Understanding Ten-Eleven Translocation-2 in Hematological and Nervous Systems

I proposed the study of two distinct aspects of Ten-Eleven Translocation 2 (TET2) protein for understanding specific functions in different body systems. In Part I, I characterized the molecular mechanisms of Tet2 in the hematological system. As the second member of Ten-Eleven Translocation protein family, TET2 is frequently mutated in leukemic patients. Previous studies have shown that the TET2 mutations frequently occur in 20% myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN), 10% T-cell lymphoma leukemia and 2% B-cell lymphoma leukemia. Genetic mouse models also display distinct phenotypes of various types of hematological malignancies. I performed 5-hydroxymethylcytosine (5hmC) chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) of hematopoietic stem/progenitor cells to determine whether the deletion of Tet2 can affect the abundance of 5hmC at myeloid, T-cell and B-cell specific gene transcription start sites, which ultimately result in various hematological malignancies. Subsequent Exome sequencing (Exome-Seq) showed that disease-specific genes are mutated in different types of tumors, which suggests that TET2 may protect the genome from being mutated. The direct interaction between TET2 and Mutator S Homolog 6 (MSH6) protein suggests TET2 is involved in DNA mismatch repair. Finally, in vivo mismatch repair studies show that the loss of Tet2 causes a mutator phenotype. Taken together, my data indicate that TET2 binds to MSH6 to protect genome integrity. In Part II, I intended to better understand the role of Tet2 in the nervous system. 5-hydroxymethylcytosine regulates epigenetic modification during neurodevelopment and aging. Thus, Tet2 may play a critical role in regulating adult neurogenesis. To examine the physiological significance of Tet2 in the nervous system, I first showed that the deletion of Tet2 reduces the 5hmC levels in neural stem cells. Mice lacking Tet2 show abnormal hippocampal neurogenesis along with 5hmC alternations at different gene promoters and corresponding gene expression downregulation. Through the luciferase reporter assay, two neural factors Neurogenic differentiation 1 (NeuroD1) and Glial fibrillary acidic protein (Gfap) were down-regulated in Tet2 knockout cells. My results suggest that Tet2 regulates neural stem/progenitor cell proliferation and differentiation in adult brain.

Theoretical Investigation of Intra- and Inter-cellular Spatiotemporal Calcium Patterns in Microcirculation

Microcirculatory vessels are lined by endothelial cells (ECs) which are surrounded by a single or multiple layer of smooth muscle cells (SMCs). Spontaneous and agonist induced spatiotemporal calcium (Ca2+) events are generated in ECs and SMCs, and regulated by complex bi-directional signaling between the two layers which ultimately determines the vessel tone. The contractile state of microcirculatory vessels is an important factor in the determination of vascular resistance, blood flow and blood pressure. This dissertation presents theoretical insights into some of the important and currently unresolved phenomena in microvascular tone regulation. Compartmental and continuum models of isolated EC and SMC, coupled EC-SMC and a multi-cellular vessel segment with deterministic and stochastic descriptions of the cellular components were developed, and the intra- and inter-cellular spatiotemporal Ca2+ mobilization was examined. Coupled EC-SMC model simulations captured the experimentally observed localized subcellular EC Ca2+ events arising from the opening of EC transient receptor vanilloid 4 (TRPV4) channels and inositol triphosphate receptors (IP3Rs). These localized EC Ca2+ events result in endothelium-derived hyperpolarization (EDH) and Nitric Oxide (NO) production which transmit to the adjacent SMCs to ultimately result in vasodilation. The model examined the effect of heterogeneous distribution of cellular components and channel gating kinetics in determination of the amplitude and spread of the Ca2+ events. The simulations suggested the necessity of co-localization of certain cellular components for modulation of EDH and NO responses. Isolated EC and SMC models captured intracellular Ca2+ wave like activity and predicted the necessity of non-uniform distribution of cellular components for the generation of Ca2+ waves. The simulations also suggested the role of membrane potential dynamics in regulating Ca2+ wave velocity. The multi-cellular vessel segment model examined the underlying mechanisms for the intercellular synchronization of spontaneous oscillatory Ca2+ waves in individual SMC. From local subcellular events to integrated macro-scale behavior at the vessel level, the developed multi-scale models captured basic features of vascular Ca2+ signaling and provide insights for their physiological relevance. The models provide a theoretical framework for assisting investigations on the regulation of vascular tone in health and disease.

Peatland depths and radiocarbon dates, recent decades, North America

Peatland ecosystems store about 500-600 Pg of organic carbon, largely accumulated since the last glaciation. Whether they continue to sequester carbon or release it as greenhouse gases, perhaps in large amounts, is important in Earth's temperature dynamics. Given both ages and depths of numerous dated sample peatlands, their rate of carbon sequestration can be estimated throughout the Holocene. Here we use average values for carbon content per unit volume, the geographical extent of peatlands, and ecological models of peatland establishment and growth, to reconstruct the time-trajectory of peatland carbon sequestration in North America and project it into the future. Peatlands there contain ~163 Pg of carbon. Ignoring effects of climate change and other major anthropogenic disturbances, the rate of carbon accumulation is projected to decline slowly over millennia as reduced net carbon accumulation in existing peatlands is largely balanced by new peatland establishment. Peatlands are one of few long-term terrestrial carbon sinks, probably important for global carbon regulation in future generations. This study contributes to a better understanding of these ecosystems that will assist their inclusion in earth-system models, and therefore their management to maintain carbon storage during climate change.

Length of stay in a neonatal intensive care unit and its association with low rates of exclusive breastfeeding in very low birth weight infants

OBJECTIVE: To identify the inpatient maternal and neonatal factors associated to the weaning of very low birth weight (VLBW) infants. METHODS: One hundred nineteen VLBW (<1500 g) infants were monitored from July 2005 through August 2006, from birth to the first ambulatory visit after maternity discharge. This maternity unit uses the Kangaroo Method and the Baby Friendly Hospital Initiative. Out of 119 VLBW infants monitored until discharge, 88 (75%) returned to the facility, 22 (25%) were on exclusive breastfeeding (EB), and 66 (75%) were weaned (partial breastfeeding or formula feeding). RESULTS: Univariate analysis found an association between weaning and lower birth weight, longer stays in the neonatal intensive care unit (NICU), and longer hospitalization times, in addition to more prolonged enteral feeding and birth weight recovery period. Logistic regression showed length of NICU stay as being the main determinant of weaning. CONCLUSION: The negative repercussion on EB of an extended stay in the NICU is a significant challenge for health professionals to provide more adequate nutrition to VLBW infants.

Length of stay in a neonatal intensive care unit and its association with low rates of exclusive breastfeeding in very low birth weight infants

OBJECTIVE: To identify the inpatient maternal and neonatal factors associated to the weaning of very low birth weight (VLBW) infants. METHODS: One hundred nineteen VLBW (<1500 g) infants were monitored from July 2005 through August 2006, from birth to the first ambulatory visit after maternity discharge. This maternity unit uses the Kangaroo Method and the Baby Friendly Hospital Initiative. Out of 119 VLBW infants monitored until discharge, 88 (75%) returned to the facility, 22 (25%) were on exclusive breastfeeding (EB), and 66 (75%) were weaned (partial breastfeeding or formula feeding). RESULTS: Univariate analysis found an association between weaning and lower birth weight, longer stays in the neonatal intensive care unit (NICU), and longer hospitalization times, in addition to more prolonged enteral feeding and birth weight recovery period. Logistic regression showed length of NICU stay as being the main determinant of weaning. CONCLUSION: The negative repercussion on EB of an extended stay in the NICU is a significant challenge for health professionals to provide more adequate nutrition to VLBW infants.

Método híbrido para projeto de superfícies seletivas em frequência

This thesis presents a hybrid technique of frequency selective surfaces project (FSS) on a isotropic dielectric layer, considering various geometries for the elements of the unit cell. Specifically, the hybrid technique uses the equivalent circuit method in conjunction with genetic algorithm, aiming at the synthesis of structures with response single-band and dual-band. The equivalent circuit method allows you to model the structure by using an equivalent circuit and also obtaining circuits for different geometries. From the obtaining of the parameters of these circuits, you can get the transmission and reflection characteristics of patterned structures. For the optimization of patterned structures, according to the desired frequency response, Matlab™ optimization tool named optimtool proved to be easy to use, allowing you to explore important results on the optimization analysis. In this thesis, numeric and experimental results are presented for the different characteristics of the analyzed geometries. For this, it was determined a technique to obtain the parameter N, which is based on genetic algorithms and differential geometry, to obtain the algebraic rational models that determine values of N more accurate, facilitating new projects of FSS with these geometries. The optimal results of N are grouped according to the occupancy factor of the cell and the thickness of the dielectric, for modeling of the structures by means of rational algebraic equations. Furthermore, for the proposed hybrid model was developed a fitness function for the purpose of calculating the error occurred in the definitions of FSS bandwidths with transmission features single band and dual band. This thesis deals with the construction of prototypes of FSS with frequency settings and band widths obtained with the use of this function. The FSS were initially reviewed through simulations performed with the commercial software Ansoft Designer ™, followed by simulation with the equivalent circuit method for obtaining a value of N in order to converge the resonance frequency and the bandwidth of the FSS analyzed, then the results obtained were compared. The methodology applied is validated with the construction and measurement of prototypes with different geometries of the cells of the arrays of FSS.

Método híbrido para projeto de superfícies seletivas em frequência

This thesis presents a hybrid technique of frequency selective surfaces project (FSS) on a isotropic dielectric layer, considering various geometries for the elements of the unit cell. Specifically, the hybrid technique uses the equivalent circuit method in conjunction with genetic algorithm, aiming at the synthesis of structures with response single-band and dual-band. The equivalent circuit method allows you to model the structure by using an equivalent circuit and also obtaining circuits for different geometries. From the obtaining of the parameters of these circuits, you can get the transmission and reflection characteristics of patterned structures. For the optimization of patterned structures, according to the desired frequency response, Matlab™ optimization tool named optimtool proved to be easy to use, allowing you to explore important results on the optimization analysis. In this thesis, numeric and experimental results are presented for the different characteristics of the analyzed geometries. For this, it was determined a technique to obtain the parameter N, which is based on genetic algorithms and differential geometry, to obtain the algebraic rational models that determine values of N more accurate, facilitating new projects of FSS with these geometries. The optimal results of N are grouped according to the occupancy factor of the cell and the thickness of the dielectric, for modeling of the structures by means of rational algebraic equations. Furthermore, for the proposed hybrid model was developed a fitness function for the purpose of calculating the error occurred in the definitions of FSS bandwidths with transmission features single band and dual band. This thesis deals with the construction of prototypes of FSS with frequency settings and band widths obtained with the use of this function. The FSS were initially reviewed through simulations performed with the commercial software Ansoft Designer ™, followed by simulation with the equivalent circuit method for obtaining a value of N in order to converge the resonance frequency and the bandwidth of the FSS analyzed, then the results obtained were compared. The methodology applied is validated with the construction and measurement of prototypes with different geometries of the cells of the arrays of FSS.

Dispersion and energy relations in periodic chains and grids

In this study wave propagation, dispersion relations, and energy relations for linear elastic periodic systems are analyzed. In particular, the dispersion relations for monoatomic chain of infinite dimension are obtained analytically by writing the Block-type wave equation for a unit cell in order to capture the dynamic behavior for chains under prescribed vibration. By comparing the discretized model (mass-spring chain) with the solid bar system, the nonlinearity of the dispersion relation for chain indicates that the periodic lattice is dispersive in contrast to the continuous rod, which is non dispersive. Further investigations have been performed considering one-dimensional diatomic linear elastic mass-spring chain. The dispersion relations, energy velocity, and group velocity have been derived. At certain range of frequencies harmonic plane waves do not propagate in contrast with monoatomic chain. Also, since the diatomic chain considered is a linear elastic chain, both of the energy velocity and the group velocity are identical. As long as the linear elastic condition is considered the results show zero flux condition without residual energy. In addition, this paper shows that the diatomic chain dispersion relations are independent on the unit cell scheme. Finally, an extension for the study covers the dispersion and energy relations for 2D- grid system. The 2x2 grid system show a periodicity of the dispersion surface in the wavenumber domain. In addition, the symmetry of the surface can be exploited to identify an Irreducible Brillouin Zone (IBZ). Compact representations of the dispersion properties of multidimensional periodic systems are obtained by plotting frequency as the wave vector’s components vary along the boundary of the IBZ, which leads to a widely accepted and effective visualization of bandgaps and overall dispersion properties.

Ferroelectric and dielectric properties of Nd2−xCexTi2O7 ceramics

The solid solution system Nd2−xCexTi2O7 has been investigated. The solubility limit of Ce in Nd2−xCexTi2O7 was found to be 0·5–0·75 according to X-ray diffraction and X-ray photoelectron spectroscopy results. Ce substitution increases the b and c axes and the volume of the unit cell due to its larger ionic radius. Nd2−xCexTi2O7 (x  = 0·05, 0·25, 0·5, 0·75) textured ceramics were fabricated using spark plasma sintering. The ferroelectric and dielectric properties of the ceramics were studied. Ce substitution decreases the Curie point Tc of Nd2−xCexTi2O7 compounds. The results suggest that the Tc of Ce2Ti2O7 is <1445°C.

Nanostructured copper oxides and phosphates from a new solid-state route

Nanostructured copper containing materials of CuO, Cu3(PO4)3 and Cu2P2O7 have been prepared by solid-state pyrolysis of molecular CuCl2·NC5H4OH (I), CuCl2·CNCH2C6H4OH (II), oligomeric [Cu(PPh3)Cl]4 (III), N3P3[OC6H4CH2CN·CuCl]6[PF6] (IV), N3P3[OC6H5]5[OC5H4N·Cu][PF6] (V), polymeric chitosan·(CuCl2)n (VI) and polystyrene-co-4-vinylpyridine PS-b-4-PVP·(CuCl2) (VII) precursors. The products strongly depend on the precursor used. The pyrolytic products from phosphorus-containing precursors (III), (IV) and (V) are Cu phosphates or pyrophosphates, while non-phosphorous-containing precursors (VI) and (VII), result in mainly CuO. The use of chitosan as a solid-state template/stabilizer induces the formation of CuO and Cu2O nanoparticles. Copper pyrophosphate (Cu2P2O7) deposited on Si using (IV) as the precursor exhibits single-crystal dots of average diameter 100 nm and heights equivalent to twice the unit cell b-axis (1.5–1.7 nm) and an areal density of 5.1–7.7 Gigadots/in.2. Cu2P2O7 deposited from precursor (VI) exhibits unique labyrinthine high surface area deposits. The morphology of CuO deposited on Si from pyrolysis of (VI) depends on the polymer/Cu meta ratio. Magnetic measurements performed using SQUID on CuO nanoparticle networks suggest superparamagnetic behavior. The results give insights into compositional, shape and morphological control of the as-formed nanostructures through the structure of the precursors.

Latent Space and Social Psychological Models of Diffusion

The problem of social diffusion has animated sociological thinking on topics ranging from the spread of an idea, an innovation or a disease, to the foundations of collective behavior and political polarization. While network diffusion has been a productive metaphor, the reality of diffusion processes is often muddier. Ideas and innovations diffuse differently from diseases, but, with a few exceptions, the diffusion of ideas and innovations has been modeled under the same assumptions as the diffusion of disease. In this dissertation, I develop two new diffusion models for "socially meaningful" contagions that address two of the most significant problems with current diffusion models: (1) that contagions can only spread along observed ties, and (2) that contagions do not change as they spread between people. I augment insights from these statistical and simulation models with an analysis of an empirical case of diffusion - the use of enterprise collaboration software in a large technology company. I focus the empirical study on when people abandon innovations, a crucial, and understudied aspect of the diffusion of innovations. Using timestamped posts, I analyze when people abandon software to a high degree of detail.

To address the first problem, I suggest a latent space diffusion model. Rather than treating ties as stable conduits for information, the latent space diffusion model treats ties as random draws from an underlying social space, and simulates diffusion over the social space. Theoretically, the social space model integrates both actor ties and attributes simultaneously in a single social plane, while incorporating schemas into diffusion processes gives an explicit form to the reciprocal influences that cognition and social environment have on each other. Practically, the latent space diffusion model produces statistically consistent diffusion estimates where using the network alone does not, and the diffusion with schemas model shows that introducing some cognitive processing into diffusion processes changes the rate and ultimate distribution of the spreading information. To address the second problem, I suggest a diffusion model with schemas. Rather than treating information as though it is spread without changes, the schema diffusion model allows people to modify information they receive to fit an underlying mental model of the information before they pass the information to others. Combining the latent space models with a schema notion for actors improves our models for social diffusion both theoretically and practically.

The empirical case study focuses on how the changing value of an innovation, introduced by the innovations' network externalities, influences when people abandon the innovation. In it, I find that people are least likely to abandon an innovation when other people in their neighborhood currently use the software as well. The effect is particularly pronounced for supervisors' current use and number of supervisory team members who currently use the software. This case study not only points to an important process in the diffusion of innovation, but also suggests a new approach -- computerized collaboration systems -- to collecting and analyzing data on organizational processes.

Pre-Clinical Models of Diffuse Intrinsic Pontine Glioma.

Diffuse intrinsic pontine glioma (DIPG) is a rare and incurable brain tumor that arises in the brainstem of children predominantly between the ages of 6 and 8. Its intricate morphology and involvement of normal pons tissue precludes surgical resection, and the standard of care today remains fractionated radiation alone. In the past 30 years, there have been no significant advances made in the treatment of DIPG. This is largely because we lack good models of DIPG and therefore have little biological basis for treatment. In recent years, however, due to increased biopsy and acquisition of autopsy specimens, research is beginning to unravel the genetic and epigenetic drivers of DIPG. Insight gleaned from these studies has led to improvements in approaches to both model these tumors in the lab and to potentially treat them in the clinic. This review will detail the initial strides toward modeling DIPG in animals, which included allograft and xenograft rodent models using non-DIPG glioma cells. Important advances in the field came with the development of in vitro cell and in vivo xenograft models derived directly from autopsy material of DIPG patients or from human embryonic stem cells. Finally, we will summarize the progress made in the development of genetically engineered mouse models of DIPG. Cooperation of studies incorporating all of these modeling systems to both investigate the unique mechanisms of gliomagenesis in the brainstem and to test potential novel therapeutic agents in a preclinical setting will result in improvement in treatments for DIPG patients.

RNA Localization and Translational Regulation on the Endoplasmic Reticulum

mRNA localization is emerging as a critical cellular mechanism for the spatiotemporal regulation of protein expression and serves important roles in oogenesis, embryogenesis, cell fate specification, and synapse formation. Signal sequence-encoding mRNAs are localized to the endoplasmic reticulum (ER) membrane by either of two mechanisms, a canonical mechanism of translation on ER-bound ribosomes (signal recognition particle pathway), or a poorly understood direct ER anchoring mechanism. In this study, we identify that the ER integral membrane proteins function as RNA-binding proteins and play important roles in the direct mRNA anchoring to the ER. We report that one of the ER integral membrane RNA-binding protein, AEG-1 (astrocyte elevated gene-1), functions in the direct ER anchoring and translational regulation of mRNAs encoding endomembrane transmembrane proteins. HITS-CLIP and PAR-CLIP analyses of the AEG-1 mRNA interactome of human hepatocellular carcinoma cells revealed a high enrichment for mRNAs encoding endomembrane organelle proteins, most notably encoding transmembrane proteins. AEG-1 binding sites were highly enriched in the coding sequence and displayed a signature cluster enrichment downstream of encoded transmembrane domains. In overexpression and knockdown models, AEG-1 expression markedly regulates translational efficiency and protein functions of two of its bound transcripts, MDR1 and NPC1. This study reveals a molecular mechanism for the selective localization of mRNAs to the ER and identifies a novel post-transcriptional gene regulation function for AEG-1 in membrane protein expression.

Elemental Analysis of Biological Matrices by Laser Ablation High Resolution Inductively Coupled Plasma Mass Spectrometry (LA-HR-ICP-MS) and High Resolution Inductively Coupled Plasma Mass Spectrometry (HR-ICP-MS)

The need for elemental analysis of biological matrices such as bone, teeth, and plant matter for sourcing purposes has emerged within the forensic and geochemical laboratories. Trace elemental analyses for the comparison of aterials such as glass by inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS has been shown to offer a high degree of discrimination between different manufacturing sources. Unit resolution ICP-MS instruments may suffer from some polyatomic interferences including 40Ar16O+, 40Ar16O1H+, and 40Ca16O+ that affect iron measurement at trace levels. Iron is an important element in the analysis of glass and also of interest for the analysis of several biological matrices. A comparison of the nalytical performance of two different ICP-MS systems for iron analysis in glass for determining the method detection limits (MDLs), accuracy, and precision of the measurement is presented. Acid digestion and laser ablation methods are also compared. Iron polyatomic interferences were reduced or resolved by using dynamic reaction cell and high resolution ICP-MS. MDLs as low as 0.03 ìg g-1 and 0.14 ìg g-1 for laser ablation and solution based analyses respectively were achieved. The use of helium as a carrier gas demonstrated improvement in the detection limits of both iron isotopes (56Fe and 57Fe) in medium resolution for the HR-ICP-MS and with a dynamic reaction cell (DRC) coupled to a quadrupole ICP-MS system. The development and application of robust analytical methods for the quantification of trace elements in biological matrices has lead to a better understanding of the potential utility of these measurements in forensic chemical analyses. Standard reference materials (SRMs) were used in the development of an analytical method using HR-ICP-MS and LA-HR-ICP-MS that was subsequently applied on the analysis of real samples. Bone, teeth and ashed marijuana samples were analyzed with the developed method. Elemental analysis of bone samples from 12 different individuals provided discrimination between individuals, when femur and humerus bones were considered separately. Discrimination of 14 teeth samples based on elemental composition was achieved with the exception of one case where samples from the same individual were not associated with each other. The discrimination of 49 different ashed plant (cannabis)samples was achieved using the developed method.

Floral and faunal characteristics and content of photosynthetic pigment in soils of northern Victoria Land, Antarctica

Although soil algae are among the main primary producers in most terrestrial ecosystems of continental Antarctica, there are very few quantitative studies on their relative proportion in the main algal groups and on how their distribution is affected by biotic and abiotic factors. Such knowledge is essential for understanding the functioning of Antarctic terrestrial ecosystems. We therefore analyzed biological soil crusts from northern Victoria Land to determine their pH, electrical conductivity (EC), water content (W), total and organic C (TC and TOC) and total N (TN) contents, and the presence and abundance of photosynthetic pigments. In particular, the latter were tested as proxies for biomass and coarse-resolution community structure. Soil samples were collected from five sites with known soil algal communities and the distribution of pigments was shown to reflect differences in the relative proportions of Chlorophyta, Cyanophyta and Bacillariophyta in these sites. Multivariate and univariate models strongly indicated that almost all soil variables (EC, W, TOC and TN) were important environmental correlates of pigment distribution. However, a significant amount of variation is independent of these soil variables and may be ascribed to local variability such as changes in microclimate at varying spatial and temporal scales. There are at least five possible sources of local variation: pigment preservation, temporal variations in water availability, temporal and spatial interactions among environmental and biological components, the local-scale patchiness of organism distribution, and biotic interactions.