Conjugated Quantum Dots Inhibit the Amyloid β (1–42) Fibrillation Process

Nanoparticles have enormous potential in diagnostic and therapeutic studies. We have demonstrated that the amyloid beta mixed with and conjugated to dihydrolipoic acid- (DHLA) capped CdSe/ZnS quantum dots (QDs) of size approximately 2.5 nm can be used to reduce the fibrillation process. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) were used as tools for analysis of fibrillation. There is a significant change in morphology of fibrils when amyloid β (1–42) (Aβ (1–42)) is mixed or conjugated to the QDs. The length and the width of the fibrils vary under modified conditions. Thioflavin T (ThT) fluorescence supports the decrease in fibril formation in presence of DHLA-capped QDs.

The Role of Splicing Factors and Small Nuclear RNAS in Spliceosomal Formation

Protein coding genes are comprised of protein-coding exons and non-protein-coding introns. The process of splicing involves removal of the introns and joining of the exons to form a mature messenger RNA, which subsequently undergoes translation into polypeptide. The spliceosome is a large, RNA/protein assembly of five small nuclear RNAs as well as over 300 proteins, which catalyzes intron removal and exon ligation. The selection of specific exons for inclusion in the mature messenger RNA is spatio-temporally regulated and results in production of an enormous diversity of polypeptides from a single gene locus. This phenomenon, known as alternative splicing, is regulated, in part, by protein splicing factors, which target the spliceosome to exon/intron boundaries. The first part of my dissertation (Chapters II and III) focuses on the discovery and characterization of the 45 kilodalton FK506 binding protein (FKBP45), which I discovered in the silk moth, Bombyx mori, as a U1 small nuclear RNA binding protein. This protein family binds the immunosuppressants FK506 and rapamycin and contains peptidyl-prolyl cis-trans isomerase activity, which converts polypeptides from cis to trans about a proline residue. This is the first time that an FKBP has been identified in the spliceosome. The second section of my dissertation (Chapters IV, V, VI and VII) is an investigation of the potential role of small nuclear RNA sequence variants in the control of splicing. I identified 46 copies of small nuclear RNAs in the 6X whole genome shotgun of the Bombyx mori p50T strain. These variants may play a role in differential binding of specific proteins that mediate alternative splicing. Along these lines, further investigation of U2 snRNA sequence variants in Bombyx mori demonstrated that some U2 snRNAs preferentially assemble into high molecular weight spliceosomal complexes over others. Expression of snRNA variants may represent another mechanism by which the cell is able to fine tune the splicing process.

Rastafarianism and the Nation of Islam as institutions for group-identity formation among blacks in the United States : a case study comparing their approaches

This dissertation explores the Rastafari movement and the Nation of Islam as institutions that provide a group-identity for their adherents. The study seeks to determine the characteristics of the identity that is institutionalized by each movement, and the nature of the institutionalization process. The research was conducted primarily in South Florida where both movements exist. An extensive literature review in conjunction with in-depth field interviews were used as the primary research methodologies. What was of particular interest were the reasons that the members of the movements chose one movement over the other, also the similarities and dissimilarities between the movements in their role as institutions for group-identity formation. The research showed that both movements imbued their members with a sense of pride, high self-esteem and a strong sense of race consciousness. In addition, it showed that there was significant variation in identity orientation within the Rastafari Movement, which contrasted with the Nation of Islam where the identity variations within the movement were negligible. This was due largely to the difference in structure between the movements, the Nation of Islam being a centrally organized movement with one leader while the Rastafari movement is a decentralized polycephalous one. Both movements were found to be millenarian in nature, essentially because of the significant utility of the concept that their members would rise to prominence through God's grace. Additionally, both movements were identified as expressive social movements, since they were determined as being primarily concerned with changing the attitudes of their members rather than effecting structural social change.

A probabilistic approach to assess hydrate formation and design preventive measures

Formation of hydrates is one of the major flow assurance problems faced by the oil and gas industry. Hydrates tend to form in natural gas pipelines with the presence of water and favorable temperature and pressure conditions, generally low temperatures and corresponding high pressures. Agglomeration of hydrates can result in blockage of flowlines and equipment, which can be time consuming to remove in subsea equipment and cause safety issues. Natural gas pipelines are more susceptible to burst and explosion owing to hydrate plugging. Therefore, a rigorous risk-assessment related to hydrate formation is required, which assists in preventing hydrate blockage and ensuring equipment integrity. This thesis presents a novel methodology to assess the probability of hydrate formation and presents a risk-based approach to determine the parameters of winterization schemes to avoid hydrate formation in natural gas pipelines operating in Arctic conditions. It also presents a lab-scale multiphase flow loop to study the effects of geometric and hydrodynamic parameters on hydrate formation and discusses the effects of geometric and hydrodynamic parameters on multiphase development length of a pipeline. Therefore, this study substantially contributes to the assessment of probability of hydrate formation and the decision making process of winterization strategies to prevent hydrate formation in Arctic conditions.

The relation between cool cluster cores and Herschel-detected star formation in brightest cluster galaxies

We present far-infrared (FIR) analysis of 68 brightest cluster galaxies (BCGs) at 0.08 < z < 1.0. Deriving total infrared luminosities directly from Spitzer and Herschel photometry spanning the peak of the dust component (24-500 μm), we calculate the obscured star formation rate (SFR). 22^+6.2 _–5.3% of the BCGs are detected in the far-infrared, with SFR = 1-150 M ☉ yr^–1. The infrared luminosity is highly correlated with cluster X-ray gas cooling times for cool-core clusters (gas cooling time <1 Gyr), strongly suggesting that the star formation in these BCGs is influenced by the cluster-scale cooling process. The occurrence of the molecular gas tracing Hα emission is also correlated with obscured star formation. For all but the most luminous BCGs (L_TIR > 2 × 10^11 L_☉), only a small (≤0.4 mag) reddening correction is required for SFR(Hα) to agree with SFR_FIR. The relatively low Hα extinction (dust obscuration), compared to values reported for the general star-forming population, lends further weight to an alternate (external) origin for the cold gas. Finally, we use a stacking analysis of non-cool-core clusters to show that the majority of the fuel for star formation in the FIR-bright BCGs is unlikely to originate from normal stellar mass loss.

Fault-controlled and stratabound dolostones in the Late Aptian-earliest Albian Benassal Formation (Maestrat Basin, E Spain) : petrology and geochemistry constrains

This study was developed under the ExxonMobil FC2 Alliance (Fundamental Controls on Flow in Carbonates). The authors wish to thank ExxonMobil Production Company and ExxonMobil Upstream Research Company for providing funding. The views in this article by Sherry L. Stafford are her own and not necessarily those of ExxonMobil. This research was supported by the Sedimentary Geology Research Group of the Generalitat de Catalunya (2014SGR251). We would like to thank Andrea Ceriani and Paola Ronchi for their critical and valuable reviews, and Associated Editor Piero Gianolla for the editorial work.

Design of experiments to study the impact of process parameters on droplet size and development of non-invasive imaging techniques in tablet coating

Atomisation of an aqueous solution for tablet film coating is a complex process with multiple factors determining droplet formation and properties. The importance of droplet size for an efficient process and a high quality final product has been noted in the literature, with smaller droplets reported to produce smoother, more homogenous coatings whilst simultaneously avoiding the risk of damage through over-wetting of the tablet core. In this work the effect of droplet size on tablet film coat characteristics was investigated using X-ray microcomputed tomography (XμCT) and confocal laser scanning microscopy (CLSM). A quality by design approach utilising design of experiments (DOE) was used to optimise the conditions necessary for production of droplets at a small (20 μm) and large (70 μm) droplet size. Droplet size distribution was measured using real-time laser diffraction and the volume median diameter taken as a response. DOE yielded information on the relationship three critical process parameters: pump rate, atomisation pressure and coating-polymer concentration, had upon droplet size. The model generated was robust, scoring highly for model fit (R2 = 0.977), predictability (Q2 = 0.837), validity and reproducibility. Modelling confirmed that all parameters had either a linear or quadratic effect on droplet size and revealed an interaction between pump rate and atomisation pressure. Fluidised bed coating of tablet cores was performed with either small or large droplets followed by CLSM and XμCT imaging. Addition of commonly used contrast materials to the coating solution improved visualisation of the coating by XμCT, showing the coat as a discrete section of the overall tablet. Imaging provided qualitative and quantitative evidence revealing that smaller droplets formed thinner, more uniform and less porous film coats.

Layered graphitic carbon host formation during liquid-free solid state growth of metal pyrophosphates

We report a successful ligand- and liquid-free solid state route to form metal pyrophosphates within a layered graphitic carbon matrix through a single step approach involving pyrolysis of previously synthesized organometallic derivatives of a cyclotriphosphazene. In this case, we show how single crystal Mn2P2O7 can be formed on either the micro- or the nanoscale in the complete absence of solvents or solutions by an efficient combustion process using rationally designed macromolecular trimer precursors, and present evidence and a mechanism for layered graphite host formation. Using in situ Raman spectroscopy, infrared spectroscopy, X-ray diffraction, high resolution electron microscopy, thermogravimetric and differential scanning calorimetric analysis, and near-edge X-ray absorption fine structure examination, we monitor the formation process of a layered, graphitic carbon in the matrix. The identification of thermally and electrically conductive graphitic carbon host formation is important for the further development of this general ligand-free synthetic approach for inorganic nanocrystal growth in the solid state, and can be extended to form a range of transition metals pyrophosphates. For important energy storage applications, the method gives the ability to form oxide and (pyro)phosphates within a conductive, intercalation possible, graphitic carbon as host–guest composites directly on substrates for high rate Li-ion battery and emerging alternative positive electrode materials

An investigation by AFM and TEM of the mechanism of anodic formation of nanoporosity in n-InP in KOH

The early stages of nanoporous layer formation, under anodic conditions in the absence of light, were investigated for n-type InP with a carrier concentration of ∼3× 1018 cm-3 in 5 mol dm-3 KOH and a mechanism for the process is proposed. At potentials less than ∼0.35 V, spectroscopic ellipsometry and transmission electron microscopy (TEM) showed a thin oxide film on the surface. Atomic force microscopy (AFM) of electrode surfaces showed no pitting below ∼0.35 V but clearly showed etch pit formation in the range 0.4-0.53 V. The density of surface pits increased with time in both linear potential sweep and constant potential reaching a constant value at a time corresponding approximately to the current peak in linear sweep voltammograms and current-time curves at constant potential. TEM clearly showed individual nanoporous domains separated from the surface by a dense ∼40 nm InP layer. It is concluded that each domain develops as a result of directionally preferential pore propagation from an individual surface pit which forms a channel through this near-surface layer. As they grow larger, domains meet, and the merging of multiple domains eventually leads to a continuous nanoporous sub-surface region.

Nanoporous InP: anodic formation and growth mechanism in aqueous electrolytes

Porous layers can be formed electrochemically on (100) oriented n-InP substrates in aqueous KOH. A nanoporous layer is obtained underneath a dense near-surface layer and the pores appear to propagate from holes through the near-surface layer. In the early stages of the anodization transmission electron microscopy (TEM) clearly shows individual porous domains that appear to have a square-based pyramidal shape. Each domain appears to develop from an individual surface pit which forms a channel through this near-surface layer. We suggest that the pyramidal structure arises as a result of preferential pore propagation along the <100> directions. AFM measurements show that the density of surface pits increases with time. Each of these pits acts as a source for a pyramidal porous domain. When the domains grow, the current density increases correspondingly. Eventually the domains meet, forming a continuous porous layer, the interface between the porous and bulk InP becomes relatively flat and its total effective surface area decreases resulting in a decrease in the current density. Current-time curves at constant potential exhibit a peak and porous layers are observed to form beneath the electrode surface. The density of pits formed on the surface increases with time and approaches a plateau value. Porous layers are also observed in highly doped InP but are not observed in wafers with doping densities below ~5 × 1017 cm-3. Numerical models of this process have been developed invoking a mechanism of directional selectivity of pore growth preferentially along the <100> lattice directions. Manipulation of the parameters controlling these curves shows that the fall-off in current is controlled by the rate of diffusion of electrolyte through the pore structure with the final decline in current being caused by the termination of growth at the pore tips through the formation of passivating films or some other irreversible modification of the pore tips.

Pitting and porous layer formation on n-InP anodes

Surface pitting occurs when InP electrodes are anodized in KOH electrolytes at concentrations in the range 2 - 5 mol dm-3. The process has been investigated using atomic force microscopy (AFM) and the results correlated with cross-sectional transmission electron microscopy (TEM) and electroanalytical measurements. AFM measurements show that pitting of the surface occurs and the density of pits is observed to increase with time under both potentiodynamic and potentiostatic conditions. This indicates a progressive pit nucleation process and implies that the development of porous domains beneath the surface is also progressive in nature. Evidence for this is seen in plan view TEM images in which individual domains are seen to be at different stages of development. Analysis of the cyclic voltammograms of InP electrodes in 5 mol dm-3 KOH indicates that, above a critical potential for pit formation, the anodic current is predominantly time dependent and there is little differential dependence of the current on potential. Thus, pores continue to grow with time when the potential is high enough to maintain depletion layer breakdown conditions.

Electrochemical pore formation on InP in alkaline solutions

The surface properties of InP electrodes were examined following anodization in (NH4)2S and KOH electrolytes. In both solutions, the observation of current peaks in the cyclic voltammetric curves was attributed to selective etching of the substrate and a film formation process. AFM images of samples anodized in the sulfide solution, revealed surface pitting and TEM micrographs revealed the porous nature of the film formed on top of the pitted substrate. After anodization in the KOH electrolyte, TEM images revealed that a porous layer extending 500 nm into the substrate had been formed. Analysis of the composition of the anodic products indicates the presence of In2S3 in films grown in (NH4)2S and an In2O3 phase within the porous network formed in KOH.

AuxAg1-x alloy seeds: A way to control growth, morphology and defect formation in Ge nanowires

Germanium (Ge) nanowires are of current research interest for high speed nanoelectronic devices due to the lower band gap and high carrier mobility compatible with high K-dielectrics and larger excitonic Bohr radius ensuing a more pronounced quantum confinement effect [1-6]. A general way for the growth of Ge nanowires is to use liquid or a solid growth promoters in a bottom-up approach which allow control of the aspect ratio, diameter, and structure of 1D crystals via external parameters, such as precursor feedstock, temperature, operating pressure, precursor flow rate etc [3, 7-11]. The Solid-phase seeding is preferred for more control processing of the nanomaterials and potential suppression of the unintentional incorporation of high dopant concentrations in semiconductor nanowires and unrequired compositional tailing of the seed-nanowire interface [2, 5, 9, 12]. There are therefore distinct features of the solid phase seeding mechanism that potentially offer opportunities for the controlled processing of nanomaterials with new physical properties. A superior control over the growth kinetics of nanowires could be achieved by controlling the inherent growth constraints instead of external parameters which always account for instrumental inaccuracy. The high dopant concentrations in semiconductor nanowires can result from unintentional incorporation of atoms from the metal seed material, as described for the Al catalyzed VLS growth of Si nanowires [13] which can in turn be depressed by solid-phase seeding. In addition, the creation of very sharp interfaces between group IV semiconductor segments has been achieved by solid seeds [14], whereas the traditionally used liquid Au particles often leads to compositional tailing of the interface [15] . Korgel et al. also described the superior size retention of metal seeds in a SFSS nanowire growth process, when compared to a SFLS process using Au colloids [12]. Here in this work we have used silver and alloy seed particle with different compositions to manipulate the growth of nanowires in sub-eutectic regime. The solid seeding approach also gives an opportunity to influence the crystallinity of the nanowires independent of the substrate. Taking advantage of the readily formation of stacking faults in metal nanoparticles, lamellar twins in nanowires could be formed.

Multimode Atomic Pattern Formation via Enhanced Light-atom Interactions

The nonlinear interaction between light and atoms is an extensive field of study with a broad range of applications in quantum information science and condensed matter physics. Nonlinear optical phenomena occurring in cold atoms are particularly interesting because such slowly moving atoms can spatially organize into density gratings, which allows for studies involving optical interactions with structured materials. In this thesis, I describe a novel nonlinear optical effect that arises when cold atoms spatially bunch in an optical lattice. I show that employing this spatial atomic bunching provides access to a unique physical regime with reduced thresholds for nonlinear optical processes and enhanced material properties. Using this method, I observe the nonlinear optical phenomenon of transverse optical pattern formation at record-low powers. These transverse optical patterns are generated by a wave- mixing process that is mediated by the cold atomic vapor. The optical patterns are highly multimode and induce rich non-equilibrium atomic dynamics. In particular, I find that there exists a synergistic interplay between the generated optical pat- terns and the atoms, wherein the scattered fields help the atoms to self-organize into new, multimode structures that are not externally imposed on the atomic sample. These self-organized structures in turn enhance the power in the optical patterns. I provide the first detailed investigation of the motional dynamics of atoms that have self-organized in a multimode geometry. I also show that the transverse optical patterns induce Sisyphus cooling in all three spatial dimensions, which is the first observation of spontaneous three-dimensional cooling. My experiment represents a unique means by which to study nonlinear optics and non-equilibrium dynamics at ultra-low required powers.

Molecular Insights of CD4+ T Cell Differentiation, Effector Formation and Helper Function

CD4+ T cells play a crucial in the adaptive immune system. They function as the central hub to orchestrate the rest of immunity: CD4+ T cells are essential governing machinery in antibacterial and antiviral responses by facilitating B cell affinity maturation and coordinating the innate and adaptive immune systems to boost the overall immune outcome; on the contrary, hyperactivation of the inflammatory lineages of CD4+ T cells, as well as the impairments of suppressive CD4+ regulatory T cells, are the etiology of various autoimmunity and inflammatory diseases. The broad role of CD4+ T cells in both physiological and pathological contexts prompted me to explore the modulation of CD4+ T cells on the molecular level.

microRNAs (miRNAs) are small RNA molecules capable of regulating gene expression post-transcriptionally. miRNAs have been shown to exert substantial regulatory effects on CD4+ T cell activation, differentiation and helper function. Specifically, my lab has previously established the function of the miR-17-92 cluster in Th1 differentiation and anti-tumor responses. Here, I further analyzed the role of this miRNA cluster in Th17 differentiation, specifically, in the context of autoimmune diseases. Using both gain- and loss-of-function approaches, I demonstrated that miRNAs in miR-17-92, specifically, miR-17 and miR-19b in this cluster, is a crucial promoter of Th17 differentiation. Consequently, loss of miR-17-92 expression in T cells mitigated the progression of experimental autoimmune encephalomyelitis and T cell-induced colitis. In combination with my previous data, the molecular dissection of this cluster establishes that miR-19b and miR-17 play a comprehensive role in promoting multiple aspects of inflammatory T cell responses, which underscore them as potential targets for oligonucleotide-based therapy in treating autoimmune diseases.

To systematically study miRNA regulation in effector CD4+ T cells, I devised a large-scale miRNAome profiling to track in vivo miRNA changes in antigen-specific CD4+ T cells activated by Listeria challenge. From this screening, I identified that miR-23a expression tightly correlates with CD4+ effector expansion. Ectopic expression and genetic deletion strategies validated that miR-23a was required for antigen-stimulated effector CD4+ T cell survival in vitro and in vivo. I further determined that miR-23a targets Ppif, a gatekeeper of mitochondrial reactive oxygen species (ROS) release that protects CD4+ T cells from necrosis. Necrosis is a type of cell death that provokes inflammation, and it is prominently triggered by ROS release and its consequent oxidative stress. My finding that miR-23a curbs ROS-mediated necrosis highlights the essential role of this miRNA in maintaining immune homeostasis.

A key feature of miRNAs is their ability to modulate different biological aspects in different cell populations. Previously, my lab found that miR-23a potently suppresses CD8+ T cell cytotoxicity by restricting BLIMP1 expression. Since BLIMP1 has been found to inhibit T follicular helper (Tfh) differentiation by antagonizing the master transcription factor BCL6, I investigated whether miR-23a is also involved in Tfh differentiation. However, I found that miR-23a does not target BLIMP1 in CD4+ T cells and loss of miR-23a even fostered Tfh differentiation. This data indicate that miR-23a may target other pathways in CD4+ T cells regarding the Tfh differentiation pathway.

Although the lineage identity and regulatory networks for Tfh cells have been defined, the differentiation path of Tfh cells remains elusive. Two models have been proposed to explain the differentiation process of Tfh cells: in the parallel differentiation model, the Tfh lineage is segregated from other effector lineages at the early stage of antigen activation; alternatively, the sequential differentiation model suggests that naïve CD4+ T cells first differentiate into various effector lineages, then further program into Tfh cells. To address this question, I developed a novel in vitro co-culture system that employed antigen-specific CD4+ T cells, naïve B cells presenting cognate T cell antigen and BAFF-producing feeder cells to mimic germinal center. Using this system, I were able to robustly generate GC-like B cells. Notably, well-differentiated Th1 or Th2 effector cells also quickly acquired Tfh phenotype and function during in vitro co-culture, which suggested a sequential differentiation path for Tfh cells. To examine this path in vivo, under conditions of classical Th1- or Th2-type immunizations, I employed a TCRβ repertoire sequencing technique to track the clonotype origin of Tfh cells. Under both Th1- and Th2- immunization conditions, I observed profound repertoire overlaps between the Teff and Tfh populations, which strongly supports the proposed sequential differentiation model. Therefore, my studies establish a new platform to conveniently study Tfh-GC B cell interactions and provide insights into Tfh differentiation processes.