The Effect of Zinc in Carbon Concentrating Mechanisms in Phaeodactylum tricornutum

Photosynthesis is crucial for life but is a slow process because the CO2 concentration near the principal carbon-assimilation enzyme RuBisCO is extremely low. Very few plants and algae perform a carbon-concentrating mechanism (CCM) to overcome the insufficiency, which are classified into biophysical and biochemical (C4) mechanism. The enzyme CA catalyzes the reversible dehydration of HCO3- to CO2 in biophysical CCMs and its active site contains a Zn2+. In this study, we hypothesized that Zn2+ availability can impact CCMs and therefore investigated the effect of Zn2+ availability on photosynthetic metabolism in a unicellular marine diatom Phaeodactylum tricornutum. P. tricornutum has a sequenced genome and can conduct both biophysical and C4 CCMs. We observed that Zn2+ has a significant effect on cell growth rate but no significant interference on intracellular metabolism, suggesting no essential compensation of C4 CCMs for biophysical CCMs even at low CA activity anticipated at low Zn2+ concentration.

Rate of Belowground Carbon Allocation Differs with Successional Habit of Two Afromontane Trees

Background: Anthropogenic disturbance of old-growth tropical forests increases the abundance of early successional tree species at the cost of late successional ones. Quantifying differences in terms of carbon allocation and the proportion of recently fixed carbon in soil CO2 efflux is crucial for addressing the carbon footprint of creeping degradation. Methodology: We compared the carbon allocation pattern of the late successional gymnosperm Podocarpus falcatus (Thunb.) Mirb. and the early successional (gap filling) angiosperm Croton macrostachyus Hochst. es Del. in an Ethiopian Afromontane forest by whole tree (CO2)-C-13 pulse labeling. Over a one-year period we monitored the temporal resolution of the label in the foliage, the phloem sap, the arbuscular mycorrhiza, and in soil-derived CO2. Further, we quantified the overall losses of assimilated C-13 with soil CO2 efflux. Principal Findings: C-13 in leaves of C. macrostachyus declined more rapidly with a larger size of a fast pool (64% vs. 50% of the assimilated carbon), having a shorter mean residence time (14 h vs. 55 h) as in leaves of P. falcatus. Phloem sap velocity was about 4 times higher for C. macrostachyus. Likewise, the label appeared earlier in the arbuscular mycorrhiza of C. macrostachyus and in the soil CO2 efflux as in case of P. falcatus (24 h vs. 72 h). Within one year soil CO2 efflux amounted to a loss of 32% of assimilated carbon for the gap filling tree and to 15% for the late successional one. Conclusions: Our results showed clear differences in carbon allocation patterns between tree species, although we caution that this experiment was unreplicated. A shift in tree species composition of tropical montane forests (e. g., by degradation) accelerates carbon allocation belowground and increases respiratory carbon losses by the autotrophic community. If ongoing disturbance keeps early successional species in dominance, the larger allocation to fast cycling compartments may deplete soil organic carbon in the long run.

Hydrothermal carbonization in the synthesis of sustainable porous carbon materials

Carbon materials are found versatile and applicable in wide range of applications. During the recent years research of carbon materials has focussed on the search of environmentally friendly, sustainable, renewable and low-cost starting material sources as well as simple cost-efficient synthesis techniques. As an alternative synthesis technique in the production of carbon materials hydrothermal carbonization (HTC) has shown a great potential. Depending on the application HTC can be performed as such or as a pretreatment technique. This technique allows synthesis of carbon materials i.e. hydrochars in closed vessel in the presence of water and self-generated pressure at relatively low temperatures (180-250 ˚C). As in many applications well developed porosity and heteroatom distribution are in a key role. Therefore in this study different techniques e.g. varying feedstock, templating and post-treatment in order to introduce these properties to the hydrochars structure were performed. Simple monosaccharides i.e. fructose or glucose and more complex compounds such as cellulose and sludge were performed as starting materials. Addition of secondary precursor e.g. thiophenecarboxaldehyde and ovalbumin was successfully exploited in order to alter heteroatom content. It was shown that well-developed porosity (SBET 550 m2/g) can be achieved via one-pot approach (i.e. exploitation of salt mixture) without conventionally used post-carbonization step. Nitrogen-enriched hydrochars indicated significant Pb(II) and Cr(VI) removal efficiency of 240 mg/g and 68 mg/g respectively. Sulphur addition into carbon network was not found to have enhancing effect on the adsorption of methylene blue or change acidity of the carbon material. However, these hydrochars were found to remove 99.9 % methylene blue and adsorption efficiency of these hydrochars remained over 90 % even after regeneration. In addition to water treatment application N-rich high temperature treated carbon materials were proven applicable as electrocatalyst and electrocatalyst support. Hydrothermal carbonization was shown to be workable technique for the production of carbon materials with variable physico-chemical properties and therefore hydrochars could be applied in several different applications e.g. as alternative low-cost adsorbent for pollutant removal from water.

Estimates of global sources and sinks of carbon from land cover and land use changes

The distribution of sources and sinks of carbon over the land surface is dominated by changes in land use such as deforestation, reforestation, and agricultural management. Despite, the importance of land-use change in dominating long-term net terrestrial fluxes of carbon, estimates of the annual flux are uncertain relative to other terms in the global carbon budget. The interaction of the nitrogen cycle via atmospheric N inputs and N limitation with the carbon cycle contributes to the uncertain effect of land use change on terrestrial carbon uptake. This study uses two different land use datasets to force the geographically explicit terrestrial carbon-nitrogen coupled component of the Integrated Science Assessment Model (ISAM) to examine the response of terrestrial carbon stocks to historical LCLUC (cropland, pastureland and wood harvest) while accounting for changes in N deposition, atmospheric CO2 and climate. One of the land use datasets is based on satellite data (SAGE) while the other uses population density maps (HYDE), which allows this study to investigate how global LCLUC data construction can affect model estimated emissions. The timeline chosen for this study starts before the Industrial Revolution in 1765 to the year 2000 because of the influence of rising population and economic development on regional LCLUC. Additionally, this study evaluates the impact that resulting secondary forests may have on terrestrial carbon uptake. The ISAM model simulations indicate that uncertainties in net terrestrial carbon fluxes during the 1990s are largely due to uncertainties in regional LCLUC data. Also results show that secondary forests increase the terrestrial carbon sink but secondary tropical forests carbon uptake are constrained due to nutrient limitation.

Electrical and optical studies on carbon nanotube arrays

Single-walled carbon nanotubes (SWNTs) have been studied as a prominent class of high performance electronic materials for next generation electronics. Their geometry dependent electronic structure, ballistic transport and low power dissipation due to quasi one dimensional transport, and their capability of carrying high current densities are some of the main reasons for the optimistic expectations on SWNTs. However, device applications of individual SWNTs have been hindered by uncontrolled variations in characteristics and lack of scalable methods to integrate SWNTs into electronic devices. One relatively new direction in SWNT electronics, which avoids these issues, is using arrays of SWNTs, where the ensemble average may provide uniformity from device to device, and this new breed of electronic material can be integrated into electronic devices in a scalable fashion. This dissertation describes (1) methods for characterization of SWNT arrays, (2) how the electrical transport in these two-dimensional arrays depend on length scales and spatial anisotropy, (3) the interaction of aligned SWNTs with the underlying substrate, and (4) methods for scalable integration of SWNT arrays into electronic devices. The electrical characterization of SWNT arrays have been realized by polymer electrolyte-gated SWNT thin film transistors (TFTs). Polymer electrolyte-gating addresses many technical difficulties inherent to electrical characterization by gating through oxide-dielectrics. Having shown polymer electrolyte-gating can be successfully applied on SWNT arrays, we have studied the length scaling dependence of electrical transport in SWNT arrays. Ultrathin films formed by sub-monolayer surface coverage of SWNT arrays are very interesting systems in terms of the physics of two-dimensional electronic transport. We have observed that they behave qualitatively different than the classical conducting films, which obey the Ohm’s law. The resistance of an ultrathin film of SWNT arrays is indeed non-linear with the length of the film, across which the transport occurs. More interestingly, a transition between conducting and insulating states is observed at a critical surface coverage, which is called percolation limit. The surface coverage of conducting SWNTs can be manipulated by turning on and off the semiconductors in the SWNT array, leading to the operation principle of SWNT TFTs. The percolation limit depends also on the length and the spatial orientation of SWNTs. We have also observed that the percolation limit increases abruptly for aligned arrays of SWNTs, which are grown on single crystal quartz substrates. In this dissertation, we also compare our experimental results with a two-dimensional stick network model, which gives a good qualitative picture of the electrical transport in SWNT arrays in terms of surface coverage, length scaling, and spatial orientation, and briefly discuss the validity of this model. However, the electronic properties of SWNT arrays are not only determined by geometrical arguments. The contact resistances at the nanotube-nanotube and nanotube-electrode (bulk metal) interfaces, and interactions with the local chemical groups and the underlying substrates are among other issues related to the electronic transport in SWNT arrays. Different aspects of these factors have been studied in detail by many groups. In fact, I have also included a brief discussion about electron injection onto semiconducting SWNTs by polymer dopants. On the other hand, we have compared the substrate-SWNT interactions for isotropic (in two dimensions) arrays of SWNTs grown on Si/SiO2 substrates and horizontally (on substrate) aligned arrays of SWNTs grown on single crystal quartz substrates. The anisotropic interactions associated with the quartz lattice between quartz and SWNTs that allow near perfect horizontal alignment on substrate along a particular crystallographic direction is examined by Raman spectroscopy, and shown to lead to uniaxial compressive strain in as-grown SWNTs on single crystal quartz. This is the first experimental demonstration of the hard-to-achieve uniaxial compression of SWNTs. Temperature dependence of Raman G-band spectra along the length of individual nanotubes reveals that the compressive strain is non-uniform and can be larger than 1% locally at room temperature. Effects of device fabrication steps on the non-uniform strain are also examined and implications on electrical performance are discussed. Based on our findings, there are discussions about device performances and designs included in this dissertation. The channel length dependences of device mobilities and on/off ratios are included for SWNT TFTs. Time response of polymer-electrolyte gated SWNT TFTs has been measured to be ~300 Hz, and a proof-of-concept logic inverter has been fabricated by using polymer electrolyte gated SWNT TFTs for macroelectronic applications. Finally, I dedicated a chapter on scalable device designs based on aligned arrays of SWNTs, including a design for SWNT memory devices.

FUNCTIONAL CHARACTERIZATION OF THE LINK BETWEEN CARBOHYDRATE METABOLISM AND THE PATHOGENESIS OF THE INVASIVE M1T1 GROUP A STREPTOCOCCUS

The Group A Streptococcus (GAS), or Streptococcus pyogenes, is a strict human pathogen that colonizes a variety of sites within the host. Infections can vary from minor and easily treatable, to life-threatening, invasive forms of disease. In order to adapt to niches, GAS utilizes environmental cues, such as carbohydrates, to coordinate the expression of virulence factors. Research efforts to date have focused on identifying how either components of the phosphoenolpyruvate-phosphotransferase system (PTS) or global transcriptional networks affect the regulation of virulence factors, but not the synergistic relationship between the two. The present study investigates the role of a putative PTS-fructose operon encoded by fruRBA and its role in virulence in the M1T1 strain 5448. Growth in fructose resulted in induction of fruRBA. RT-PCR showed that fruRBA formed an operon, which was repressed by FruR in the absence of fructose. Growth and carbon utilization profiles revealed that although the entire fruRBA operon was required for growth in fructose, FruA was the main fructose transporter. The ability of both ΔfruR and ΔfruB mutants to survive in whole human blood or neutrophils was impaired. However, the phenotypes were not reproduced in murine whole blood or in a mouse intraperitoneal infection, indicating a human-specific mechanism. While it is known that the PTS can affect activity of the Mga virulence regulator, further characterization of the mechanism by which sugars and its protein domains affect activity have not been studied. Transcriptional studies revealed that the core Mga regulon is activated more in a glucose-rich than a glucose-poor environment. This activation correlates with the differential phosphorylation of Mga at its PTS regulatory domains (PRDs). Using a 5448 mga mutant, transcriptome studies in THY or C media established that the Mga regulon reflects the media used. Interestingly, Mga regulates phage-encoded DNases in a low glucose environment. We also show that Mga activity is dependent on C-terminal amino acid interactions that aid in the formation of homodimers. Overall, the studies presented sought to define how external environmental cues, specifically carbohydrates, control complex regulatory networks used by GAS, contribute to pathogenesis, and aid in adaptation to various nutrient conditions encountered.