Differential susceptibility of mitochondrial complex II to inhibition by oxaloacetate in brain and heart

Mitochondrial Complex II is a key mitochondrial enzyme connecting the tricarboxylic acid (TCA) cycle and the electron transport chain. Studies of complex II are clinically important since new roles for this enzyme have recently emerged in cell signalling, cancer biology, immune response and neurodegeneration. Oxaloacetate (OAA) is an intermediate of the TCA cycle and at the same time is an inhibitor of complex II with high affinity (Kd ~ 10− 8 M). Whether or not OAA inhibition of complex II is a physiologically relevant process is a significant, but still controversial topic. We found that complex II from mouse heart and brain tissue has similar affinity to OAA and that only a fraction of the enzyme in isolated mitochondrial membranes (30.2 ± 6.0% and 56.4 ± 5.6% in the heart and brain, respectively) is in the free, active form. Since OAA could bind to complex II during isolation, we established a novel approach to deplete OAA in the homogenates at the early stages of isolation. In heart, this treatment significantly increased the fraction of free enzyme, indicating that OAA binds to complex II during isolation. In brain the OAA-depleting system did not significantly change the amount of free enzyme, indicating that a large fraction of complex II is already in the OAA-bound inactive form. Furthermore, short-term ischemia resulted in a dramatic decline of OAA in tissues, but it did not change the amount of free complex II. Our data show that in brain OAA is an endogenous effector of complex II, potentially capable of modulating the activity of the enzyme.

Molecular Mechanism of the Response to Hydrogen Sulfide in C. elegans

Thesis (Ph.D.)--University of Washington, 2016-08

Effects of copper on the photosynthesis of intact chloroplasts: interaction with manganese

Highly purified, intact chloroplasts were prepared from pea (Pisum sativum L.) and spinach (Spinacia oleracea L.) following an identical procedure, and were used to investigate the cupric cation inhibition on the photosynthetic activity. In both species, copper inhibition showed a similar inhibitor concentration that decreases the enzyme activity by 50% (IC(50) approximately 1.8 microM) and did not depend on the internal or external phosphate (Pi) concentration, indicating that copper did not interact with the Pi translocator. Fluorescence analysis suggested that the presence of copper did not facilitate photoinhibition, because there were no changes in maximal fluorescence (F(m)) nor in basal fluorescence (F(o)) of copper-treated samples. The electron transport through the photosystem II (PSII) was also not affected (operating efficiency of PSII-F'v/F'm similar in all conditions). Yet, under Cu(2+) stress, the proportion of open PSII reaction centers was dramatically decreased, and the first quinone acceptor (Q(A)) reoxidation was fully inhibited, as demonstrated by the constant photochemical quenching (q(P)) along experiment time. The quantum yield of PSII electron transport (Phi(PSII)) was also clearly affected by copper, and therefore reduced the photochemistry efficiency. Manganese, when added simultaneously with copper, delayed the inhibition, as measured by oxygen evolution and chlorophyll fluorescence, but neither reversed the copper effect when added to copper-inhibited plastids, nor prevented the inhibition of the Hill activity of isolated copper-treated thylakoids. Our results suggest that manganese competed with copper to penetrate the chloroplast envelope. This competition seems to be specific because other divalent cations e.g. magnesium and calcium, did not interfere with the copper action in intact chloroplasts. All results do suggest that, under these conditions, the stroma proteins, such as the Calvin-Benson cycle enzymes or others are the most probable first target for the Cu(2+) action, resulting in the total inhibition of chloroplast photosynthesis and in the consequent unbalanced rate of production and consumption of the reducing power.

Growth and application of planar III-V semiconductor nanowires grown with MOCVD

The semiconductor nanowire has been widely studied over the past decade and identified as a promising nanotechnology building block with application in photonics and electronics. The flexible bottom-up approach to nanowire growth allows for straightforward fabrication of complex 1D nanostructures with interesting optical, electrical, and mechanical properties. III-V nanowires in particular are useful because of their direct bandgap, high carrier mobility, and ability to form heterojunctions and have been used to make devices such as light-emitting diodes, lasers, and field-effect transistors. However, crystal defects are widely reported for III-V nanowires when grown in the common out-of-plane <111>B direction. Furthermore, commercialization of nanowires has been limited by the difficulty of assembling nanowires with predetermined position and alignment on a wafer-scale. In this thesis, planar III-V nanowires are introduced as a low-defect and integratable nanotechnology building block grown with metalorganic chemical vapor deposition. Planar GaAs nanowires grown with gold seed particles self-align along the <110> direction on the (001) GaAs substrate. Transmission electron microscopy reveals that planar GaAs nanowires are nearly free of crystal defects and grow laterally and epitaxially on the substrate surface. The nanowire morphology is shown to be primarily controlled through growth temperature and an ideal growth window of 470 +\- 10 °C is identified for planar GaAs nanowires. Extension of the planar growth mode to other materials is demonstrated through growth of planar InAs nanowires. Using a sacrificial layer, the transfer of planar GaAs nanowires onto silicon substrates with control over the alignment and position is presented. A metal-semiconductor field-effect transistor fabricated with a planar GaAs nanowire shows bulk-like low-field electron transport characteristics with high mobility. The aligned planar geometry and excellent material quality of planar III-V nanowires may lead to highly integrated III-V nanophotonics and nanoelectronics.

Macrophage adaptation leads to parallel evolution of genetically diverseEscherichia colismall-colony variants with increased fitness in vivo and antibiotic collateral sensitivity

Small-colony variants (SCVs) are commonly observed in evolution experiments and clinical isolates, being associated with antibiotic resistance and persistent infections. We recently observed the repeated emergence of Escherichia coli SCVs during adaptation to the interaction with macrophages. To identify the genetic targets underlying the emergence of this clinically relevant morphotype, we performed whole-genome sequencing of independently evolved SCV clones. We uncovered novel mutational targets, not previously associated with SCVs (e.g. cydA, pepP) and observed widespread functional parallelism. All SCV clones had mutations in genes related to the electron-transport chain. As SCVs emerged during adaptation to macrophages, and often show increased antibiotic resistance, we measured SCV fitness inside macrophages and measured their antibiotic resistance profiles. SCVs had a fitness advantage inside macrophages and showed increased aminoglycoside resistance in vitro, but had collateral sensitivity to other antibiotics (e.g. tetracycline). Importantly, we observed similar results in vivo. SCVs had a fitness advantage upon colonization of the mouse gut, which could be tuned by antibiotic treatment: kanamycin (aminoglycoside) increased SCV fitness, but tetracycline strongly reduced it. Our results highlight the power of using experimental evolution as the basis for identifying the causes and consequences of adaptation during host-microbe interactions.

Exploring complex chemical systems: insights from mass spectrometry, electrochemistry and continuous cell culture

The work presented herein covers a broad range of research topics and so, in the interest of clarity, has been presented in a portfolio format. Accordingly, each chapter consists of its own introductory material prior to presentation of the key results garnered, this is then proceeded by a short discussion on their significance. In the first chapter, a methodology to facilitate the resolution and qualitative assessment of very large inorganic polyoxometalates was designed and implemented employing ion-mobility mass spectrometry. Furthermore, the potential of this technique for ‘mapping’ the conformational space occupied by this class of materials was demonstrated. These claims are then substantiated by the development of a tuneable, polyoxometalate-based calibration protocol that provided the necessary platform for quantitative assessments of similarly large, but unknown, polyoxometalate species. In addition, whilst addressing a major limitation of travelling wave ion mobility, this result also highlighted the potential of this technique for solution-phase cluster discovery. The second chapter reports on the application of a biophotovoltaic electrochemical cell for characterising the electrogenic activity inherent to a number of mutant Synechocystis strains. The intention was to determine the key components in the photosynthetic electron transport chain responsible for extracellular electron transfer. This would help to address the significant lack of mechanistic understanding in this field. Finally, in the third chapter, the design and fabrication of a low-cost, highly modular, continuous cell culture system is presented. To demonstrate the advantages and suitability of this platform for experimental evolution investigations, an exploration into the photophysiological response to gradual iron limitation, in both the ancestral wild type and a randomly generated mutant library population, was undertaken. Furthermore, coupling random mutagenesis to continuous culture in this way is shown to constitute a novel source of genetic variation that is open to further investigation.

The development of planar high-K/III-V p-channel MOSFETs for post-silicon CMOS

Conventional Si complementary-metal-oxide-semiconductor (CMOS) scaling is fast approaching its limits. The extension of the logic device roadmap for future enhancements in transistor performance requires non-Si materials and new device architectures. III-V materials, due to their superior electron transport properties, are well poised to replace Si as the channel material beyond the 10nm technology node to mitigate the performance loss of Si transistors from further reductions in supply voltage to minimise power dissipation in logic circuits. However several key challenges, including a high quality dielectric/III-V gate stack, a low-resistance source/drain (S/D) technology, heterointegration onto a Si platform and a viable III-V p-metal-oxide-semiconductor field-effect-transistor (MOSFET), need to be addressed before III-Vs can be employed in CMOS. This Thesis specifically addressed the development and demonstration of planar III-V p-MOSFETs, to complement the n-MOSFET, thereby enabling an all III-V CMOS technology to be realised. This work explored the application of InGaAs and InGaSb material systems as the channel, in conjunction with Al2O3/metal gate stacks, for p-MOSFET development based on the buried-channel flatband device architecture. The body of work undertaken comprised material development, process module development and integration into a robust fabrication flow for the demonstration of p-channel devices. The parameter space in the design of the device layer structure, based around the III-V channel/barrier material options of In_x≥0.53Ga_1-xAs/In_0.52Al_0.48As and In_x≥0.1Ga_1-xSb/AlSb, was systematically examined to improve hole channel transport. A mobility of 433 cm²/Vs, the highest room temperature hole mobility of any InGaAs quantum-well channel reported to date, was obtained for the In_0.85Ga_0.15As (2.1% strain) structure. S/D ohmic contacts were developed based on thermally annealed Au/Zn/Au metallisation and validated using transmission line model test structures. The effects of metallisation thickness, diffusion barriers and de-oxidation conditions were examined. Contacts to InGaSb-channel structures were found to be sensitive to de-oxidation conditions. A fabrication process, based on a lithographically-aligned double ohmic patterning approach, was realised for deep submicron gate-to-source/drain gap (L_side) scaling to minimise the access resistance, thereby mitigating the effects of parasitic S/D series resistance on transistor performance. The developed process yielded gaps as small as 20nm. For high-k integration on GaSb, ex-situ ammonium sulphide ((NH₄)₂S) treatments, in the range 1%-22%, for 10min at 295K were systematically explored for improving the electrical properties of the Al₂O₃/GaSb interface. Electrical and physical characterisation indicated the 1% treatment to be most effective with interface trap densities in the range of 4 - 10×10¹²cm^-2eV^-1 in the lower half of the bandgap. An extended study, comprising additional immersion times at each sulphide concentration, was further undertaken to determine the surface roughness and the etching nature of the treatments on GaSb. A number of p-MOSFETs based on III-V-channels with the most promising hole transport and integration of the developed process modules were successfully demonstrated in this work. Although the non-inverted InGaAs-channel devices showed good current modulation and switch-off characteristics, several aspects of performance were non-ideal; depletion-mode operation, modest drive current (I_d,sat=1.14mA/mm), double peaked transconductance (g_m=1.06mS/mm), high subthreshold swing (SS=301mV/dec) and high on-resistance (R_on=845kΩ.μm). Despite demonstrating substantial improvement in the on-state metrics of I_d,sat (11×), g_m (5.5×) and R_on (5.6×), inverted devices did not switch-off. Scaling gate-to-source/drain gap (L_side) from 1μm down to 70nm improved I_d,sat (72.4mA/mm) by a factor of 3.6 and gm (25.8mS/mm) by a factor of 4.1 in inverted InGaAs-channel devices. Well-controlled current modulation and good saturation behaviour was observed for InGaSb-channel devices. In the on-state In_0.3Ga_0.7Sb-channel (I_d,sat=49.4mA/mm, g_m=12.3mS/mm, R_on=31.7kΩ.μm) and In_0.4Ga_0.6Sb-channel (I_d,sat=38mA/mm, g_m=11.9mS/mm, R_on=73.5kΩ.μm) devices outperformed the InGaAs-channel devices. However the devices could not be switched off. These findings indicate that III-V p-MOSFETs based on InGaSb as opposed to InGaAs channels are more suited as the p-channel option for post-Si CMOS.

Life without complex I: proteome analyses of an Arabidopsis mutant lacking the mitochondrial NADH dehydrogenase complex

The mitochondrial NADH dehydrogenase complex (complex I) is of particular importance for the respiratory chain in mitochondria. It is the major electron entry site for the mitochondrial electron transport chain (mETC) and therefore of great significance for mitochondrial ATP generation. We recently described an Arabidopsis thaliana double-mutant lacking the genes encoding the carbonic anhydrases CA1 and CA2, which both form part of a plant-specific 'carbonic anhydrase domain' of mitochondrial complex I. The mutant lacks complex I completely. Here we report extended analyses for systematically characterizing the proteome of the ca1ca2 mutant. Using various proteomic tools, we show that lack of complex I causes reorganization of the cellular respiration system. Reduced electron entry into the respiratory chain at the first segment of the mETC leads to induction of complexes II and IV as well as alternative oxidase. Increased electron entry at later segments of the mETC requires an increase in oxidation of organic substrates. This is reflected by higher abundance of proteins involved in glycolysis, the tricarboxylic acid cycle and branched-chain amino acid catabolism. Proteins involved in the light reaction of photosynthesis, the Calvin cycle, tetrapyrrole biosynthesis, and photorespiration are clearly reduced, contributing to the significant delay in growth and development of the double-mutant. Finally, enzymes involved in defense against reactive oxygen species and stress symptoms are much induced. These together with previously reported insights into the function of plant complex I, which were obtained by analysing other complex I mutants, are integrated in order to comprehensively describe 'life without complex I'.

Reduced graphene oxide wrapped Cu2O supported on C3N4: An efficient visible light responsive semiconductor photocatalyst

Herein, Cu 2O spheres were prepared and encapsulated with reduced graphene oxide (rGO). The Cu 2O–rGO–C3N4 composite covered the whole solar spectrum with significant absorption intensity. rGO wrapped Cu 2O loading caused a red shift in the absorption with respect to considering the absorption of bare C3N4. The photoluminescence study confirms that rGO exploited as an electron transport layer at the interface of Cu 2O and C3N4 heterojunction. Utmost, ∼2 fold synergistic effect was achieved with Cu 2O–rGO–C3N4 for the photocatalytic reduction of 4-nitrophenol to 4-aminophenol in comparison with Cu 2O–rGO and C3N4. The Cu 2O–rGO–C3N4 photocatalyst was reused for four times without loss in its activity.

High On/Off ratio memristive switching of manganite/cuprate bilayer by interfacial magnetoelectricity

Memristive switching serves as the basis for a new generation of electronic devices. Memristors are two-terminal devices in which the current is turned on and off by redistributing point defects, e.g., vacancies, which is difficult to control. Memristors based on alternative mechanisms have been explored, but achieving both the high On/Off ratio and the low switching energy desirable for use in electronics remains a challenge. Here we report memristive switching in a La_(0.7)Ca_(0.3)MnO_(3)/PrBa_(2)Cu_(3)O_(7) bilayer with an On/Off ratio greater than 103 and demonstrate that the phenomenon originates from a new type of interfacial magnetoelectricity. Using results from firstprinciples calculations, we show that an external electric-field induces subtle displacements of the interfacial Mn ions, which switches on/off an interfacial magnetic “dead” layer, resulting in memristive behavior for spin-polarized electron transport across the bilayer. The interfacial nature of the switching entails low energy cost about of a tenth of atto Joule for write/erase a “bit”. Our results indicate new opportunities for manganite/cuprate systems and other transition-metal-oxide junctions in memristive applications.

The transition from health to sickness via the chloroplast

Microbe associated molecular pattern (MAMP) receptors in plants recognize MAMPs and activate basal defences; however a complete understanding of the molecular and physiological mechanisms conferring immunity remains elusive. Pathogens suppress active defence in plants through the combined action of effector proteins. This talk presents results showing the chloroplast as a key component of early immune responses. MAMP perception triggers the rapid, large-scale suppression of nuclear encoded chloroplast-targeted genes (NECGs). Virulent Pseudomonas syringae effectors reprogramme NECG expression in Arabidopsis, target the chloroplast and inhibit photosynthetic CO2 assimilation through disruption of photosystem II. This activity prevents a chloroplastic reactive oxygen burst. These physiological changes precede bacterial multiplication and coincide with pathogen-induced abscisic acid (ABA) accumulation. MAMP pretreatment protects chloroplasts from effector manipulation, whereas application of ABA or the inhibitor of photosynthetic electron transport, DCMU, abolishes the MAMP-induced chloroplastic reactive oxygen burst, and enhances growth of a P. syringae hrpA mutant that fails to secrete effectors.

Controlled electronic transport in single-walled carbon nanotube networks : selecting electron hopping and chemical doping mechanisms

The electronic transport in both intrinsic and acid-treated single-walled carbon nanotube networks containing more than 90% semiconducting nanotubes is investigated using temperature-dependent resistance measurements. The semiconducting behavior observed in the intrinsic network is attributed to the three-dimensional electron hopping mechanism. In contrast, the chemical doping mechanism in the acid-treated network is found to be responsible for the revealed metal-like linear resistivity dependence in a broad temperature range. This effective method to control the electrical conductivity of single-walled carbon nanotube networks is promising for future nanoscale electronics, thermometry, and bolometry. © 2010 American Institute of Physics.

Analyzing hysteresis behavior of capacitance-voltage characteristics of IZO/C₆₀/pentacene/Au diodes with a hole-transport electron-blocking polyterpenol layer by electric-field-induced optical second-harmonic generation measurement

By using electric-field-induced optical second-harmonic generation (EFISHG) measurement, we analyzed hysteresis behavior of capacitance-voltage (C-V) characteristics of IZO/polyterpenol (PT)/C₆₀/pentacene/Au diodes, where PT layer is actively working as a hole-transport electron-blocking layer. The EFISHG measurement verified the presence of interface accumulated charges in the diodes, and showed that a space charge electric field from accumulated excess electrons (holes) that remain at the PT/C₆₀ (C₆₀/pentacene) interface is responsible for the hysteresis loop observed in the C-V characteristics.

Transport through an electrostatically defined quantum dot lattice in a two-dimensional electron gas

Quantum dot lattices (QDLs) have the potential to allow for the tailoring of optical, magnetic, and electronic properties of a user-defined artificial solid. We use a dual gated device structure to controllably tune the potential landscape in a GaAs/AlGaAs two-dimensional electron gas, thereby enabling the formation of a periodic QDL. The current-voltage characteristics, I (V), follow a power law, as expected for a QDL. In addition, a systematic study of the scaling behavior of I (V) allows us to probe the effects of background disorder on transport through the QDL. Our results are particularly important for semiconductor-based QDL architectures which aim to probe collective phenomena.

Macroscopic Transport of Mega-ampere Electron Currents in Aligned Carbon-Nanotube Arrays

We demonstrate that aligned carbon-nanotube arrays are efficient transporters of laser-generated megaampere electron currents over distances as large as a millimeter. A direct polarimetric measurement of the temporal and the spatial evolution of the megagauss magnetic fields (as high as 120 MG) at the target rear at an intensity of (10(18)-10(19)) W/cm(2) was corroborated by the rear-side hot electron spectra. Simulations show that such high magnetic flux densities can only be generated by a very well collimated fast electron bunch.