Unraveling the molecular underpinnings of Philadelphia-negative myeloproliferative neoplasms: implications for future therapeutic strategies

The present thesis encompasses the two researches projects I conducted during my PhD program in Molecular Biology and Pathology. The common thread is represented by the analysis of the signaling pathways implicated in the pathophysiology of the two most aggressive Philadelphia-negative myeloproliferative neoplasms, namely, atypical chronic myeloid leukemia (aCML) and primary myelofibrosis (PMF). In the last decade, since the description of the JAK2V617F mutation in 2005, the field of the molecular characterization of Philadelphia-negative myeloproliferative neoplasms has experienced an astonishing implementation that led to the discovery of 16 new mutations involving signal transduction, epigenetic modifiers, cell cycle regulators. Nevertheless, their pathogenetic relevance and whether they could represent good “druggable” candidates have to be proved yet. In the first section I provide the first report of the signaling cascade down-stream the rare cytogenetic lesion t(8;9)(p22;p24)/PCM1-JAK2 associated with aCML, finding that it selectively activates the ERK1/2 signaling without affecting JAK/STAT phosphorylation. In the second part, I investigated the implication of the ε isoform of novel Protein kinase Cs (PKCs) in the pathophysiology of the aberrant megakaryocytopoiesis in PMF, concluding that the over-expression of PKCε detains a crucial relevance in the aberrant behavior of PMF megakaryocytes and its inhibition is capable to restore their normal differentiation and abrogate the anti-apoptotic signaling. Both results are discussed in the view of their therapeutic implications. In case PCM1/JAK2-related hematologic neoplasms, ERK-inhibitors rather than JAK-inhibitors (i.e. ruxolitinib) should be considered as a “tailored” drugs. In case of PMF, PKCε-inhibitors (i.e. εV1-2 peptide) configure as an appealing strategy to re-direct the megakaryocytic neoplastic clone.

Multiple system atrophy: laminar distribution of the pathological changes in frontal and temporal neocortex--a study in ten patients

OBJECTIVE: To determine the distribution of the pathological changes in the neocortex in multiple-system atrophy (MSA). METHOD: The vertical distribution of the abnormal neurons (neurons with enlarged or atrophic perikarya), surviving neurons, glial cytoplasmic inclusions (GCI) and neuronal cytoplasmic inclusions (NI) were studied in alpha-synuclein-stained material of frontal and temporal cortex in ten cases of MSA. RESULTS: Abnormal neurons exhibited two common patterns of distribution, viz., density was either maximal in the upper cortex or a bimodal distribution was present with a density peak in the upper and lower cortex. The NI were either located in the lower cortex or were more uniformly distributed down the cortical profile. The distribution of the GCI varied considerably between gyri and cases. The density of the glial cell nuclei was maximal in the lower cortex in the majority of gyri. In a number of gyri, there was a positive correlation between the vertical densities of the abnormal neurons, the total number of surviving neurons, and the glial cell nuclei. The vertical densities of the GCI were not correlated with those of the surviving neurons or glial cells but the GCI and NI were positively correlated in a small number of gyri. CONCLUSION: The data suggest that there is significant degeneration of the frontal and temporal lobes in MSA, the lower laminae being affected more significantly than the upper laminae. Cortical degeneration in MSA is likely to be secondary to pathological changes occurring within subcortical areas.

Computational mechanics of molecular systems:quantifying high-dimensional dynamics by distribution of Poincaré recurrence times

A framework that connects computational mechanics and molecular dynamics has been developed and described. As the key parts of the framework, the problem of symbolising molecular trajectory and the associated interrelation between microscopic phase space variables and macroscopic observables of the molecular system are considered. Following Shalizi and Moore, it is shown that causal states, the constituent parts of the main construct of computational mechanics, the e-machine, define areas of the phase space that are optimal in the sense of transferring information from the micro-variables to the macro-observables. We have demonstrated that, based on the decay of their Poincare´ return times, these areas can be divided into two classes that characterise the separation of the phase space into resonant and chaotic areas. The first class is characterised by predominantly short time returns, typical to quasi-periodic or periodic trajectories. This class includes a countable number of areas corresponding to resonances. The second class includes trajectories with chaotic behaviour characterised by the exponential decay of return times in accordance with the Poincare´ theorem.

Origins of molecular neurobiology:The role of the physicists

The revolution in the foundations of physics at the beginning of the twentieth century suggested to several of its most prominent workers that biology was ripe for something similar. In consequence, a number of physicists moved into biology. They were highly influential in initiating a molecular biology in the 1950s. Two decades later it seemed to several of these migrants, and those they had influenced, that the major problems in molecular biology had been solved, and that it was time to move on to what seemed to them the final problem: the nervous system, consciousness, and the age-old mind-body problem. This paper reviews this "double migration" and shows how the hopes of the first generation of physicist-biologists were both realized and dashed. No new physical principles were discovered at work in the foundations of biology or neuroscience. On the other hand, the mind-set of those trained in physics proved immensely valuable in analyzing fundamental issues in both biology and neuroscience. It has been argued that the outcome of the molecular biology of the 1950s was a change in the concept of the gene from that of "a mysterious entity into that of a real molecular object" (Watson, 1965, p.6); the gates and channels which play such crucial roles in the functioning of nervous systems have been transformed in a similar way. Studies on highly simplified systems have also opened the prospect of finding the neural correlatives of numerous behaviors and neuropathologies. This increasing understanding at the molecular level is invaluable not only in devising rational therapies but also, by defining the material substrate of consciousness, in bringing the mind-body problem into sharper focus. Copyright © Taylor & Francis Inc.

Studies in the anionic polymerization of methyl methacrylate

A study has been made of the anionic polymerization of methyl methacrylate using butyllithium and polystyryl lithium as initiators and using aluminium triisobutyl as a cocatalyst. The aspects of the polymerization that were examined were the effect of changing the order of addition of reagents, the temperature at which polymerization takes place and the polarity of the solvent. Trends were assessed in terms of molecular weight, molecular weight distribution and tacticity. In addition, a second monomer addition test was carried out to verify that the polymerization was truly a living one, and a kinetic study was attempted. Studies to investigate the effect of changing the order of addition of reagents showed that polymer with similar polydispersities and tacticities are produced whether the pre-mixing (mixing initiator and cocatalyst before addition of monomer) or the post-mixing (mixing monomer and cocatalyst before addition of initiator) method were used. However, polymerizations using the post-mixing mixing method demonstrated lower initiator efficiencies, possibly indicating a different initiating species. Investigations into the effect of changing the polymerization temperature show the molecular weight distribution to narrow as the temperature decreases, although a small amount of low molecular weight tailing was also observed at low temperature. A clear relationship between tacticity and temperature was observed with syndiotacticity increasing with decreasing temperature. Changes in solvent polarity were achieved by using mixtures of the standard solvent, toluene, with varying amounts of cyclohexane, tetrahydrofuran or dichloromethane. Experiments at low solvent polarity (using toluene/cyclohexane mixtures) showed problems with initiator solubility but produced polymer with lower polydispersity and higher syndiotacticity than in toluene alone. Experiments using toluene/THF mixtures yielded no polymer, thought to be owing to a side reaction between THF and aluminium triisobutyl. Increased solvent polarity, achieved using toluene/dichloromethane mixtures produced polymer with higher polydispersity and at lower yields than the conventional system, but also with higher syndiotacticity. Second monomer addition reactions demonstrated that the polymerization was 'living' since an increase in molecular weight was observed with no increase in polydispersity. Kinetic studies demonstrated the high speed of the polymerization but yielded no useful data.

Electrophysiological studies of the visual pathways in Alzheimer's and Parkinson's disease

It is known that parallel pathways exist within the visual system. These have been described as magnocellular and parvocellular as a result of the layered organisation of the lateral geniculate nucleus and extend from the retina to the cortex. Dopamine (DA) and acetylcholine (ACH) are neurotransmitters that are present in the visual pathway. DA is present in the retina and is associated with the interplexiform cells and horizontal cells. ACH is also present in the retina and is associated with displaced amacrine cells; it is also present in the superior colliculus. DA is found to be significantly depleted in the brain of Parkinson's disease (PD) patients and ACH in Alzheimer's disease (AD) patients. For this reason these diseases were used to assess the function of DA and ACH in the electrophysiology of the visual pathway. Experiments were conducted on young normals to design stimuli that would preferentially activate the magnocellular or parvocellular pathway. These stimuli were then used to evoke visual evoked potentials (VEP) in patients with PD and AD, in order to assess the function of DA and ACH in the visual pathway. Electroretinograms (ERGs) were also measured in PD patients to assess the role of DA in the retina. In addition, peripheral ACH function was assessed by measuring VEPs, ERGs and contrast sensitivity (CS) in young normals following the topical instillation of hyoscine hydrobromide (an anticholinergic drug). The results indicate that the magnocellular pathway can be divided into two: a cholinergic tectal-association area pathway carrying luminance information, and a non-cholinergic geniculo-cortical pathway carrying spatial information. It was also found that depletion of DA had very little effect on the VEPs or ERGs, confirming a general regulatory function for this neurotransmitter.

Immunoinformatics and the in silico prediction of immunogenicity:an introduction

Immunoinformatics is the application of informatics techniques to molecules of the immune system. One of its principal goals is the effective prediction of immunogenicity, be that at the level of epitope, subunit vaccine, or attenuated pathogen. Immunogenicity is the ability of a pathogen or component thereof to induce a specific immune response when first exposed to surveillance by the immune system, whereas antigenicity is the capacity for recognition by the extant machinery of the adaptive immune response in a recall response. In thisbook, we introduce these subjects and explore the current state of play in immunoinformatics and the in silico prediction of immunogenicity.

Dynamic complexity of chaotic transitions in high-dimensional classical dynamics:Leu-Enkephalin folding

Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A ß-turn transition is investigated by calculating the topological complexity (in the "computational mechanics" framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the ß-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a "quasi-regular" dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated. © Springer-Verlag Berlin Heidelberg 2006.

A pilot study to evaluate the self-medication system for liver transplant patients at the Queen Elizabeth Hospital in Birmingham

Background and Objective: Medication non-compliance is a considerable obstacle in achievinga therapeutic goal, whichcan result in poorerhealthcare outcomes, increased expenditure, wastage and potential for medication resistance. The UK Government’s Audit Commission’s publication ‘A Spoonful of Sugar’1 addresses these issues and promotes self-medication systems as a possible solution. The self-medication system within the Liver Transplant Unit (LTU) was implemented to induct patients onto new post- transplantation medication regimes ready for discharge. The system involves initial consultations with both the Liver Transplant Pharmacist and Trans- plant Co-ordinator, supported with additional advice as and when necessary. Design: Following ethical approval, evaluation of the self-medication sys- tem for liver transplant patients was conducted between January and March 2004 via two methods: audit and structured post-transplantation interview. The audit enabled any discrepancies between current Hospital guidelines and Liver Transplant Unit (LTU) practices to be highlighted. Patient interviews generated a retrospective insight into patient acceptance of the self-medication system. Setting: LTU, Queen Elizabeth Hospital, Birmingham, England. Main Outcome Measures: LTU compliance with Hospital self-medication guidelines and patient insight into self-medication system. Results: A total of seven patients were audited. Findings illustrated that self- medication by transplant patients is a complex process which was not fully addressed by current Hospital self-medication guidelines. Twenty-three patients were interviewed, showing an overwhelming positive attitude to- wards participating in their own care and a high level of understanding towards their individual medication regimes. Following a drugs counselling session, 100% of patients understood why they were taking their medica- tion, and their doses, 95% understood how to take their medication and 85% were aware of potential side effects. Conclusions: From this pilot evaluation it can be stated that the LTU self-medication system is appreciated by patients and assists them in fully understanding their medication regimes. There appear to be no major defects in the system. However areas such as communication barriers and on-going internet education were illustrated as areas for possible future investigation. References: 1. Audit Commission. A spoonful of sugar – medicines management in NHS hospitals. London: Audit Commission; 2001.

Complexity of classical dynamics of molecular systems. I. Methodology

Methods for the calculation of complexity have been investigated as a possible alternative for the analysis of the dynamics of molecular systems. “Computational mechanics” is the approach chosen to describe emergent behavior in molecular systems that evolve in time. A novel algorithm has been developed for symbolization of a continuous physical trajectory of a dynamic system. A method for calculating statistical complexity has been implemented and tested on representative systems. It is shown that the computational mechanics approach is suitable for analyzing the dynamic complexity of molecular systems and offers new insight into the process.

Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model

Two-dimensional 'Mercedes Benz' (MB) or BN2D water model (Naim, 1971) is implemented in Molecular Dynamics. It is known that the MB model can capture abnormal properties of real water (high heat capacity, minima of pressure and isothermal compressibility, negative thermal expansion coefficient) (Silverstein et al., 1998). In this work formulas for calculating the thermodynamic, structural and dynamic properties in microcanonical (NVE) and isothermal-isobaric (NPT) ensembles for the model from Molecular Dynamics simulation are derived and verified against known Monte Carlo results. The convergence of the thermodynamic properties and the system's numerical stability are investigated. The results qualitatively reproduce the peculiarities of real water making the model a visually convenient tool that also requires less computational resources, thus allowing simulations of large (hydrodynamic scale) molecular systems. We provide the open source code written in C/C++ for the BN2D water model implementation using Molecular Dynamics.

Oligodendrocyte pathology in neurodegenerative disease

Oligodendrocytes have multiple functions in the central nervous system including mechanical support of neurons, production of myelin sheaths, and uptake and inactivation of chemical neurotransmitters released by neurons. Consequently, oligodendrocytes could be involved in the pathology of a number of neurodegenerative diseases. Although, the molecular mechanisms involved require further elucidation, it is likely that oligodendrocyte dysfunction is important in Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), and multiple sclerosis (MS). In addition, abnormal protein aggregates in the form of oligodendrocyte inclusions (OI) have been observed in several other disorders, most notable in multiple system atrophy (MSA), in which the glial cytoplasmic inclusion (GCI) is the ‘signature’ pathology of the disease. OI have also been identified in argyrophilic grain disease (AGD), progressive supranuclear palsy (PSP) (Armstrong et al 2007), and various forms of frontotemporal lobar degeneration (FTLD) (Armstrong et al 2010), although their role in the pathology of these disorders is less clear. It is likely that future research will expand the range of disorders in which oligodendrocytes play a significant role in neurodegeneration.

Characterization, sources, and transformations of dissolved organic matter (DOM) in Florida coastal Everglades (FCE)

Dissolved organic matter (DOM) is one of the largest carbon reservoirs on this planet and is present in aquatic environments as a highly complex mixture of organic compounds. The Florida coastal Everglades (FCE) is one of the largest wetlands in the world. DOM in this system is an important biogeochemical component as most of the nitrogen (N) and phosphorous (P) are in organic forms. Achieving a better understanding of DOM dynamics in large coastal wetlands is critical, and a particularly important issue in the context of Everglades restoration. In this work, the environmental dynamics of surface water DOM on spatial and temporal scales was investigated. In addition, photo- and bio-reactivity of this DOM was determined, surface-to-groundwater exchange of DOM was investigated, and the size distribution of freshwater DOM in Everglades was assessed. The data show that DOM dynamics in this ecosystem are controlled by both hydrological and ecological drivers and are clearly different on spatial scales and variable seasonally. The DOM reactivity data, modeled with a multi-pool first order degradation kinetics model, found that fluorescent DOM in FCE is generally photo-reactive and bio-refractory. Yet the sequential degradation proved a “priming effect” of sunlight on the bacterial uptake and reworking of this subtropical wetland DOM. Interestingly, specific PARAFAC components were found to have different photo- and bio-degradation rates, suggesting a highly heterogeneous nature of fluorophores associated with the DOM. Surface-to-groundwater exchange of DOM was observed in different regions of the system, and compositional differences were associated with source and photo-reactivity. Lastly, the high degree of heterogeneity of DOM associated fluorophores suggested based on the degradation studies was confirmed through the EEM-PARAFAC analysis of DOM along a molecular size continuum, suggesting that the fluorescence characteristics of DOM are highly controlled by different size fractions and as such can exhibit significant differences in reactivity.

Chemical characteristics of dissolved organic matter in an oligotrophic subtropical wetland/estuarine ecosystem

Fluorescence properties of whole water samples and molecular characteristics of ultrafiltrated dissolved organic matter (UDOM > 1,000 D) such as lignin phenol and neutral sugar compositions and 13C nuclear magnetic resonance (NMR) spectra were determined along a freshwater to marine gradient in Everglades National Park. Furthermore, UDOM samples were categorized by hierarchical cluster analysis based on their pyrolysis gas chromatography/mass spectrometry products. Fluorescence properties suggest that autochthonous DOM leached/exuded from biomass is quantitatively important in this system. 13C NMR spectra showed that UDOM from the oligotrophic Taylor Slough (TS) and Florida Bay (FB) ecosystems has low aromatic C (13% ± 3% for TS; 2% ± 2% for FB) and very high O-alkyl C (54% ± 4% for TS; 75% ± 4% for FB) concentrations. High O-alkyl C concentrations in FB suggest seagrass/phytoplankton communities as dominant sources of UDOM. The amount of neutral sugars was not appreciably different between the TS and FB sites (115 ± 12 mg C g C-1 UDOM) but their concentrations suggest a low level of diagenesis and high production rates of this material in this oligotrophic environment. Total yield of lignin phenols (vanillyl + syringyl phenols) in TS was low (0.20–0.39 mg 100 mg C-1 UDOM) compared with other riverine environments and even lower in FB (0.04–0.07 mg 100 mg C-1 UDOM) and could be a result of photodegradation and/or dilution by other utochthonous DOM. The high O-alkyl and low aromatic nature of this UDOM suggests significant biogenic inputs (as compared with soils) and limited bioavailability in this ecosystem.

Hybrid Power System Intelligent Operation and Protection Involving Plug-in Electric Vehicles

Two key solutions to reduce the greenhouse gas emissions and increase the overall energy efficiency are to maximize the utilization of renewable energy resources (RERs) to generate energy for load consumption and to shift to low or zero emission plug-in electric vehicles (PEVs) for transportation. The present U.S. aging and overburdened power grid infrastructure is under a tremendous pressure to handle the issues involved in penetration of RERS and PEVs. The future power grid should be designed with for the effective utilization of distributed RERs and distributed generations to intelligently respond to varying customer demand including PEVs with high level of security, stability and reliability. This dissertation develops and verifies such a hybrid AC-DC power system. The system will operate in a distributed manner incorporating multiple components in both AC and DC styles and work in both grid-connected and islanding modes. The verification was performed on a laboratory-based hybrid AC-DC power system testbed as hardware/software platform. In this system, RERs emulators together with their maximum power point tracking technology and power electronics converters were designed to test different energy harvesting algorithms. The Energy storage devices including lithium-ion batteries and ultra-capacitors were used to optimize the performance of the hybrid power system. A lithium-ion battery smart energy management system with thermal and state of charge self-balancing was proposed to protect the energy storage system. A grid connected DC PEVs parking garage emulator, with five lithium-ion batteries was also designed with the smart charging functions that can emulate the future vehicle-to-grid (V2G), vehicle-to-vehicle (V2V) and vehicle-to-house (V2H) services. This includes grid voltage and frequency regulations, spinning reserves, micro grid islanding detection and energy resource support. The results show successful integration of the developed techniques for control and energy management of future hybrid AC-DC power systems with high penetration of RERs and PEVs.