scientists. NOW! enables the provision of early results using significantly fewer resources thereby enabling a substantial reduction in the cost incurred during such analytics. Finally, I propose NSCALE, a system for efficient and cost-effective complex analytics on large-scale graph-structured data in the Cloud. The system is based on the key observation that a wide range of complex analysis tasks over graph data require processing and reasoning about a large number of multi-hop neighborhoods or subgraphs in the graph; examples include ego network analysis, motif counting in biological networks, finding social circles in social networks, personalized recommendations, link prediction, etc. These tasks are not well served by existing vertex-centric graph processing frameworks whose computation and execution models limit the user program to directly access the state of a single vertex, resulting in high execution overheads. Further, the lack of support for extracting the relevant portions of the graph that are of interest to an analysis task and loading it onto distributed memory leads to poor scalability. NSCALE allows users to write programs at the level of neighborhoods or subgraphs rather than at the level of vertices, and to declaratively specify the subgraphs of interest. It enables the efficient distributed execution of these neighborhood-centric complex analysis tasks over largescale graphs, while minimizing resource consumption and communication cost, thereby substantially reducing the overall cost of graph data analytics in the Cloud. The results of our extensive experimental evaluation of these prototypes with several real-world data sets and applications validate the effectiveness of our techniques which provide orders-of-magnitude reductions in the overheads of distributed data querying and analysis in the Cloud.

Identifying health inequalities in individuals with major mental illness (MMI) using routine data

Abstract and Summary of Thesis: Background: Individuals with Major Mental Illness (such as schizophrenia and bipolar disorder) experience increased rates of physical health comorbidity compared to the general population. They also experience inequalities in access to certain aspects of healthcare. This ultimately leads to premature mortality. Studies detailing patterns of physical health comorbidity are limited by their definitions of comorbidity, single disease approach to comorbidity and by the study of heterogeneous groups. To date the investigation of possible sources of healthcare inequalities experienced by individuals with Major Mental Illness (MMI) is relatively limited. Moreover studies detailing the extent of premature mortality experienced by individuals with MMI vary both in terms of the measure of premature mortality reported and age of the cohort investigated, limiting their generalisability to the wider population. Therefore local and national data can be used to describe patterns of physical health comorbidity, investigate possible reasons for health inequalities and describe mortality rates. These findings will extend existing work in this area. Aims and Objectives: To review the relevant literature regarding: patterns of physical health comorbidity, evidence for inequalities in physical healthcare and evidence for premature mortality for individuals with MMI. To examine the rates of physical health comorbidity in a large primary care database and to assess for evidence for inequalities in access to healthcare using both routine primary care prescribing data and incentivised national Quality and Outcome Framework (QOF) data. Finally to examine the rates of premature mortality in a local context with a particular focus on cause of death across the lifespan and effect of International Classification of Disease Version 10 (ICD 10) diagnosis and socioeconomic status on rates and cause of death. Methods: A narrative review of the literature surrounding patterns of physical health comorbidity, the evidence for inequalities in physical healthcare and premature mortality in MMI was undertaken. Rates of physical health comorbidity and multimorbidity in schizophrenia and bipolar disorder were examined using a large primary care dataset (Scottish Programme for Improving Clinical Effectiveness in Primary Care (SPICE)). Possible inequalities in access to healthcare were investigated by comparing patterns of prescribing in individuals with MMI and comorbid physical health conditions with prescribing rates in individuals with physical health conditions without MMI using SPICE data. Potential inequalities in access to health promotion advice (in the form of smoking cessation) and prescribing of Nicotine Replacement Therapy (NRT) were also investigated using SPICE data. Possible inequalities in access to incentivised primary healthcare were investigated using National Quality and Outcome Framework (QOF) data. Finally a pre-existing case register (Glasgow Psychosis Clinical Information System (PsyCIS)) was linked to Scottish Mortality data (available from the Scottish Government Website) to investigate rates and primary cause of death in individuals with MMI. Rate and primary cause of death were compared to the local population and impact of age, socioeconomic status and ICD 10 diagnosis (schizophrenia vs. bipolar disorder) were investigated. Results: Analysis of the SPICE data found that sixteen out of the thirty two common physical comorbidities assessed, occurred significantly more frequently in individuals with schizophrenia. In individuals with bipolar disorder fourteen occurred more frequently. The most prevalent chronic physical health conditions in individuals with schizophrenia and bipolar disorder were: viral hepatitis (Odds Ratios (OR) 3.99 95% Confidence Interval (CI) 2.82-5.64 and OR 5.90 95% CI 3.16-11.03 respectively), constipation (OR 3.24 95% CI 3.01-3.49 and OR 2.84 95% CI 2.47-3.26 respectively) and Parkinson’s disease (OR 3.07 95% CI 2.43-3.89 and OR 2.52 95% CI 1.60-3.97 respectively). Both groups had significantly increased rates of multimorbidity compared to controls: in the schizophrenia group OR for two comorbidities was 1.37 95% CI 1.29-1.45 and in the bipolar disorder group OR was 1.34 95% CI 1.20-1.49. In the studies investigating inequalities in access to healthcare there was evidence of: under-recording of cardiovascular-related conditions for example in individuals with schizophrenia: OR for Atrial Fibrillation (AF) was 0.62 95% CI 0.52 - 0.73, for hypertension 0.71 95% CI 0.67 - 0.76, for Coronary Heart Disease (CHD) 0.76 95% CI 0.69 - 0.83 and for peripheral vascular disease (PVD) 0.83 95% CI 0.72 - 0.97. Similarly in individuals with bipolar disorder OR for AF was 0.56 95% CI 0.41-0.78, for hypertension 0.69 95% CI 0.62 - 0.77 and for CHD 0.77 95% CI 0.66 - 0.91. There was also evidence of less intensive prescribing for individuals with schizophrenia and bipolar disorder who had comorbid hypertension and CHD compared to individuals with hypertension and CHD who did not have schizophrenia or bipolar disorder. Rate of prescribing of statins for individuals with schizophrenia and CHD occurred significantly less frequently than in individuals with CHD without MMI (OR 0.67 95% CI 0.56-0.80). Rates of prescribing of 2 or more anti-hypertensives were lower in individuals with CHD and schizophrenia and CHD and bipolar disorder compared to individuals with CHD without MMI (OR 0.66 95% CI 0.56-0.78 and OR 0.55 95% CI 0.46-0.67, respectively). Smoking was more common in individuals with MMI compared to individuals without MMI (OR 2.53 95% CI 2.44-2.63) and was particularly increased in men (OR 2.83 95% CI 2.68-2.98). Rates of ex-smoking and non-smoking were lower in individuals with MMI (OR 0.79 95% CI 0.75-0.83 and OR 0.50 95% CI 0.48-0.52 respectively). However recorded rates of smoking cessation advice in smokers with MMI were significantly lower than the recorded rates of smoking cessation advice in smokers with diabetes (88.7% vs. 98.0%, p<0.001), smokers with CHD (88.9% vs. 98.7%, p<0.001) and smokers with hypertension (88.3% vs. 98.5%, p<0.001) without MMI. The odds ratio of NRT prescription was also significantly lower in smokers with MMI without diabetes compared to smokers with diabetes without MMI (OR 0.75 95% CI 0.69-0.81). Similar findings were found for smokers with MMI without CHD compared to smokers with CHD without MMI (OR 0.34 95% CI 0.31-0.38) and smokers with MMI without hypertension compared to smokers with hypertension without MMI (OR 0.71 95% CI 0.66-0.76). At a national level, payment and population achievement rates for the recording of body mass index (BMI) in MMI was significantly lower than the payment and population achievement rates for BMI recording in diabetes throughout the whole of the UK combined: payment rate 92.7% (Inter Quartile Range (IQR) 89.3-95.8 vs. 95.5% IQR 93.3-97.2, p<0.001 and population achievement rate 84.0% IQR 76.3-90.0 vs. 92.5% IQR 89.7-94.9, p<0.001 and for each country individually: for example in Scotland payment rate was 94.0% IQR 91.4-97.2 vs. 96.3% IQR 94.3-97.8, p<0.001. Exception rate was significantly higher for the recording of BMI in MMI than the exception rate for BMI recording in diabetes for the UK combined: 7.4% IQR 3.3-15.9 vs. 2.3% IQR 0.9-4.7, p<0.001 and for each country individually. For example in Scotland exception rate in MMI was 11.8% IQR 5.4-19.3 compared to 3.5% IQR 1.9-6.1 in diabetes. Similar findings were found for Blood Pressure (BP) recording: across the whole of the UK payment and population achievement rates for BP recording in MMI were also significantly reduced compared to payment and population achievement rates for the recording of BP in chronic kidney disease (CKD): payment rate: 94.1% IQR 90.9-97.1 vs.97.8% IQR 96.3-98.9 and p<0.001 and population achievement rate 87.0% IQR 81.3-91.7 vs. 97.1% IQR 95.5-98.4, p<0.001. Exception rates again were significantly higher for the recording of BP in MMI compared to CKD (6.4% IQR 3.0-13.1 vs. 0.3% IQR 0.0-1.0, p<0.001). There was also evidence of differences in rates of recording of BMI and BP in MMI across the UK. BMI and BP recording in MMI were significantly lower in Scotland compared to England (BMI:-1.5% 99% CI -2.7 to -0.3%, p<0.001 and BP: -1.8% 99% CI -2.7 to -0.9%, p<0.001). While rates of BMI and BP recording in diabetes and CKD were similar in Scotland compared to England (BMI: -0.5 99% CI -1.0 to 0.05, p=0.004 and BP: 0.02 99% CI -0.2 to 0.3, p=0.797). Data from the PsyCIS cohort showed an increase in Standardised Mortality Ratios (SMR) across the lifespan for individuals with MMI compared to the local Glasgow and wider Scottish populations (Glasgow SMR 1.8 95% CI 1.6-2.0 and Scotland SMR 2.7 95% CI 2.4-3.1). Increasing socioeconomic deprivation was associated with an increased overall rate of death in MMI (350.3 deaths/10,000 population/5 years in the least deprived quintile compared to 794.6 deaths/10,000 population/5 years in the most deprived quintile). No significant difference in rate of death for individuals with schizophrenia compared with bipolar disorder was reported (6.3% vs. 4.9%, p=0.086), but primary cause of death varied: with higher rates of suicide in individuals with bipolar disorder (22.4% vs. 11.7%, p=0.04). Discussion: Local and national datasets can be used for epidemiological study to inform local practice and complement existing national and international studies. While the strengths of this thesis include the large data sets used and therefore their likely representativeness to the wider population, some limitations largely associated with using secondary data sources are acknowledged. While this thesis has confirmed evidence of increased physical health comorbidity and multimorbidity in individuals with MMI, it is likely that these findings represent a significant under reporting and likely under recognition of physical health comorbidity in this population. This is likely due to a combination of patient, health professional and healthcare system factors and requires further investigation. Moreover, evidence of inequality in access to healthcare in terms of: physical health promotion (namely smoking cessation advice), recording of physical health indices (BMI and BP), prescribing of medications for the treatment of physical illness and prescribing of NRT has been found at a national level. While significant premature mortality in individuals with MMI within a Scottish setting has been confirmed, more work is required to further detail and investigate the impact of socioeconomic deprivation on cause and rate of death in this population. It is clear that further education and training is required for all healthcare staff to improve the recognition, diagnosis and treatment of physical health problems in this population with the aim of addressing the significant premature mortality that is seen. Conclusions: Future work lies in the challenge of designing strategies to reduce health inequalities and narrow the gap in premature mortality reported in individuals with MMI. Models of care that allow a much more integrated approach to diagnosing, monitoring and treating both the physical and mental health of individuals with MMI, particularly in areas of social and economic deprivation may be helpful. Strategies to engage this “hard to reach” population also need to be developed. While greater integration of psychiatric services with primary care and with specialist medical services is clearly vital the evidence on how best to achieve this is limited. While the National Health Service (NHS) is currently undergoing major reform, attention needs to be paid to designing better ways to improve the current disconnect between primary and secondary care. This should then help to improve physical, psychological and social outcomes for individuals with MMI.

MLCut: exploring multi-level cuts in dendrograms for biological data.

Choosing a single similarity threshold for cutting dendrograms is not sufficient for performing hierarchical clustering analysis of heterogeneous data sets. In addition, alternative automated or semi-automated methods that cut dendrograms in multiple levels make assumptions about the data in hand. In an attempt to help the user to find patterns in the data and resolve ambiguities in cluster assignments, we developed MLCut: a tool that provides visual support for exploring dendrograms of heterogeneous data sets in different levels of detail. The interactive exploration of the dendrogram is coordinated with a representation of the original data, shown as parallel coordinates. The tool supports three analysis steps. Firstly, a single-height similarity threshold can be applied using a dynamic slider to identify the main clusters. Secondly, a distinctiveness threshold can be applied using a second dynamic slider to identify “weak-edges” that indicate heterogeneity within clusters. Thirdly, the user can drill-down to further explore the dendrogram structure - always in relation to the original data - and cut the branches of the tree at multiple levels. Interactive drill-down is supported using mouse events such as hovering, pointing and clicking on elements of the dendrogram. Two prototypes of this tool have been developed in collaboration with a group of biologists for analysing their own data sets. We found that enabling the users to cut the tree at multiple levels, while viewing the effect in the original data, is a promising method for clustering which could lead to scientific discoveries.

Comparison of five popular normalization methods using a spike-in proteomics data set

Mass spectrometry (MS)-based proteomics has seen significant technical advances during the past two decades and mass spectrometry has become a central tool in many biosciences. Despite the popularity of MS-based methods, the handling of the systematic non-biological variation in the data remains a common problem. This biasing variation can result from several sources ranging from sample handling to differences caused by the instrumentation. Normalization is the procedure which aims to account for this biasing variation and make samples comparable. Many normalization methods commonly used in proteomics have been adapted from the DNA-microarray world. Studies comparing normalization methods with proteomics data sets using some variability measures exist. However, a more thorough comparison looking at the quantitative and qualitative differences of the performance of the different normalization methods and at their ability in preserving the true differential expression signal of proteins, is lacking. In this thesis, several popular and widely used normalization methods (the Linear regression normalization, Local regression normalization, Variance stabilizing normalization, Quantile-normalization, Median central tendency normalization and also variants of some of the forementioned methods), representing different strategies in normalization are being compared and evaluated with a benchmark spike-in proteomics data set. The normalization methods are evaluated in several ways. The performance of the normalization methods is evaluated qualitatively and quantitatively on a global scale and in pairwise comparisons of sample groups. In addition, it is investigated, whether performing the normalization globally on the whole data or pairwise for the comparison pairs examined, affects the performance of the normalization method in normalizing the data and preserving the true differential expression signal. In this thesis, both major and minor differences in the performance of the different normalization methods were found. Also, the way in which the normalization was performed (global normalization of the whole data or pairwise normalization of the comparison pair) affected the performance of some of the methods in pairwise comparisons. Differences among variants of the same methods were also observed.

Dinoflagellate Genomic Organization and Phylogenetic Marker Discovery Utilizing Deep Sequencing Data

Dinoflagellates possess large genomes in which most genes are present in many copies. This has made studies of their genomic organization and phylogenetics challenging. Recent advances in sequencing technology have made deep sequencing of dinoflagellate transcriptomes feasible. This dissertation investigates the genomic organization of dinoflagellates to better understand the challenges of assembling dinoflagellate transcriptomic and genomic data from short read sequencing methods, and develops new techniques that utilize deep sequencing data to identify orthologous genes across a diverse set of taxa. To better understand the genomic organization of dinoflagellates, a genomic cosmid clone of the tandemly repeated gene Alchohol Dehydrogenase (AHD) was sequenced and analyzed. The organization of this clone was found to be counter to prevailing hypotheses of genomic organization in dinoflagellates. Further, a new non-canonical splicing motif was described that could greatly improve the automated modeling and annotation of genomic data. A custom phylogenetic marker discovery pipeline, incorporating methods that leverage the statistical power of large data sets was written. A case study on Stramenopiles was undertaken to test the utility in resolving relationships between known groups as well as the phylogenetic affinity of seven unknown taxa. The pipeline generated a set of 373 genes useful as phylogenetic markers that successfully resolved relationships among the major groups of Stramenopiles, and placed all unknown taxa on the tree with strong bootstrap support. This pipeline was then used to discover 668 genes useful as phylogenetic markers in dinoflagellates. Phylogenetic analysis of 58 dinoflagellates, using this set of markers, produced a phylogeny with good support of all branches. The Suessiales were found to be sister to the Peridinales. The Prorocentrales formed a monophyletic group with the Dinophysiales that was sister to the Gonyaulacales. The Gymnodinales was found to be paraphyletic, forming three monophyletic groups. While this pipeline was used to find phylogenetic markers, it will likely also be useful for finding orthologs of interest for other purposes, for the discovery of horizontally transferred genes, and for the separation of sequences in metagenomic data sets.

Kinetic modelling of in vitro data of PI3K, mTOR1, PTEN enzymes and on-target inhibitors Rapamycin, BEZ235, and LY294002

The phosphatidylinositide 3-kinases (PI3K) and mammalian target of rapamycin-1 (mTOR1) are two key targets for anti-cancer therapy. Predicting the response of the PI3K/AKT/mTOR1 signalling pathway to targeted therapy is made difficult because of network complexities. Systems biology models can help explore those complexities but the value of such models is dependent on accurate parameterisation. Motivated by a need to increase accuracy in kinetic parameter estimation, and therefore the predictive power of the model, we present a framework to integrate kinetic data from enzyme assays into a unified enzyme kinetic model. We present exemplar kinetic models of PI3K and mTOR1, calibrated on in vitro enzyme data and founded on Michaelis-Menten (MM) approximation. We describe the effects of an allosteric mTOR1 inhibitor (Rapamycin) and ATP-competitive inhibitors (BEZ2235 and LY294002) that show dual inhibition of mTOR1 and PI3K. We also model the kinetics of phosphatase and tensin homolog (PTEN), which modulates sensitivity of the PI3K/AKT/mTOR1 pathway to these drugs. Model validation with independent data sets allows investigation of enzyme function and drug dose dependencies in a wide range of experimental conditions. Modelling of the mTOR1 kinetics showed that Rapamycin has an IC50 independent of ATP concentration and that it is a selective inhibitor of mTOR1 substrates S6K1 and 4EBP1: it retains 40% of mTOR1 activity relative to 4EBP1 phosphorylation and inhibits completely S6K1 activity. For the dual ATP-competitive inhibitors of mTOR1 and PI3K, LY294002 and BEZ235, we derived the dependence of the IC50 on ATP concentration that allows prediction of the IC50 at different ATP concentrations in enzyme and cellular assays. Comparison of the drug effectiveness in enzyme and cellular assays showed that some features of these drugs arise from signalling modulation beyond the on-target action and MM approximation and require a systems-level consideration of the whole PI3K/PTEN/AKT/mTOR1 network in order to understand mechanisms of drug sensitivity and resistance in different cancer cell lines. We suggest that using these models in systems biology investigation of the PI3K/AKT/mTOR1 signalling in cancer cells can bridge the gap between direct drug target action and the therapeutic response to these drugs and their combinations.