Intercepting Cyclic Dinucleotide Signaling with Small Molecules

Bacterial infections, especially the ones that are caused by multidrug-resistant strains, are becoming increasingly difficult to treat and put enormous stress on healthcare systems. Recently President Obama announced a new initiative to combat the growing problem of antibiotic resistance. New types of antibiotic drugs are always in need to catch up with the rapid speed of bacterial drug-resistance acquisition. Bacterial second messengers, cyclic dinucleotides, play important roles in signal transduction and therefore are currently generating great buzz in the microbiology community because it is believed that small molecules that inhibit cyclic dinucleotide signaling could become next-generation antibacterial agents. The first identified cyclic dinucleotide, c-di-GMP, has now been shown to regulate a large number of processes, such as virulence, biofilm formation, cell cycle, quorum sensing, etc. Recently, another cyclic dinucleotide, c-di-AMP, has emerged as a regulator of key processes in Gram-positive and mycobacteria. C-di-AMP is now known to regulate DNA damage sensing, fatty acid synthesis, potassium ion transport, cell wall homeostasis and host type I interferon response induction. Due to the central roles that cyclic dinucleotides play in bacteria, we are interested in small molecules that intercept cyclic dinucleotide signaling with the hope that these molecules would help us learn more details about cyclic dinucleotide signaling or could be used to inhibit bacterial viability or virulence. This dissertation documents the development of several small molecule inhibitors of a cyclic dinucleotide synthase (DisA from B. subtilis) and phosphodiesterases (RocR from P. aeruginosa and CdnP from M. tuberculosis). We also demonstrate that an inhibitor of RocR PDE can inhibit bacterial swarming motility, which is a virulence factor.

Ceramic Materials Development for Intermediate Temperature Solid Oxide Fuel Cell (IT-SOFC)

Solid oxide fuel cell (SOFC) is an electrochemical device that converts chemical energy into electric power with high efficiency. Traditional SOFC has its disadvantages, such as redox cycling instability and carbon deposition while using hydrocarbon fuels. It is because traditional SOFC uses Ni-cermet as anode. In order to solve these problems, ceramic anode is a good candidate to replace Ni. However, the conductivity of most ceramic anode materials are much lower than Ni metal, and it introduces high ohmic resistance. How to increase the conductivity is a hot topic in this research field. Based on our proposed mechanism, several types of ceramic materials have been developed. Vanadium doped perovskite, Sr1-x/2VxTi1-xO3 (SVT) and Sr0.2Na0.8Nb1-xVxO3 (SNNV), achieved the conductivity as high as 300 S*cm-1 in hydrogen, without any high temperature reduction. GDC electrolyte supported cell was fabricated with Sr0.2Na0.8Nb0.9V0.1O3 and the performance was measured in hydrogen and methane respectively. Due to vanadium’s intrinsic problems, the anode supported cell is not easy. Fe doped double perovskite Sr2CoMoO6 (SFCM) was also developed. By carefully doping Fe, the conductivity was improved over one magnitude, without any vigorous reducing conditions. SFCM anode supported cell was successfully fabricated with GDC as the electrolyte. By impregnating Ni-GDC nano particles into the anode, the cell can be operated at lower temperatures while having higher performance than the traditional Ni-cermet cells. Meanwhile, this SFCM anode supported SOFC has long term stability in the reformate containing methane. During the anode development, cathode improvement caused by a thin Co-GDC layer was observed. By adding this Co-GDC layer between the electrolyte and the cathode, the interfacial resistance decreases due to fast oxygen ion transport. This mechanism was confirmed via isotope exchange. This Co-GDC layer works with multiple kinds of cathodes and the modified cell’s performance is 3 times as the traditional Ni-GDC cell. With this new method, lowering the SOFC operation temperature is feasible.

Exploring the Function and Regulation of Arabidopsis EIN2 in Ethylene Signaling

Ethylene is an essential plant hormone involved in nearly all stages of plant growth and development. EIN2 (ETHYLENE INSENSITIVE2) is a master positive regulator in the ethylene signaling pathway, consisting of an N-terminal domain and a C-terminal domain. The EIN2 N-terminal domain localizes to the endoplasmic reticulum (ER) membrane and shows sequence similarity to Nramp metal ion transporters. The cytosolic C-terminal domain is unique to plants and signals downstream. There have been several major gaps in our knowledge of EIN2 function. It was unknown how the ethylene signal gets relayed from the known upstream component CTR1 (CONSTITUTIVE RESPONSE1) a Ser/Thr kinase at the ER, to EIN2. How the ethylene signal was transduced from EIN2 to the next downstream component transcription factor EIN3 (ETHYLENE INSENSITIVE3) in the nucleus was also unknown. The N-terminal domain of EIN2 shows homology to Nramp metal ion transporters and whether EIN2 can also function as a metal transporter has been a question plaguing the ethylene field for almost two decades. Here, EIN2 was found to interact with the CTR1 protein kinase, leading to the discovery that CTR1 phosphorylates the C-terminal domain of EIN2 in Arabidopsis thaliana. Using tags at the termini of EIN2, it was deduced that in the presence of ethylene, the EIN2 C-terminal domain is cleaved and translocates into the nucleus, where it could somehow activate downstream ethylene responses. The EIN2 C-terminal domain interacts with nuclear proteins, RTE3 and EER5, which are components of the TREX-2 mRNA export complex, although the role of these interactions remains unclear. The EIN2 N-terminal domain was found to be capable of divalent metal transport when expressed in E. coli and S. cerevisiae leading to the hypothesis that metal transport plays a role in ethylene signaling. This hypothesis was tested using a novel missense allele, ein2 G36E, substituting a highly conserved residue that is required for metal transport in Nramp proteins. This G36E substitution did not disrupt metal ion transport of EIN2, but the ethylene insensitive phenotype of this mutant indicates that the EIN2 N-terminal domain is important for positively regulating the C-terminal domain. The defect of the ein2 G36E mutant does not prevent proper expression or subcellular localization, but might affect protein modifications. The ein2 G36E allele is partially dominant, mostly likely displaying haploinsufficiency. Overexpression of the EIN2 N-terminal domain in the ein2 G36E mutant did not rescue ethylene insensitivity, suggesting the N-terminal domain functions in cis to regulate the C-terminal domain. These findings advance our knowledge of EIN2, which is critical to understanding ethylene signaling.

Nano-Engineering of Densely Packed Electrochemical Energy Storage Architectures by Atomic Layer Deposition

Nanostructures are highly attractive for future electrical energy storage devices because they enable large surface area and short ion transport time through thin electrode layers for high power devices. Significant enhancement in power density of batteries has been achieved by nano-engineered structures, particularly anode and cathode nanostructures spatially separated far apart by a porous membrane and/or a defined electrolyte region. A self-aligned nanostructured battery fully confined within a single nanopore presents a powerful platform to determine the rate performance and cyclability limits of nanostructured storage devices. Atomic layer deposition (ALD) has enabled us to create and evaluate such structures, comprised of nanotubular electrodes and electrolyte confined within anodic aluminum oxide (AAO) nanopores. The V2O5- V2O5 symmetric nanopore battery displays exceptional power-energy performance and cyclability when tested as a massively parallel device (~2billion/cm2), each with ~1m3 volume (~1fL). Cycled between 0.2V and 1.8V, this full cell has capacity retention of 95% at 5C rate and 46% at 150C, with more than 1000 charge/discharge cycles. These results demonstrate the promise of ultrasmall, self-aligned/regular, densely packed nanobattery structures as a testbed to study ionics and electrodics at the nanoscale with various geometrical modifications and as a building block for high performance energy storage systems[1, 2]. Further increase of full cell output potential is also demonstrated in asymmetric full cell configurations with various low voltage anode materials. The asymmetric full cell nanopore batteries, comprised of V2O5 as cathode and prelithiated SnO2 or anatase phase TiO2 as anode, with integrated nanotubular metal current collectors underneath each nanotubular storage electrode, also enabled by ALD. By controlling the amount of lithium ion prelithiated into SnO2 anode, we can tune full cell output voltage in the range of 0.3V and 3V. This asymmetric nanopore battery array displays exceptional rate performance and cyclability. When cycled between 1V and 3V, it has capacity retention of approximately 73% at 200C rate compared to 1C, with only 2% capacity loss after more than 500 charge/discharge cycles. With increased full cell output potential, the asymmetric V2O5-SnO2 nanopore battery shows significantly improved energy and power density. This configuration presents a more realistic test - through its asymmetric (vs symmetric) configuration – of performance and cyclability in nanoconfined environment. This dissertation covers (1) Ultra small electrochemical storage platform design and fabrication, (2) Electron and ion transport in nanostructured electrodes inside a half cell configuration, (3) Ion transport between anode and cathode in confined nanochannels in symmetric full cells, (4) Scale up energy and power density with geometry optimization and low voltage anode materials in asymmetric full cell configurations. As a supplement, selective growth of ALD to improve graphene conductance will also be discussed[3]. References: 1. Liu, C., et al., (Invited) A Rational Design for Batteries at Nanoscale by Atomic Layer Deposition. ECS Transactions, 2015. 69(7): p. 23-30. 2. Liu, C.Y., et al., An all-in-one nanopore battery array. Nature Nanotechnology, 2014. 9(12): p. 1031-1039. 3. Liu, C., et al., Improving Graphene Conductivity through Selective Atomic Layer Deposition. ECS Transactions, 2015. 69(7): p. 133-138.

MANIPULATION OF IONS, ELECTRONS, AND PHOTONS IN 2D MATERIALS BY ION INTERCALATION

2D materials have attracted tremendous attention due to their unique physical and chemical properties since the discovery of graphene. Despite these intrinsic properties, various modification methods have been applied to 2D materials that yield even more exciting results. Among all modification methods, the intercalation of 2D materials provides the highest possible doping and/or phase change to the pristine 2D materials. This doping effect highly modifies 2D materials, with extraordinary electrical transport as well as optical, thermal, magnetic, and catalytic properties, which are advantageous for optoelectronics, superconductors, thermoelectronics, catalysis and energy storage applications. To study the property changes of 2D materials, we designed and built a planar nanobattery that allows electrochemical ion intercalation in 2D materials. More importantly, this planar nanobattery enables characterization of electrical, optical and structural properties of 2D materials in situ and real time upon ion intercalation. With this device, we successfully intercalated Li-ions into few layer graphene (FLG) and ultrathin graphite, heavily dopes the graphene to 0.6 x 10^15 /cm2, which simultaneously increased its conductivity and transmittance in the visible range. The intercalated LiC6 single crystallite achieved extraordinary optoelectronic properties, in which an eight-layered Li intercalated FLG achieved transmittance of 91.7% (at 550 nm) and sheet resistance of 3 ohm/sq. We extend the research to obtain scalable, printable graphene based transparent conductors with ion intercalation. Surfactant free, printed reduced graphene oxide transparent conductor thin film with Na-ion intercalation is obtained with transmittance of 79% and sheet resistance of 300 ohm/sq (at 550 nm). The figure of merit is calculated as the best pure rGO based transparent conductors. We further improved the tunability of the reduced graphene oxide film by using two layers of CNT films to sandwich it. The tunable range of rGO film is demonstrated from 0.9 um to 10 um in wavelength. Other ions such as K-ion is also studied of its intercalation chemistry and optical properties in graphitic materials. We also used the in situ characterization tools to understand the fundamental properties and improve the performance of battery electrode materials. We investigated the Na-ion interaction with rGO by in situ Transmission electron microscopy (TEM). For the first time, we observed reversible Na metal cluster (with diameter larger than 10 nm) deposition on rGO surface, which we evidenced with atom-resolved HRTEM image of Na metal and electron diffraction pattern. This discovery leads to a porous reduced graphene oxide sodium ion battery anode with record high reversible specific capacity around 450 mAh/g at 25mA/g, a high rate performance of 200 mAh/g at 250 mA/g, and stable cycling performance up to 750 cycles. In addition, direct observation of irreversible formation of Na2O on rGO unveils the origin of commonly observed low 1st Columbic Efficiency of rGO containing electrodes. Another example for in situ characterization for battery electrode is using the planar nanobattery for 2D MoS2 crystallite. Planar nanobattery allows the intrinsic electrical conductivity measurement with single crystalline 2D battery electrode upon ion intercalation and deintercalation process, which is lacking in conventional battery characterization techniques. We discovered that with a “rapid-charging” process at the first cycle, the lithiated MoS2 undergoes a drastic resistance decrease, which in a regular lithiation process, the resistance always increases after lithiation at its final stage. This discovery leads to a 2- fold increase in specific capacity with with rapid first lithiated MoS2 composite electrode material, compare with the regular first lithiated MoS2 composite electrode material, at current density of 250 mA/g.