Bayesian meta-analysis for identifying periodically expressed genes in fission yeast cell cycle

The effort to identify genes with periodic expression during the cell cycle from genome-wide microarray time series data has been ongoing for a decade. However, the lack of rigorous modeling of periodic expression as well as the lack of a comprehensive model for integrating information across genes and experiments has impaired the effort for the accurate identification of periodically expressed genes. To address the problem, we introduce a Bayesian model to integrate multiple independent microarray data sets from three recent genome-wide cell cycle studies on fission yeast. A hierarchical model was used for data integration. In order to facilitate an efficient Monte Carlo sampling from the joint posterior distribution, we develop a novel Metropolis–Hastings group move. A surprising finding from our integrated analysis is that more than 40% of the genes in fission yeast are significantly periodically expressed, greatly enhancing the reported 10–15% of the genes in the current literature. It calls for a reconsideration of the periodically expressed gene detection problem.Statistic

Towards self-powered wireless sensor networks

Ubiquitous computing aims at creating smart environments in which computational and communication capabilities permeate the word at all scales, improving the human experience and quality of life in a totally unobtrusive yet completely reliable manner. According to this vision, an huge variety of smart devices and products (e.g., wireless sensor nodes, mobile phones, cameras, sensors, home appliances and industrial machines) are interconnected to realize a network of distributed agents that continuously collect, process, share and transport information. The impact of such technologies in our everyday life is expected to be massive, as it will enable innovative applications that will profoundly change the world around us. Remotely monitoring the conditions of patients and elderly people inside hospitals and at home, preventing catastrophic failures of buildings and critical structures, realizing smart cities with sustainable management of traffic and automatic monitoring of pollution levels, early detecting earthquake and forest fires, monitoring water quality and detecting water leakages, preventing landslides and avalanches are just some examples of life-enhancing applications made possible by smart ubiquitous computing systems. To turn this vision into a reality, however, new raising challenges have to be addressed, overcoming the limits that currently prevent the pervasive deployment of smart devices that are long lasting, trusted, and fully autonomous. In particular, the most critical factor currently limiting the realization of ubiquitous computing is energy provisioning. In fact, embedded devices are typically powered by short-lived batteries that severely affect their lifespan and reliability, often requiring expensive and invasive maintenance. In this PhD thesis, we investigate the use of energy-harvesting techniques to overcome the energy bottleneck problem suffered by embedded devices, particularly focusing on Wireless Sensor Networks (WSNs), which are one of the key enablers of pervasive computing systems. Energy harvesting allows to use energy readily available from the environment (e.g., from solar light, wind, body movements, etc.) to significantly extend the typical lifetime of low-power devices, enabling ubiquitous computing systems that can last virtually forever. However, the design challenges posed both at the hardware and at the software levels by the design of energy-autonomous devices are many. This thesis addresses some of the most challenging problems of this emerging research area, such as devising mechanisms for energy prediction and management, improving the efficiency of the energy scavenging process, developing protocols for harvesting-aware resource allocation, and providing solutions that enable robust and reliable security support. %, including the design of mechanisms for energy prediction and management, improving the efficiency of the energy harvesting process, the develop of protocols for harvesting-aware resource allocation, and providing solutions that enable robust and reliable security support

Multivariate hydrometeorological extreme events and their impacts on vegetation: potential methods and applications

Trockenheiten und Hitzewellen beeinflussen unsere Gesellschaft und die Vegetation. Insbesondere im Zusammenhang mit dem Klimawandel sind die Auswirkungen auf die Vegetation von besonderer Bedeutung. Im globalen Kohlenstoffkreislauf sind terrestrische Ökosysteme normalerweise Senken von Kohlenstoffdioxid, können sich aber während und nach Klimaextremereignissen in Kohlenstoffquellen verwandeln. Ein entscheidender Aspekt hierbei ist die Rolle verschiedener Pflanzenarten und Vegetationstypen auf verschiedenen Skalen, die die Auswirkungen auf den Kohlenstoffkreislauf beeinflussen. Obwohl durch physiologische Unterschiede zwischen verschiedenen Pflanzenarten unterschiedliche Reaktionen auf Extremereignisse naheliegen, sind diese Unterschiede auf globaler Ebene nicht systematisch ausgewertet und vollständig verstanden. Ein weiter Aspekt ist, dass Klimaextremereignissen von Natur aus multivariat sind. Beispielsweise kann heiße Luft mehr Wasser aufnehmen als kalte Luft. Extremereignisse mit starken Auswirkungen waren in der Vergangenheit häufig multivariat, wie beispielsweise in Europa 2003, Russland 2012, oder den USA 2012. Diese multivariate Natur von Klimaextremen erfordert eine multivariate Perspektive auf diese Ereignisse. Bisher werden meistens einzelne Variablen zu Detektion von Extremereignissen genutzt und keine Kovariation oder Nichtlinearitäten berücksichtigt. Neue generische Workflows, die solche multivariaten Strukturen berücksichtigen, müssen erst entwickelt oder aus anderen Disziplinen übertragen werden, um uns eine multivariate Perspektive auf Klimaextreme zu bieten. Das übergeordnete Ziel der Dissertation ist es, die Erkennung und das Verständnis von Klimaextremen und deren Auswirkungen auf die Vegetation zu verbessern, indem eine breitere multivariate Perspektive ermöglicht wird, die bisherige Ansätze zur Erkennung von Extremereignissen ergänzt

Prognostic and pathophysiological features of uraemic cardiomyopathy using cardiovascular magnetic resonance imaging

Premature cardiovascular (CV) death is the commonest cause of death in patients with end stage renal disease (ESRD), which includes those receiving or close to requiring renal replacement therapy. In ESRD patients, CV deaths are most commonly caused by cardiac arrhythmia and sudden cardiac death compared to the general population where myocardial ischaemia and infarction predominate. Higher CV disease burden is due to accumulation of “conventional” risk factors (e.g. hypertension, diabetes mellitus, smoking) and “novel” risk factors (e.g. oxidative stress, proteinuria, anaemia, inflammation) in ESRD patients. In addition, risk factors specific to patients with renal disease have been identified including alteration in left ventricular (LV) structure, called uraemic cardiomyopathy. These structural abnormalities are common in patients with ESRD (between 60-80% of subjects upon initiation of dialysis) and include left ventricular hypertrophy (LVH), systolic dysfunction (LVSD) and dilatation. These changes in LV structure confer adverse CV outcome in ESRD patients and have proven difficult to reverse. Detection of these abnormalities is usually performed using echocardiography, however this technique is inaccurate in ESRD patients due to significant alterations in LV shape and geometric assumptions made during calculation of myocardial mass. Cardiovascular MRI (CMR) negates these assumptions and is the most accurate, reproducible and reliable method of assessing LV dimensions independent of intravascular volume, particularly in patients with altered myocardial architecture. Furthermore, maximal left atrial volume can be measured using CMR. The principle aims of the studies presented in this thesis were to elucidate prognostic and pathophysiological features of uraemic cardiomyopathy using CMR. In a large study (n=246) of haemodialysis patients, the determinants of each LV abnormality of uraemic cardiomyopathy were identified from past clinical history, haemodialysis and blood parameters and other LV measurements. For LV changes, major determinants were clinical features associated with advanced renal disease, namely expansion of intravascular/ extracellular fluid compartment, abnormal bone mineral biochemistry and hypertension. Furthermore, presence of one LV abnormality was one of the strongest predictors of presence of another, perhaps indicating differing stages of uraemic cardiomyopathy development. In a subsequent prognostic study including these patients (n=446), presence of LVSD and LV dilatation on CMR were significantly associated with poorer all cause and CV mortality. Presence of LVH, which is by far the most common structural change, was associated with poorer cardiovascular survival only. In addition, presence of two or three abnormalities (commonly LVH with another abnormality) had a significantly poorer prognosis and independently predicted CV and all cause mortality. This has implications for therapeutic strategies which should aim to slow or reverse cardiac changes of ESRD and prevent progression from one cardiac abnormality to 2 or more. In a further study (n=201) investigating additional prognostic features of ESRD patients with LVH, maximal left atrial volume (LAV) was measured using the bi-plane area length method at end LV systole. Elevated LAV and presence of LVSD were significantly associated with poorer all cause survival and were independent predictors of death. The most likely causes of elevated LAV in ESRD patients are LV diastolic dysfunction and expanded extracellular compartment and may provide a target for therapeutic intervention. The electrophysiological features of uraemic cardiomyopathy were assessed using microvolt T wave alternans (MTWA) which is a novel, non-invasive method of measuring small variations in surface electrocardiogram (ECG) T wave morphology and thus ventricular repolarisation. This technique has been used to stratify other cohorts at elevated risk of sudden cardiac death (such as ischaemic and non ischaemic cardiomyopathy, hypertensive LVH). A study presented in this thesis, compared MTWA results between ESRD (n=200) and hypertensive patients with LVH on echocardiography (n=30). Abnormal MTWA result was significantly more common in ESRD patients compared to hypertensive patients with LVH. Furthermore, abnormal MTWA result was significantly associated with myocardial abnormalities of uraemic cardiomyopathy and a history of macrovascular atheromatous disease in ESRD patients. Despite preservation of LV function on CMR, the frequency of abnormal MTWA result in ESRD patients was similar to previous studies in subjects with heart failure. 31Phosphorus magnetic resonance spectroscopy is a novel, non-invasive technique of estimating cardiac energetic status and high energy phosphate (HEP) metabolism in a myocardial area of interest and has previously been used to assess patients with global myocardial disease (dilated cardiomyopathy, hypertensive LVH). High energy phosphate metabolism was compared between patients with ESRD (n=53) and hypertensive LVH (n=30) and despite similar LV mass between both groups, PCr: ATP (an indicator of HEP metabolism) was significantly reduced in ESRD patients. These findings are most likely due to cardiac interstitial fibrosis and the alteration of tissue composition within the area of interest, and changes in metabolic function within cardiomyocytes of uraemic hearts. Finally, a small study (n=50) investigated the effect of successful renal transplantation on LV mass measured by CMR. On comparison of patients who remained on the renal transplant waiting list, there was no significant difference in LV mass in patients who received a renal transplant. It is likely that previous echocardiography studies that demonstrated significant regression of LVH, measured improvement in fluid control rather that actual reduction in myocardial mass. Future studies investigating benefit of therapeutic intervention may require identification of individuals at higher CV risk and the results of studies presented in this thesis aim to provide information for selecting such ESRD patients. With these results in mind, further prospective studies will be able to carefully select groups of ESRD patients with differing left ventricular, left atrial, electrophysiological and biochemical properties to demonstrate survival benefit with interventional agents. In this way, future therapies for ESRD patients can be tailored to improve cardiovascular survival

Oscillations and noise in gene expression: a dialogue between theory and experiments

El carácter estocástico de las reacciones bioquímicas y las fluctuaciones del ambiente celular introducen variabilidad en la expresión y regulación genética como en todos los procesos a nivel celular. Sin embargo a pesar de las fluctuaciones, las células son capaces de realizar tareas complejas y funcionar en forma confiable y reproducible. A través de redes de regulación genética, las células toman decisiones y generan patrones precisos de actividad temporal y espacial. Un ejemplo en el que confluyen las redes de regulación, la dinámica en la expresión, la formación de patrones, y el control del ruido es el surgimiento de las estructuras que dan origen a las vertebras durante el desarrollo embrioario de los vertebrados, en el que se genera un patrón oscilatorio de expresión genética controlado por un reloj de segmentación. En esta tesis nos centramos en distintos aspectos que surgen del diálogo entre la teoría y los experimentos cuyos ingredientes en común son las redes de regulación genética, las oscilaciones, el ruido y el reloj de segmentación. Las células pueden controlar las fluctuaciones en los niveles de proteína por medio del feedback negativo, donde las proteínas se unen a sitios en el ADN para reprimir su propia producción. Los estudios teóricos usualmente asumen la existencia de un único sitio de unión para el represor, mientras que en la mayoría de las especies existen múltiples sitios de unión. En la primer parte de esta tesis, estudiamos una descripción estocástica de una red de feedback negativo con múltiples sitios de unión para el represor. Encontramos que el aumento del número de sitios de unión induce la expresión regular de los productos genéticos.. Al ajustar el umbral de la represión, mostramos que los múltiples sitios de unión también pueden suprimir las fluctuaciones en la expresión genética. Los resultados de este trabajo abren posibles aplicaciones en la biología sintética así como un marco teórico para entender la existencia de múltiples sitios de unión en diversos genes. Un ejemplo paradigmático de las redes de regulación y la dinámica en la expresión, la formación de patrones, y control del ruido es la estructura segmentada y repetitiva en los vertebrados en la que los segmentos que dan origen a las vertebras se originan durante el desarrollo embrionario de manera secuencial y rítmica. El ritmo de formación de los segmentos es controlado por un reloj de segmentación, basado en la idea de que existe una red genética que tiene una expresión oscilatoria y que es capaz de generar oscilaciones autónomas en las células del reloj. Si bien la evidencia es consistente con la idea de un reloj celular, debido a las altas fluctuaciones y a la complejidad y limitaciones del proceso de medición como a la cuantificación de dicho patrón de expresión, aún no es claro que exista una red genética capaz de generar oscilaciones a nivel autónomo. En la segunda parte de esta tesis estudiamos si las células individuales son capaces de producir oscilaciones. Para ello estudiamos series temporales de la concentración de las proteínas del reloj de segmentación obtenidas de células individuales de un reportero transgénico en zebrafish. A partir de la estadística de las series temporales y una forma normal de Hopf con ruido de color en la amplitud logramos mostrar que las células individuales se comportan como osciladores y que exhiben una dinámica heterogénea oscilatoria. Las fluctuaciones limitan la precisión temporal de un oscilador. Esta precisión puede ser caracterizada por el quality factor que cuantifica el número de ciclos en los cuál la serie es coherente. En una serie temporal, esta precisión puede ser determinada a partir de la función de autocorrelación o del periodograma. Sin embargo, una característica de todas las series temporales experimentales es que tienen una longitud finita, y en particular en biología, las series oscilatorias suelen tener un número pequeño de ciclos. Esto introduce grandes limitaciones para cuantificar la precisión de las oscilaciones a través del quality factor. En este trabajo mostramos que el valor del quality factor de las series temporales depende del método usado y para series temporales cortas puede haber grandes discrepancias entre el valor estimado y el valor real, limitando la precisión de la cuantificación. A partir de un oscilador de fases con ruido, y utilizando una teoría de First Passage Time encontramos un estimador para el quality factor que se basa en la estadística de los periodos y que converge rápidamente al valor real y es robusto inclusive en series temporales cortas. Mostramos que este estimador es robusto y preciso para distintos modelos de osciladores no lineales e inclusive en presencia de fluctuaciones de amplitud. Si bien el quality factor puede ser un estimador robusto de la precisión, cuando los periodos de la serie oscilatoria se encuentran correlacionados temporalmente, este estimador no logra capturar completamente la precision de las oscilaciones. A partir de un oscilador de fase con ruido de color, generamos series de tiempo oscilatorias con el periodo correlacionado y generalizamos la noción de quality factor definiendo un quality factor generalizado. En el cuarto capítulo mostramos que este estimador logra cuantificar correctamente la precisión temporal en series temporales cuyos periodos se encuentran correlacionados en el tiempo inclusive cuando las series temporales son cortas. Por último utilizando el método propuesto para calcular el quality factor basado en la estadística de los periodos, revisamos los resultados previos y discutimos las diferencias entre los distintos métodos de cuantificación. Para concluir, en esta tesis estudiamos aspectos complementarios para avanzar sobre el entendimiento y la cuantificación de la regulación genética, las fluctuaciones, las oscilaciones, y el reloj de segmentación a partir de un enfoque teórico.The stochastic nature of biochemical reactions and fluctuations in the cellular environment introduce variability in genetic expression and regulation as in all processes at the cellular level. However, despite fluctuations, the cells are able to perform complex tasks and function reliably. By means of gene regulatory networks, cells take decisions and generate precise patterns of temporal and spatial activity. An example where the regulatory networks, the dynamics of expression, the formation of patterns, and the control of noise converge is the emergence of the structures that give rise to vertebrae during the embryonic development of vertebrates controlled by the segmentation clock. In this thesis we study aspects that arise from the dialogue between theory and experiments whose common ingredients are the gene regulatory networks, oscillations,noise and the segmentation clock. Cells can control protein level fluctuations through negative feedback, in which proteins bind to specific sites in DNA and suppress their own production. Theoretical studies usually assume the existence of a single binding site for the repressor, while most species have multiple binding sites. In the first part of this thesis, we study a stochastic description of a negative feedback network with multiple sites for the repressor. We find that the increase in the number of binding sites induces the regular expression of gene products. By adjusting the repression threshold, we show that multiple binding sites can also enhance noise suppression in gene expression. These results open up possible applications in synthetic biology as well as a theoretical framework for understanding the existence of multiple binding sites in different genes. A paradigmatic example of regulatory networks and dynamics in gene expression, pattern formation, and noise control is the segmented and repetitive structure in vertebrates, in which the segments that give rise to vertebrae originate during embryonic development in a sequential and rhythmic manner. The rhythm of the formation of the segments is controlled by a segmentation clock, based on the idea that there is a genetic network that has an oscillatory expression and that is able to generate autonomous oscillations in the cells of the clock. Although the evidence is consistent with the idea of a cellular clock, due to the fluctuations and the complexity and limitations of the measurement process as well as the quantification of this pattern of expression, it is yet not clear whether there is a genetic network capable of generate autonomous oscillations at cellular level. In the second part of this thesis we study whether individual cells are capable of producing oscillations autonomously. We analyse time series of the concentration of the segmentation clock proteins obtained from individual cells of a transgenic reporter in zebrafish. By analysing the time series and using a Hopf normal form with colour noise in the amplitude we show that single cells behave like oscillators and exhibit a heterogeneous oscillatory dynamics. Fluctuations limit the temporal precision of an oscillator. Temporal precision can be characterised by a quality factor, which quantifies the number of coherent cycles. For an experimental time series, the quality factor can be determined either from the autocorrelation function or the periodogram. A feature of experimental time series is that they have a finite duration, and particularly in biology, oscillatory series usually have a small number of cycles. This introduces major limitations for quantifying the properties of time series, such as quantifying the accuracy of oscillations through quality factor. We show that the quality factor value of time series depends on the method used and for short time series there can be large discrepancies between the estimated value and the actual value, limiting the accuracy of quantification. From a phase oscillator with noise, and using a First Passage Time theory we find an estimator for the quality factor that is based on the statistics of the periods and that converges quickly to the real value and is robust even in short time series. We show that this estimator is robust and accurate for different models of non-linear oscillators and even in the presence of amplitude fluctuations. While the quality factor can be a robust precision estimator, when the periods of the oscillatory series are time correlated, this estimator fails to fully capture the precision of the oscillations.From a phase oscillator with additive colour noise, we generate oscillatory time series with correlated period and we generalise the notion of quality factor by defining a generalized quality factor. We show that this estimator correctly quantifies time accuracy in time series whose periods are correlated in time even when time series are short. Finally, using the proposed method to calculate the quality factor based on the period statistics, we review the previous results and we discuss the differences between the different methods of quantification. To conclude, in this thesis we study complementary aspects to advance on the understanding and quantification of gene regulation, gene expression dynamics, fluctuations, oscillations, and the segmentation clock using a theoretical approach.Fil: Lengyel, Iván M.. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina

Clinical and Mechanistic Insights into Novel Probiotic Functions and Formulations

Using a combination of hypothesis and discovery based approaches, the goal of this thesis was to better describe novel probiotic functions and their mechanisms while striving to better understand the effect of formulation on Bifidobacterium animalis subsp. lactis, Lactobacillus paracasei and L. rhamnosus. Using RNA-Seq, a bacterial metatranscriptome analysis of a commonly consumed probiotic yogurt showed that the organisms adapted to storage time and flavor additions. This led to the discovery that in addition to the probiotic health benefits, members of the L. casei group (L. rhamnosus and L. paracasei) produce volatile sulfur compounds mediated by a novel sulfur/taurine metabolism gene cluster that affect taste and texture. The benefits of selected probiotic strains were tested in a further series of human studies. A systems biology approach was developed and a double-blind, placebo-controlled clinical trial of post-menopausal women showed that vaginally administered probiotics could influence the microbiota and host responses. Changes in the vaginal microbiota were noted in late pregnancy in a rural Tanzanian population, and maternal intake of Moringa supplemented L. rhamnosus GR-1 yogurt appeared to improve the gut microbiota profile of the newborn babies. Having discovered that L. rhamnosus GR-1, and selected other lactobacilli, could sequester heavy metals in vitro, a randomized open-label pilot study was performed and showed a reduction in toxic metal uptake in Tanzanian pregnant women and school children. The latter series of findings led to the discovery, development and characterization of a new strain, L. rhamnosus Lr60, with high potential to reduce toxic metal accumulation in the host. Using a mouse model, strains of L. rhamnosus were tested to better understand mechanisms of protection against mercury as well as to examine potential modulation of host xenobiotic metabolism by probiotics. Data suggest it is possible to sequester mercury and prevent it from entering the bloodstream. Collectively, these studies have increased our knowledge of probiotic mechanisms as well as lead to the development of novel applications of relevance to human health

Advances in Forensic Genetics

The book has 25 articles about the status and new directions in forensic genetics. Approximately half of the articles are invited reviews, and the remaining articles deal with new forensic genetic methods. The articles cover aspects such as sampling DNA evidence at the scene of a crime; DNA transfer when handling evidence material and how to avoid DNA contamination of items, laboratory, etc.; identification of body fluids and tissues with RNA; forensic microbiome analysis with molecular biology methods as a supplement to the examination of human DNA; forensic DNA phenotyping for predicting visible traits such as eye, hair, and skin colour; new ancestry informative DNA markers for estimating ethnic origin; new genetic genealogy methods for identifying distant relatives that cannot be identified with conventional forensic DNA typing; sensitive DNA methods, including single-cell DNA analysis and other highly specialised and sensitive methods to examine ancient DNA from unidentified victims of war; forensic animal genetics; genetics of visible traits in dogs; statistical tools for interpreting forensic DNA analyses, including the most used IT tools for forensic STR-typing and DNA sequencing; haploid markers (Y-chromosome and mitochondria DNA); inference of ethnic origin; a comprehensive logical framework for the interpretation of forensic genetic DNA data; and an overview of the ethical aspects of modern forensic genetics

Emerging Hydro-Climatic Patterns, Teleconnections and Extreme Events in Changing World at Different Timescales

This Special Issue is expected to advance our understanding of these emerging patterns, teleconnections, and extreme events in a changing world for more accurate prediction or projection of their changes especially on different spatial–time scales