Biomethane production from food waste and organic residues

Anaerobic digestion (AD) of biodegradable waste is an environmentally and economically sustainable solution which incorporates waste treatment and energy recovery. The organic fraction of municipal solid waste (OFMSW), which comprises mostly of food waste, is highly degradable under anaerobic conditions. Biogas produced from OFMSW, when upgraded to biomethane, is recognised as one of the most sustainable renewable biofuels and can also be one of the cheapest sources of biomethane if a gate fee is associated with the substrate. OFMSW is a complex and heterogeneous material which may have widely different characteristics depending on the source of origin and collection system used. The research presented in this thesis investigates the potential energy resource from a wide range of organic waste streams through field and laboratory research on real world samples. OFMSW samples collected from a range of sources generated methane yields ranging from 75 to 160 m3 per tonne. Higher methane yields are associated with source segregated food waste from commercial catering premises as opposed to domestic sources. The inclusion of garden waste reduces the specific methane yield from household organic waste. In continuous AD trials it was found that a conventional continuously stirred tank reactor (CSTR) gave the highest specific methane yields at a moderate organic loading rate of 2 kg volatile solids (VS) m-3 digester day-1 and a hydraulic retention time of 30 days. The average specific methane yield obtained at this loading rate in continuous digestion was 560 ± 29 L CH4 kg-1 VS which exceeded the biomethane potential test result by 5%. The low carbon to nitrogen ratio (C: N <14:1) associated with canteen food waste lead to increasing concentrations of volatile fatty acids in line with high concentrations of ammonia nitrogen at higher organic loading rates. At an organic loading rate of 4 kg VS m-3day-1 the specific methane yield dropped considerably (381 L CH4 kg-1 VS), the pH rose to 8.1 and free ammonia (NH3 ) concentrations reached toxicity levels towards the end of the trial (ca. 950 mg L-1). A novel two phase AD reactor configuration consisting of a series of sequentially fed leach bed reactors connected to an upflow anaerobic sludge blanket (UASB) demonstrated a high rate of organic matter decay but resulted in lower specific methane yields (384 L CH4 kg-1 VS) than the conventional CSTR system.

Exploring the Zionist evolution of Robert Briscoe: History and memory

Robert Briscoe was the Dublin born son of Lithuanian and German-Jewish immigrants. As a young man he joined Sinn Féin and was an important figure in the War of Independence due to a role as one of the IRA’s main gun-procuring agents. He took the anti-Treaty side during an internecine Civil War, mainly due to the influence of Eamon de Valera and retained a filial devotion towards him for the rest of his life. In 1926 he was a founding member of Fianna Fáil, de Valera’s breakaway republican party, which would dominate twentieth-century Irish politics. He was first elected as a Fianna Fáil T.D. (Teachta Dála, Deputy to the Dáil) in 1927, and successfully defended his seat eleven times becoming the first Jewish Lord Mayor of Dublin in 1956, an honour that was repeated in 1961. On this basis alone, it can be argued that Briscoe was a significant presence in an embryonic Irish political culture; however, when his role in the 1930s Jewish immigration endeavor is acknowledged, it is clear that he played a unique part in one of the most contentious political and social discourses of the pre-war years. This was reinforced when Briscoe embraced Zionism in a belated realisation that the survival of his European co-religionists could only be guaranteed if an independent Jewish state existed. This information is to a certain degree public knowledge; however, the full extent of his involvement as an immigration advocate for potential Jewish refugees, and the seniority he achieved in the New Zionist Organisation (Revisionists) has not been fully recognised. This is partly explicable because researchers have based their assessment of Briscoe on an incomplete political archive in the National Library of Ireland (NLI). The vast majority of documentation pertaining to his involvement in the immigration endeavor has not been available to scholars and remains the private property of Robert Briscoe’s son, Ben Briscoe. The lack of immigration files in the NLI was reinforced by the fact that information about Briscoe’s Revisionist engagement was donated to the Jabotinsky Institute in Tel Aviv and can only be accessed physically by visiting Israel. Therefore, even though these twin endeavors have been commented on by a number of academics, their assessments have tended to be based on an incomplete archive, which was supplemented by Briscoe’s autobiographical memoir published in 1958. This study will attempt to fill in the missing gaps in Briscoe’s complex political narrative by incorporating the rarely used private papers of Robert Briscoe, and the difficult to access Briscoe files in Tel Aviv. This undertaking was only possible when Mr.Ben Briscoe graciously granted me full and unrestricted access to his father’s papers, and after a month-long research trip to the Jabotinsky Institute in Tel Aviv. Access to this rarely used documentation facilitated a holistic examination of Briscoe’s complex and multifaceted political reality. It revealed the full extent of Briscoe’s political and social evolution as the Nazi instigated Jewish emigration crisis reached catastrophic proportions. He was by turn Fianna Fáil nationalist, Jewish immigration advocate and senior Revisionist actor on a global stage. The study will examine the contrasting political and social forces that initiated each stage of Briscoe’s Zionist awakening, and in the process will fill a major gap in Irish-Jewish historiography by revealing the full extent of his Revisionist engagement.

A novel activation mechanism for Clostridial bacteriophage endolysins

Bacteriophage-encoded endolysins are produced at the end of the phage lytic cycle for the degradation of the host bacterial cell. Endolysins offer the potential as alternatives to antibiotics as biocontrol agents or therapeutics. The lytic mechanisms of three bacteriophage endolysins that target Clostridium species living under different conditions were investigated. For these endolysins a trigger and release mechanism is proposed for their activation. During host lysis, holin lesion formation suddenly permeabilises the membrane which exposes the cytosol-sequestered endolysins to a sudden environmental shock. This shock is suggested to trigger a conformational switch of the endolysins between two distinct dimer states. The switch between dimer states is proposed to activate a novel autocleavage mechanism that cleaves the linker connecting the N-terminal catalytic domain and the C-terminal domain to release the catalytic domain for more efficient digestion of the bacterial cell wall. Crystal structures of cleaved fragments of CD27L and CTP1L were previously obtained. In these structures cleavage occurs at the stem of the linker connected to the C-terminal domain. Despite a sequence identity of only 22% between 81 residues of the C-terminal domains of CD27L and CTP1L, they represent a novel fold that is identified in a number of different lysins. Within the crystal structures the two distinct dimerization modes are represented: the elongated head‐on dimer and the side-by‐side dimer. Introducing mutations that inhibit either of the dimerization states caused a decrease in the efficiency of both the autocleavage mechanism and the lytic activity of the endolysins. The two dimer states were validated for the full-length endolysins in solution by using right angle light scattering, small angle X‐ray scattering and cross-linking experiments. Overall, the data represents a new type of regulation governed by the C-terminal domains that is used to activate these endolysins once they enter the bacterial cell wall.

Novel structured emulsions for delivering of food flavours

Flavour release from food is determined by the binding of flavours to other food ingredients and the partition of flavour molecules among different phases. Food emulsions are used as delivery systems for food flavours, and tailored structuring in emulsions provides novel means to better control flavour release. The current study investigated four structured oil-in-water emulsions with structuring in the oil phase, oil-water interface, and water phase. Oil phase structuring was achieved by the formation of monoglyceride (MG) liquid crystals in the oil droplets (MG structured emulsions). Structured interface was created by the adsorption of a whey protein isolate (WPI)-pectin double layer at the interface (multilayer emulsion). Water phase structured emulsions referred to emulsion filled protein gels (EFP gels), where emulsion droplets were embedded in WPI gel network, and emulsions with maltodextrins (MDs) of different dextrose-equivalent (DE) values. Flavour compounds with different physicochemical properties were added into the emulsions, and flavour release (release rate, headspace concentration and air-emulsion partition coefficient) was described by GC headspace analysis. Emulsion structures, including crystalline structure, particle size, emulsion stability, rheology, texture, and microstructures, were characterized using differential scanning calorimetry and X-ray diffraction, light scattering, multisample analytical centrifuge, rheometry, texture analysis, and confocal laser scanning microscopy, respectively. In MG structured emulsions, MG self-assembled into liquid crystalline structures and stable β-form crystals were formed after 3 days of storage at 25 °C. The inclusion of MG crystals allowed tween 20 stabilized emulsions to present viscoelastic properties, and it made WPI stabilized emulsions more sensitive to the change of pH and NaCl concentrations. Flavour compounds in MG structured emulsions had lower initial headspace concentration and air-emulsion partition coefficients than those in unstructured emulsions. Flavour release can be modulated by changing MG content, oil content and oil type. WPI-pectin multilayer emulsions were stable at pH 5.0, 4.0, and 3.0, but they presented extensive creaming when subjected to salt solutions with NaCl ≥ 150 mM and mixed with artificial salivas. Increase of pH from 5.0 to 7.0 resulted in higher headspace concentration but unchanged release rate, and increase of NaCl concentration led to increased headspace concentration and release rate. The study also showed that salivas could trigger higher release of hydrophobic flavours and lower release of hydrophilic flavours. In EFP gels, increases in protein content and oil content contributed to gels with higher storage modulus and force at breaking. Flavour compounds had significantly reduced release rates and air-emulsion partition coefficients in the gels than the corresponding ungelled emulsions, and the reduction was in line with the increase of protein content. Gels with stronger gel network but lower oil content were prepared, and lower or unaffected release rates of the flavours were observed. In emulsions containing maltodextrins, water was frozen at a much lower temperature, and emulsion stability was greatly improved when subjected to freeze-thawing. Among different MDs, MD DE 6 offered the emulsion the highest stability. Flavours had lower air-emulsion partition coefficients in the emulsions with MDs than those in the emulsion without MD. Moreover, the involvement of MDs in the emulsions allowed most flavours had similar release profiles before and after freeze-thaw treatment. The present study provided information about different structured emulsions as delivery systems for flavour compounds, and on how food structure can be designed to modulate flavour release, which could be helpful in the development of functional foods with improved flavour profile.

Biomethane production from grass silage: laboratory assessment to maximise yields

On-farm biogas production is typically associated with forage maize as the biomass source. Digesters are designed and operated with the focus of optimising the conditions for this feedstock. Thus, such systems may not be ideally suited to the digestion of grass. Ireland has ca. 3.85 million ha of grassland. Annual excess grass, surplus to livestock requirements, could potentially fuel an anaerobic digestion industry. Biomethane associated with biomass from 1.1 % of grassland in Ireland, could potentially generate over 10 % renewable energy supply in transport. This study aims to identify and optimise technologies for the production of biomethane from grass silage. Mono-digestion of grass silage and co-digestion with slurry, as would occur on Irish farms, is investigated in laboratory trials. Grass silage was shown to have 7 times greater methane potential than dairy slurry on a fresh weight basis (107 m3 t-1 v 16 m3 t-1). However, comprehensive trace element profiles indicated that cobalt, iron and nickel are deficient in mono-digestion of grass silage at a high organic loading rate (OLR) of 4.0 kg VS m-3 d-1. The addition of a slurry co-substrate was beneficial due to its wealth of essential trace elements. To stimulate hydrolysis of high lignocellulose grass silage, particle size reduction (physical) and rumen fluid addition (biological) were investigated. In a continuous trial, digestion of grass silage of <1 cm particle size achieved a specific methane yield of 371 L CH4 kg-1 VS when coupled with rumen fluid addition. The concept of demand driven biogas was also examined in a two-phase digestion system (leaching with UASB). When demand for electricity is low it is recommended to disconnect the UASB from the system and recirculate rumen fluid to increase volatile fatty acid (VFA) and soluble chemical oxygen demand (SCOD) production whilst minimising volatile solids (VS) destruction. At times of high demand for electricity, connection of the UASB increases the destruction of volatiles and associated biogas production. The above experiments are intended to assess a range of biogas production options from grass silage with a specific focus on maximising methane yields and provide a guideline for feasible design and operation of on-farm digesters in Ireland.

Eleanor Roosevelt: supporting Zion, denying Palestine

Eleanor Roosevelt, as a renowned humanitarian, portrayed an inconsistency by supporting Zionist ambitions for a national homeland in Palestine while simultaneously ignoring the rights of the indigenous Palestinians. Because of this dichotomy, this dissertation explores her attitudes, her disposition and her position in light of the conflict in the region. It conveys how her particular character traits interplayed with the cultural influences prevalent in mid-century America and encouraged her empathy with the plight of European Jews after the Holocaust. As she evolved politically, initially under the tutelage of Franklin Roosevelt and latterly as a UN delegate, she outgrew the anti-Semitism of the period to become a committed Zionist. Judging the Palestinians as ‘primitives’ incapable of self-government and heartened by Jewish development, she supported the partition of Palestine in November 1947. After the 1948 Arab-Israeli war the 800,000 Palestinian refugees encamped in neighbouring Arab states threatened to destabilise the region. Her solution was to discourage repatriation and to re-settle them in Iraq – a plan that directly contravened the principles of the December 1948 Universal Declaration of Human Rights proclaimed by the UN committee she had chaired. No detailed work has been conducted on these aspects of Eleanor Roosevelt’s life; this dissertation reveals a complex person rather than a model of ‘humanitarianism’, and one whose activities cannot be so simply categorised. In the eight chapters that follow, her own thoughts are disclosed through her ‘My Day’ newspaper column, through letters to friends and to members of the public that petitioned her, through a scrutiny of her articles, books and autobiography. This information was attained as a result of archival research in the US and in The Netherlands and was considered against an extensive range of secondary literature. During the Cold War, to offset Soviet incursion, Eleanor Roosevelt promoted Jewish usurpation of Palestinian lands with equanimity in order that an industrious Western-style democracy would bring stability to the region. These events facilitated the exposure of a latent Orientalism and an imperialistic lien that fostered paternalism in a woman new to the nuances of international diplomacy.

Biogas production from novel substrates

Biogas production is the conversion of the organic material into methane (CH4) and carbon dioxide (CO2) under anaerobic conditions. Anaerobic digestion (AD) is widely used in continental and Scandinavian communities as both a waste treatment option and a source of renewable energy. Ireland however lags behind this European movement. Numerous feedstocks exist which could be digested and used to fuel a renewable transport fleet in Ireland. An issue exists with the variety of feedstocks; these need to be assessed and quantified to ascertain their potential resource and application to AD. From literature the ideal C:N ratio is between 25 and 30:1. Low levels of C:N (<15) can lead to problems with ammonia inhibition. Within the digester a plentiful supply of nutrients and a balanced C:N is required for stable performance. Feedstocks were sampled from a range of over 100 different substrates in Ireland including for first, second and third generation feedstocks. The C:N ranged from 81:1 (Winter Oats) to 7:1 (Silage Effluent). The BMP yields were recorded ranging from 38 ± 2.0 L CH4 kg−1 VS for pig slurry (weaning pigs) to 805 ± 57 L CH4 kg−1 VS for used cooking oil (UCO). However the selection of the best preforming feedstock in terms of C:N ratio or BMP yield alone is not sufficiently adequate. A total picture has to be created which includes C:N ratio, BMP yield, harvest yield and availability. Potential feedstocks which best meet these requirements include for Grass silage, Milk processing waste (MPW) and Saccharina latissima. MPW has a potential of meeting over 6 times the required energy for Ireland’s 2020 transport in energy targets. S. Latissima recorded a yield of over 10,000 GJ ha-1 yr-1 which out ranks traditional second generation biofuels by a factor of more than 4.

Design Optimization and Security For Communication Networks

In this work we introduce a new mathematical tool for optimization of routes, topology design, and energy efficiency in wireless sensor networks. We introduce a vector field formulation that models communication in the network, and routing is performed in the direction of this vector field at every location of the network. The magnitude of the vector field at every location represents the density of amount of data that is being transited through that location. We define the total communication cost in the network as the integral of a quadratic form of the vector field over the network area. With the above formulation, we introduce a mathematical machinery based on partial differential equations very similar to the Maxwell's equations in electrostatic theory. We show that in order to minimize the cost, the routes should be found based on the solution of these partial differential equations. In our formulation, the sensors are sources of information, and they are similar to the positive charges in electrostatics, the destinations are sinks of information and they are similar to negative charges, and the network is similar to a non-homogeneous dielectric media with variable dielectric constant (or permittivity coefficient). In one of the applications of our mathematical model based on the vector fields, we offer a scheme for energy efficient routing. Our routing scheme is based on changing the permittivity coefficient to a higher value in the places of the network where nodes have high residual energy, and setting it to a low value in the places of the network where the nodes do not have much energy left. Our simulations show that our method gives a significant increase in the network life compared to the shortest path and weighted shortest path schemes. Our initial focus is on the case where there is only one destination in the network, and later we extend our approach to the case where there are multiple destinations in the network. In the case of having multiple destinations, we need to partition the network into several areas known as regions of attraction of the destinations. Each destination is responsible for collecting all messages being generated in its region of attraction. The complexity of the optimization problem in this case is how to define regions of attraction for the destinations and how much communication load to assign to each destination to optimize the performance of the network. We use our vector field model to solve the optimization problem for this case. We define a vector field, which is conservative, and hence it can be written as the gradient of a scalar field (also known as a potential field). Then we show that in the optimal assignment of the communication load of the network to the destinations, the value of that potential field should be equal at the locations of all the destinations. Another application of our vector field model is to find the optimal locations of the destinations in the network. We show that the vector field gives the gradient of the cost function with respect to the locations of the destinations. Based on this fact, we suggest an algorithm to be applied during the design phase of a network to relocate the destinations for reducing the communication cost function. The performance of our proposed schemes is confirmed by several examples and simulation experiments. In another part of this work we focus on the notions of responsiveness and conformance of TCP traffic in communication networks. We introduce the notion of responsiveness for TCP aggregates and define it as the degree to which a TCP aggregate reduces its sending rate to the network as a response to packet drops. We define metrics that describe the responsiveness of TCP aggregates, and suggest two methods for determining the values of these quantities. The first method is based on a test in which we drop a few packets from the aggregate intentionally and measure the resulting rate decrease of that aggregate. This kind of test is not robust to multiple simultaneous tests performed at different routers. We make the test robust to multiple simultaneous tests by using ideas from the CDMA approach to multiple access channels in communication theory. Based on this approach, we introduce tests of responsiveness for aggregates, and call it CDMA based Aggregate Perturbation Method (CAPM). We use CAPM to perform congestion control. A distinguishing feature of our congestion control scheme is that it maintains a degree of fairness among different aggregates. In the next step we modify CAPM to offer methods for estimating the proportion of an aggregate of TCP traffic that does not conform to protocol specifications, and hence may belong to a DDoS attack. Our methods work by intentionally perturbing the aggregate by dropping a very small number of packets from it and observing the response of the aggregate. We offer two methods for conformance testing. In the first method, we apply the perturbation tests to SYN packets being sent at the start of the TCP 3-way handshake, and we use the fact that the rate of ACK packets being exchanged in the handshake should follow the rate of perturbations. In the second method, we apply the perturbation tests to the TCP data packets and use the fact that the rate of retransmitted data packets should follow the rate of perturbations. In both methods, we use signature based perturbations, which means packet drops are performed with a rate given by a function of time. We use analogy of our problem with multiple access communication to find signatures. Specifically, we assign orthogonal CDMA based signatures to different routers in a distributed implementation of our methods. As a result of orthogonality, the performance does not degrade because of cross interference made by simultaneously testing routers. We have shown efficacy of our methods through mathematical analysis and extensive simulation experiments.

The effects of osmotic stress on the structure and function of the cell nucleus.

Osmotic stress is a potent regulator of the normal function of cells that are exposed to osmotically active environments under physiologic or pathologic conditions. The ability of cells to alter gene expression and metabolic activity in response to changes in the osmotic environment provides an additional regulatory mechanism for a diverse array of tissues and organs in the human body. In addition to the activation of various osmotically- or volume-activated ion channels, osmotic stress may also act on the genome via a direct biophysical pathway. Changes in extracellular osmolality alter cell volume, and therefore, the concentration of intracellular macromolecules. In turn, intracellular macromolecule concentration is a key physical parameter affecting the spatial organization and pressurization of the nucleus. Hyper-osmotic stress shrinks the nucleus and causes it to assume a convoluted shape, whereas hypo-osmotic stress swells the nucleus to a size that is limited by stretch of the nuclear lamina and induces a smooth, round shape of the nucleus. These behaviors are consistent with a model of the nucleus as a charged core/shell structure pressurized by uneven partition of macromolecules between the nucleoplasm and the cytoplasm. These osmotically-induced alterations in the internal structure and arrangement of chromatin, as well as potential changes in the nuclear membrane and pores are hypothesized to influence gene transcription and/or nucleocytoplasmic transport. A further understanding of the biophysical and biochemical mechanisms involved in these processes would have important ramifications for a range of fields including differentiation, migration, mechanotransduction, DNA repair, and tumorigenesis.

Quality control autophagy: a joint effort of ubiquitin, protein deacetylase and actin cytoskeleton.

Autophagy has been predominantly studied as a nonselective self-digestion process that recycles macromolecules and produces energy in response to starvation. However, autophagy independent of nutrient status has long been known to exist. Recent evidence suggests that this form of autophagy enforces intracellular quality control by selectively disposing of aberrant protein aggregates and damaged organelles--common denominators in various forms of neurodegenerative diseases. By definition, this form of autophagy, termed quality-control (QC) autophagy, must be different from nutrient-regulated autophagy in substrate selectivity, regulation and function. We have recently identified the ubiquitin-binding deacetylase, HDAC6, as a key component that establishes QC. HDAC6 is not required for autophagy activation per se; rather, it is recruited to ubiquitinated autophagic substrates where it stimulates autophagosome-lysosome fusion by promoting F-actin remodeling in a cortactin-dependent manner. Remarkably, HDAC6 and cortactin are dispensable for starvation-induced autophagy. These findings reveal that autophagosomes associated with QC are molecularly and biochemically distinct from those associated with starvation autophagy, thereby providing a new molecular framework to understand the emerging complexity of autophagy and therapeutic potential of this unique machinery.

Latent Stick-Breaking Processes.

We develop a model for stochastic processes with random marginal distributions. Our model relies on a stick-breaking construction for the marginal distribution of the process, and introduces dependence across locations by using a latent Gaussian copula model as the mechanism for selecting the atoms. The resulting latent stick-breaking process (LaSBP) induces a random partition of the index space, with points closer in space having a higher probability of being in the same cluster. We develop an efficient and straightforward Markov chain Monte Carlo (MCMC) algorithm for computation and discuss applications in financial econometrics and ecology. This article has supplementary material online.

Intake, digestibility, and passage of a commercially designed diet by two Propithecus species.

The digestibility and passage of an experimental diet was used to compare the digestive physiology of two Propithecus species: P. verreauxi and P. tattersalli. Though both animals have a similar feeding ecology, the captive status of P. verreauxi is considered more stable than that of P. tattersalli. The test diet included a local tree species, Rhus copallina, at 15% of dry matter intake (DMI) and Mazuri Leafeater Primate Diet at 85% of DMI. The chemical composition of the diet (dry matter basis) was 25% crude protein, 34% neutral detergent fiber (NDF), and 22% acid detergent fiber (ADF) with a gross energy of 4.52 kcal/g. After a 6 week acclimation to the experimental diet, animals were placed in research caging. After a 7 day adjustment period, animals were dosed with chromium mordant and Co-EDTA as markers for digesta passage and all feed refusals and feces were collected at timed intervals for 7 days. Digestibility values, similar for both species, were approximately 65% for dry matter, crude protein, and energy, and 40% and 35% respectively, for NDF and ADF. Transit times (17-18.5 hr) and mean retention times (31-34 hr) were not significantly different between species, and there was no difference between the chromium mordant and Co-EDTA. Serum values for glucose, urea, and non-esterified fatty acids (NEFA) were obtained during four different time periods to monitor nutritional status. While there was no change in serum glucose, serum urea increased over time. The NEFAs increased across all four time periods for P. verreauxi and increased for the first three periods then decreased in the last period for P. tattersalli. Results obtained indicate no difference in digestibility nor digesta passage between species, and that both Propithecus species were similar to other post-gastric folivores.

Thermodynamic and dynamic contributions to future changes in regional precipitation variance: focus on the Southeastern United States

© 2014, Springer-Verlag Berlin Heidelberg.The frequency and severity of extreme events are tightly associated with the variance of precipitation. As climate warms, the acceleration in hydrological cycle is likely to enhance the variance of precipitation across the globe. However, due to the lack of an effective analysis method, the mechanisms responsible for the changes of precipitation variance are poorly understood, especially on regional scales. Our study fills this gap by formulating a variance partition algorithm, which explicitly quantifies the contributions of atmospheric thermodynamics (specific humidity) and dynamics (wind) to the changes in regional-scale precipitation variance. Taking Southeastern (SE) United States (US) summer precipitation as an example, the algorithm is applied to the simulations of current and future climate by phase 5 of Coupled Model Intercomparison Project (CMIP5) models. The analysis suggests that compared to observations, most CMIP5 models (~60 %) tend to underestimate the summer precipitation variance over the SE US during the 1950–1999, primarily due to the errors in the modeled dynamic processes (i.e. large-scale circulation). Among the 18 CMIP5 models analyzed in this study, six of them reasonably simulate SE US summer precipitation variance in the twentieth century and the underlying physical processes; these models are thus applied for mechanistic study of future changes in SE US summer precipitation variance. In the future, the six models collectively project an intensification of SE US summer precipitation variance, resulting from the combined effects of atmospheric thermodynamics and dynamics. Between them, the latter plays a more important role. Specifically, thermodynamics results in more frequent and intensified wet summers, but does not contribute to the projected increase in the frequency and intensity of dry summers. In contrast, atmospheric dynamics explains the projected enhancement in both wet and dry summers, indicating its importance in understanding future climate change over the SE US. The results suggest that the intensified SE US summer precipitation variance is not a purely thermodynamic response to greenhouse gases forcing, and cannot be explained without the contribution of atmospheric dynamics. Our analysis provides important insights to understand the mechanisms of SE US summer precipitation variance change. The algorithm formulated in this study can be easily applied to other regions and seasons to systematically explore the mechanisms responsible for the changes in precipitation extremes in a warming climate.

Computational Inference of Genome-Wide Protein-DNA Interactions Using High-Throughput Genomic Data

Transcriptional regulation has been studied intensively in recent decades. One important aspect of this regulation is the interaction between regulatory proteins, such as transcription factors (TF) and nucleosomes, and the genome. Different high-throughput techniques have been invented to map these interactions genome-wide, including ChIP-based methods (ChIP-chip, ChIP-seq, etc.), nuclease digestion methods (DNase-seq, MNase-seq, etc.), and others. However, a single experimental technique often only provides partial and noisy information about the whole picture of protein-DNA interactions. Therefore, the overarching goal of this dissertation is to provide computational developments for jointly modeling different experimental datasets to achieve a holistic inference on the protein-DNA interaction landscape.

We first present a computational framework that can incorporate the protein binding information in MNase-seq data into a thermodynamic model of protein-DNA interaction. We use a correlation-based objective function to model the MNase-seq data and a Markov chain Monte Carlo method to maximize the function. Our results show that the inferred protein-DNA interaction landscape is concordant with the MNase-seq data and provides a mechanistic explanation for the experimentally collected MNase-seq fragments. Our framework is flexible and can easily incorporate other data sources. To demonstrate this flexibility, we use prior distributions to integrate experimentally measured protein concentrations.

We also study the ability of DNase-seq data to position nucleosomes. Traditionally, DNase-seq has only been widely used to identify DNase hypersensitive sites, which tend to be open chromatin regulatory regions devoid of nucleosomes. We reveal for the first time that DNase-seq datasets also contain substantial information about nucleosome translational positioning, and that existing DNase-seq data can be used to infer nucleosome positions with high accuracy. We develop a Bayes-factor-based nucleosome scoring method to position nucleosomes using DNase-seq data. Our approach utilizes several effective strategies to extract nucleosome positioning signals from the noisy DNase-seq data, including jointly modeling data points across the nucleosome body and explicitly modeling the quadratic and oscillatory DNase I digestion pattern on nucleosomes. We show that our DNase-seq-based nucleosome map is highly consistent with previous high-resolution maps. We also show that the oscillatory DNase I digestion pattern is useful in revealing the nucleosome rotational context around TF binding sites.

Finally, we present a state-space model (SSM) for jointly modeling different kinds of genomic data to provide an accurate view of the protein-DNA interaction landscape. We also provide an efficient expectation-maximization algorithm to learn model parameters from data. We first show in simulation studies that the SSM can effectively recover underlying true protein binding configurations. We then apply the SSM to model real genomic data (both DNase-seq and MNase-seq data). Through incrementally increasing the types of genomic data in the SSM, we show that different data types can contribute complementary information for the inference of protein binding landscape and that the most accurate inference comes from modeling all available datasets.

This dissertation provides a foundation for future research by taking a step toward the genome-wide inference of protein-DNA interaction landscape through data integration.

Elucidating the Molecular Composition of Cartilage by Proteomics.

Articular cartilage consists of chondrocytes and two major components, a collagen-rich framework and highly abundant proteoglycans. Most prior studies defining the zonal distribution of cartilage have extracted proteins with guanidine-HCl. However, an unextracted collagen-rich residual is left after extraction. In addition, the high abundance of anionic polysaccharide molecules extracted from cartilage adversely affects the chromatographic separation. In this study, we established a method for removing chondrocytes from cartilage sections with minimal extracellular matrix protein loss. The addition of surfactant to guanidine-HCl extraction buffer improved protein solubility. Ultrafiltration removed interference from polysaccharides and salts. Almost four-times more collagen peptides were extracted by the in situ trypsin digestion method. However, as expected, proteoglycans were more abundant within the guanidine-HCl extraction. These different methods were used to extract cartilage sections from different cartilage layers (superficial, intermediate, and deep), joint types (knee and hip), and disease states (healthy and osteoarthritic), and the extractions were evaluated by quantitative and qualitative proteomic analyses. The results of this study led to the identifications of the potential biomarkers of osteoarthritis (OA), OA progression, and the joint specific biomarkers.