The C. elegans ALA neuron : its transcriptome and role in inducing sleep

A long-standing yet to be accomplished task in understanding behavior is to dissect the function of each gene involved in the development and function of a neuron. The C. elegans ALA neuron was chosen in this study for its known function in sleep, an ancient but less understood animal behavior. Single-cell transcriptome profiling identified 8,133 protein-coding genes in the ALA neuron, of which 57 are neuropeptide-coding genes. The most enriched genes are also neuropeptides. In combination with gain-of-function and loss-of-function assays, here I showed that the ALA-enriched FMRFamide neuropeptides, FLP-7, FLP-13, and FLP-24, are sufficient and necessary for inducing C. elegans sleep. These neuropeptides act as neuromodulators through GPCRs, NPR-7, and NPR-22. Further investigation in zebrafish indicates that FMRFamide neuropeptides are sleep-promoting molecules in animals. To correlate the behavioral outputs with genomic context, I constructed a gene regulatory network of the relevant genes controlling C. elegans sleep behavior through EGFR signaling in the ALA neuron. First, I identified an ALA cell-specific motif to conduct a genome-wide search for possible ALA-expressed genes. I then filtered out non ALA-expressed genes by comparing the motif-search genes with ALA transcriptomes from single-cell profiling. In corroborating with ChIP-seq data from modENCODE, I sorted out direct interaction of ALA-expressed transcription factors and differentiation genes in the EGFR sleep regulation pathway. This approach provides a network reference for the molecular regulation of C. elegans sleep behavior, and serves as an entry point for the understanding of functional genomics in animal behaviors.

Phase behavior of complex superprotonic solid acids

Superprotonic phase transitions and thermal behaviors of three complex solid acid systems are presented, namely Rb3H(SO4)2-RbHSO4 system, Rb3H(SeO4)2-Cs3H(SeO4)2 solid solution system, and Cs6(H2SO4)3(H1.5PO4)4. These material systems present a rich set of phase transition characteristics that set them apart from other, simpler solid acids. A.C. impedance spectroscopy, high-temperature X-ray powder diffraction, and thermal analysis, as well as other characterization techniques, were employed to investigate the phase behavior of these systems.

Rb3H(SO4)2 is an atypical member of the M3H(XO4)2 class of compounds (M = alkali metal or NH4+ and X = S or Se) in that a transition to a high-conductivity state involves disproportionation into two phases rather than a simple polymorphic transition [1]. In the present work, investigations of the Rb3H(SO4)2-RbHSO4 system have revealed the disproportionation products to be Rb2SO4 and the previously unknown compound Rb5H3(SO4)4. The new compound becomes stable at a temperature between 25 and 140 °C and is isostructural to a recently reported trigonal phase with space group P3̅m of Cs5H3(SO4)4 [2]. At 185 °C the compound undergoes an apparently polymorphic transformation with a heat of transition of 23.8 kJ/mol and a slight additional increase in conductivity.

The compounds Rb3H(SeO4)2 and Cs3H(SeO4)2, though not isomorphous at ambient temperatures, are quintessential examples of superprotonic materials. Both adopt monoclinic structures at ambient temperatures and ultimately transform to a trigonal (R3̅m) superprotonic structure at slightly elevated temperatures, 178 and 183 °C, respectively. The compounds are completely miscible above the superprotonic transition and show extensive solubility below it. Beyond a careful determination of the phase boundaries, we find a remarkable 40-fold increase in the superprotonic conductivity in intermediate compositions rich in Rb as compared to either end-member.

The compound Cs6(H2SO4)3(H1.5PO4)4 is unusual amongst solid acid compounds in that it has a complex cubic structure at ambient temperature and apparently transforms to a simpler cubic structure of the CsCl-type (isostructural with CsH2PO4) at its transition temperature of 100-120 °C [3]. Here it is found that, depending on the level of humidification, the superprotonic transition of this material is superimposed with a decomposition reaction, which involves both exsolution of (liquid) acid and loss of H2O. This reaction can be suppressed by application of sufficiently high humidity, in which case Cs6(H2SO4)3(H1.5PO4)4 undergoes a true superprotonic transition. It is proposed that, under conditions of low humidity, the decomposition/dehydration reaction transforms the compound to Cs6(H2-0.5xSO4)3(H1.5PO4)4-x, also of the CsCl structure type at the temperatures of interest, but with a smaller unit cell. With increasing temperature, the decomposition/dehydration proceeds to greater and greater extent and unit cell of the solid phase decreases. This is identified to be the source of the apparent negative thermal expansion behavior.

References

[1] L.A. Cowan, R.M. Morcos, N. Hatada, A. Navrotsky, S.M. Haile, Solid State Ionics 179 (2008) (9-10) 305.

[2] M. Sakashita, H. Fujihisa, K.I. Suzuki, S. Hayashi, K. Honda, Solid State Ionics 178 (2007) (21-22) 1262.

[3] C.R.I. Chisholm, Superprotonic Phase Transitions in Solid Acids: Parameters affecting the presence and stability of superprotonic transitions in the MHnXO4 family of compounds (X=S, Se, P, As; M=Li, Na, K, NH4, Rb, Cs), Materials Science, California Institute of Technology, Pasadena, California (2003).

Exploring the Kinetics of Domain Switching in Ferroelectrics for Structural Applications

The complex domain structure in ferroelectrics gives rise to electromechanical coupling, and its evolution (via domain switching) results in a time-dependent (i.e. viscoelastic) response. Although ferroelectrics are used in many technological applications, most do not attempt to exploit the viscoelastic response of ferroelectrics, mainly due to a lack of understanding and accurate models for their description and prediction. Thus, the aim of this thesis research is to gain better understanding of the influence of domain evolution in ferroelectrics on their dynamic mechanical response. There have been few studies on the viscoelastic properties of ferroelectrics, mainly due to a lack of experimental methods. Therefore, an apparatus and method called Broadband Electromechanical Spectroscopy (BES) was designed and built. BES allows for the simultaneous application of dynamic mechanical and electrical loading in a vacuum environment. Using BES, the dynamic stiffness and loss tangent in bending and torsion of a particular ferroelectric, viz. lead zirconate titanate (PZT), was characterized for different combinations of electrical and mechanical loading frequencies throughout the entire electric displacement hysteresis. Experimental results showed significant increases in loss tangent (by nearly an order of magnitude) and compliance during domain switching, which shows promise as a new approach to structural damping. A continuum model of the viscoelasticity of ferroelectrics was developed, which incorporates microstructural evolution via internal variables and associated kinetic relations. For the first time, through a new linearization process, the incremental dynamic stiffness and loss tangent of materials were computed throughout the entire electric displacement hysteresis for different combinations of mechanical and electrical loading frequencies. The model accurately captured experimental results. Using the understanding gained from the characterization and modeling of PZT, two applications of domain switching kinetics were explored by using Micro Fiber Composites (MFCs). Proofs of concept of set-and-hold actuation and structural damping using MFCs were demonstrated.

Investigating the Role of the GET3-GET4/GET5 Interaction During Tail-Anchor Protein Targeting

The proper targeting of membrane proteins is essential to the viability of all cells. Tail-anchored (TA) proteins, defined as having a single transmembrane helix at their C-terminus, are post-translationally targeted to the endoplasmic reticulum (ER) membrane by the GET pathway (Guided Entry of TA proteins). In the yeast pathway, the handover of TA substrates is mediated by the heterotetrameric Get4/Get5 (Get4/5) complex, which tethers the co-chaperone Sgt2 to the central targeting factor, the Get3 ATPase. Although binding of Get4/5 to Get3 is critical for efficient TA targeting, the mechanisms by which Get4 regulates Get3 are unknown. To understand the molecular basis of Get4 function, we used a combination of structural biology, biochemistry, and cell biology. Get4/5 binds across the Get3 dimer interface, in an orientation only compatible with a closed Get3, providing insight into the role of nucleotide in complex formation. Additionally, this structure reveals two functionally distinct binding interfaces for anchoring and ATPase regulation, and loss of the regulatory interface leads to strong defects in vitro and in vivo. Additional crystal structures of the Get3-Get4/5 complex give rise to an alternate conformation, which represents an initial binding interaction mediated by electrostatics that facilitates the rate of subsequent inhibited complex formation. This interface is supported by an in-depth kinetic analysis of the Get3-Get4/5 interaction confirming the two-step complex formation. These results allow us to generate a refined model for Get4/5 function in TA targeting.

Theory of the positive column of a gas discharge

An attempt is made to provide a theoretical explanation of the effect of the positive column on the voltage-current characteristic of a glow or an arc discharge. Such theories have been developed before, and all are based on balancing the production and loss of charged particles and accounting for the energy supplied to the plasma by the applied electric field. Differences among the theories arise from the approximations and omissions made in selecting processes that affect the particle and energy balances. This work is primarily concerned with the deviation from the ambipolar description of the positive column caused by space charge, electron-ion volume recombination, and temperature inhomogeneities.

The presentation is divided into three parts, the first of which involved the derivation of the final macroscopic equations from kinetic theory. The final equations are obtained by taking the first three moments of the Boltzmann equation for each of the three species in the plasma. Although the method used and the equations obtained are not novel, the derivation is carried out in detail in order to appraise the validity of numerous approximations and to justify the use of data from other sources. The equations are applied to a molecular hydrogen discharge contained between parallel walls. The applied electric field is parallel to the walls, and the dependent variables—electron and ion flux to the walls, electron and ion densities, transverse electric field, and gas temperature—vary only in the direction perpendicular to the walls. The mathematical description is given by a sixth-order nonlinear two-point boundary value problem which contains the applied field as a parameter. The amount of neutral gas and its temperature at the walls are held fixed, and the relation between the applied field and the electron density at the center of the discharge is obtained in the process of solving the problem. This relation corresponds to that between current and voltage and is used to interpret the effect of space charge, recombination, and temperature inhomogeneities on the voltage-current characteristic of the discharge.

The complete solution of the equations is impractical both numerically and analytically, and in Part II the gas temperature is assumed uniform so as to focus on the combined effects of space charge and recombination. The terms representing these effects are treated as perturbations to equations that would otherwise describe the ambipolar situation. However, the term representing space charge is not negligible in a thin boundary layer or sheath near the walls, and consequently the perturbation problem is singular. Separate solutions must be obtained in the sheath and in the main region of the discharge, and the relation between the electron density and the applied field is not determined until these solutions are matched.

In Part III the electron and ion densities are assumed equal, and the complicated space-charge calculation is thereby replaced by the ambipolar description. Recombination and temperature inhomogeneities are both important at high values of the electron density. However, the formulation of the problem permits a comparison of the relative effects, and temperature inhomogeneities are shown to be important at lower values of the electron density than recombination. The equations are solved by a direct numerical integration and by treating the term representing temperature inhomogeneities as a perturbation.

The conclusions reached in the study are primarily concerned with the association of the relation between electron density and axial field with the voltage-current characteristic. It is known that the effect of space charge can account for the subnormal glow discharge and that the normal glow corresponds to a close approach to an ambipolar situation. The effect of temperature inhomogeneities helps explain the decreasing characteristic of the arc, and the effect of recombination is not expected to appear except at very high electron densities.

Structural Design under Seismic Risk Using Multiple Performance Objectives

Structural design is a decision-making process in which a wide spectrum of requirements, expectations, and concerns needs to be properly addressed. Engineering design criteria are considered together with societal and client preferences, and most of these design objectives are affected by the uncertainties surrounding a design. Therefore, realistic design frameworks must be able to handle multiple performance objectives and incorporate uncertainties from numerous sources into the process.

In this study, a multi-criteria based design framework for structural design under seismic risk is explored. The emphasis is on reliability-based performance objectives and their interaction with economic objectives. The framework has analysis, evaluation, and revision stages. In the probabilistic response analysis, seismic loading uncertainties as well as modeling uncertainties are incorporated. For evaluation, two approaches are suggested: one based on preference aggregation and the other based on socio-economics. Both implementations of the general framework are illustrated with simple but informative design examples to explore the basic features of the framework.

The first approach uses concepts similar to those found in multi-criteria decision theory, and directly combines reliability-based objectives with others. This approach is implemented in a single-stage design procedure. In the socio-economics based approach, a two-stage design procedure is recommended in which societal preferences are treated through reliability-based engineering performance measures, but emphasis is also given to economic objectives because these are especially important to the structural designer's client. A rational net asset value formulation including losses from uncertain future earthquakes is used to assess the economic performance of a design. A recently developed assembly-based vulnerability analysis is incorporated into the loss estimation.

The presented performance-based design framework allows investigation of various design issues and their impact on a structural design. It is a flexible one that readily allows incorporation of new methods and concepts in seismic hazard specification, structural analysis, and loss estimation.