Solution structure and characterization of the LGR8 receptor binding surface of insulin-like peptide 3

Insulin-like peptide 3 (INSL3), a member of the relaxin peptide family, is produced in testicular Leydig cells and ovarian thecal cells. Gene knock-out experiments have identified a key biological role in initiating testes descent during fetal development. Additionally, INSL3 has an important function in mediating male and female germ cell function. These actions are elicited via its recently identified receptor, LGR8, a member of the leucine-rich repeat-containing G-protein- coupled receptor family. To identify the structural features that are responsible for the interaction of INSL3 with its receptor, its solution structure was determined by NMR spectroscopy together with in vitro assays of a series of B-chain alanine-substituted analogs. Synthetic human INSL3 was found to adopt a characteristic relaxin/ insulin-like fold in solution but is a highly dynamic molecule. The four termini of this two-chain peptide are disordered, and additional conformational exchange is evident in the molecular core. Alanine-substituted analogs were used to identify the key residues of INSL3 that are responsible for the interaction with the ectodomain of LGR8. These include Arg(B16) and Val(B19), with His(B12) and Arg(B20) playing a secondary role, as evident from the synergistic effect on the activity in double and triple mutants involving these residues. Together, these amino acids combine with the previously identified critical residue, Trp(B27), to form the receptor binding surface. The current results provide clear direction for the design of novel specific agonists and antagonists of this receptor.

The construction and optimization of a surface plasmon resonance sensor for the studies of bio-molecular interactions

Bio-molecular interactions exist ubiquitously in all biological systems. This dissertation project was to construct a powerful surface plasmon resonance (SPR) sensor. The SPR system is used to study bio-molecular interactions in real time and without labeling. Surface plasmon is the oscillation of free electrons in metals coupled with surface electromagnetic waves. These surface electromagnetic waves provide a sensitive probe to study bio-molecular interactions on metal surfaces. This project resulted in the successful construction and optimization of a homemade SPR sensor and the development of several new powerful protocols to study bio-molecular interactions. It was discovered through this project that the limitations of earlier SPR sensors are related not only to the instrumentation design and operating procedures, but also to the complex behaviors of bio-molecules on sensor surfaces that were very different from that in solution. Based on these discoveries the instrumentation design and operating procedures were fully optimized. A set of existing sensor surface treatment protocols were tested and evaluated and new protocols were developed in this project. The new protocols have demonstrated excellent performance to study biomolecular interactions. The optimized home-made SPR sensor was used to study protein-surface interactions. These protein-surface interactions are responsible for many complex organic cell activities. The co-existence of different driving forces and their correlation with the structure of the protein and the surface make the understanding of the fundamental mechanism of protein-surface interactions a very challenging task. Using the improved SPR sensor, the electrostatic interaction and hydrophobic interaction were studied separately. The results of this project directly confirmed the theoretical predictions for electrostatic force between the protein and surface. In addition, this project demonstrated that the strength of the protein-surface hydrophobic interaction does not solely depend on the hydrophobicity as reported earlier. Surface structure also plays a significant role.

Discharge measurements and storm event chemistry at the San Francisco River station (Planta) in 2007-2008

To improve our knowledge of the influence of land-use on solute behaviour and export rates in neotropical montane catchments we investigated total organic carbon (TOC), Ca, Mg, Na, K, NO3 and SO4 concentrations during April 2007-May 2008 at different flow conditions and over time in six forested and pasture-dominated headwaters (0.7-76 km2) in Ecuador. NO3 and SO4 concentrations decreased during the study period, with a continual decrease in NO3 and an abrupt decrease in February 2008 for SO4. We attribute this to changing weather regimes connected to a weakening La Niña event. Stream Na concentration decreased in all catchments, and Mg and Ca concentration decreased in all but the forested catchments during storm flow. Under all land-uses TOC increased at high flows. The differences in solute behaviour during storm flow might be attributed to largely shallow subsurface and surface flow paths in pasture streams on the one hand, and a predominant origin of storm flow from the organic layer in the forested streams on the other hand. Nutrient export rates in the forested streams were comparable to the values found in literature for tropical streams. They amounted to 6-8 kg/ha/y for Ca, 7-8 kg/ha/y for K, 4-5 kg/ha/y for Mg, 11-14 kg/ha/y for Na, 19-22 kg/ha/y for NO3 (i.e. 4.3-5.0 kg/ha/y NO3-N) and 17 kg/ha/y for SO4. Our data contradict the assumption that nutrient export increases with the loss of forest cover. For NO3 we observed a positive correlation of export value and percentage forest cover.

Seawater carbonate chemistry, tissue-skeleton interface and calcification in reef corals in a laboratory experiment

Insight into the response of reef corals and other major marine calcifiers to ocean acidification is limited by a lack of knowledge about how seawater pH and carbonate chemistry impact the physiological processes that drive biomineralization. Ocean acidification is proposed to reduce calcification rates in corals by causing declines in internal pH at the calcifying tissue-skeleton interface where biomineralization takes place. Here, we performed an in vivo study on how partial-pressure CO(2)-driven seawater acidification impacts intracellular pH in coral calcifying cells and extracellular pH in the fluid at the tissue-skeleton interface [subcalicoblastic medium (SCM)] in the coral Stylophora pistillata. We also measured calcification in corals grown under the same conditions of seawater acidification by measuring lateral growth of colonies and growth of aragonite crystals under the calcifying tissue. Our findings confirm that seawater acidification decreases pH of the SCM, but this decrease is gradual relative to the surrounding seawater, leading to an increasing pH gradient between the SCM and seawater. Reductions in calcification rate, both at the level of crystals and whole colonies, were only observed in our lowest pH treatment when pH was significantly depressed in the calcifying cells in addition to the SCM. Overall, our findings suggest that reef corals may mitigate the effects of seawater acidification by regulating pH in the SCM, but they also highlight the role of calcifying cell pH homeostasis in determining the response of reef corals to changes in external seawater pH and carbonate chemistry.

Mg/Ca ratio, Sr/Ca ratio and stable isotopes of the foraminifera Oridorsalis umbonatus in surface sediment samples

We investigate the influence of carbonate system parameters (carbonate ion concentration, [CO3**2-]; carbonate ion saturation, Delta [CO3**2-]) on the trace element and stable isotope ratios in the endobenthic foraminifera Oridorsalis umbonatus. Data from modern core top samples from the Namibian continental slope suggest that the shell composition of this species is influenced by the chemistry of the pore-water. For these organic-rich sediments, the impact of ocean bottom water properties on both pore-water and shell chemistry is surprisingly small. Sr/Ca correlates positively with [CO3**2-] and to a lesser extent with Delta [CO3**2-], which is opposed to previous results. A [CO3**2-] decrease of 10 µmol/kg leads to an increase of 0.05 mmol/mol in Sr/Ca. We observe a correlation between shell d18O (corrected for temperature and d18O seawater) and [CO3**2-], however, the variability of the corrected d18O is close to the analytical limit. No clear dependences were observed for d13C and Mg/Ca.

Sediment and pore water chemistry and physical oceanography of samples obtained during Baltic Sea research cruises

Sediment samples from approximately 40 stations in the Western, middle and eastern Baltic Sea were investigated for manganese and iron content. In a series of interstitial water samples and numerous deep and surface water samples, the manganese content was likewise determined. A strong enrichment of these elements in the basin sediments was shown. In many instances, several percent manganese were present. As a maximum value, 13% was found in a 1 mm thick layer. Furthermore, a distinct decrease in manganese content with increasing sediment depth was shown in the upper 10 to 20 cm of the Sediment at almost all stations. Both phenomena may be explained by the release of manganese from the Sediment through diffusion. In the flat parts of the Baltic and those parts having good bottom water circulation, this diffusion progresses especially vigorously as a result of a steep gradient of the Mn++ concentration in the interstitial water-deep water interface. The manganese which hereby passes into the water overlying the bottom (manganese contents between 10 and 100 y Mn/l were determined in numerous deep water samples) is partly reprecipitated on the Sediment surface, and partly carried by currents into the deeper basins where it is finallv deposited. It is bound there as a manganese-rich mixed carbonate, the composition of which can be proved chemically and by x-ray methods. Iron is likewise of higher content in the basinal sediments, however, the extent of its enrichment is far less since it is less soluble than manganese under the reducing conditions in the sediments. The fine bands of manganese- and iron-rich layers in the basin sediments may likewise be explained as a result of diffusion.

(Table 1) Water chemistry of groundwater and snow samples from three sites in Ontario, Canada

Snow samples collected from hand-dug pits at two sites in Simcoe County, Ontario, Canada were analysed for major and trace elements using the clean lab methods established for polar ice. Potentially toxic, chalcophile elements are highly enriched in snow, relative to their natural abundance in crustal rocks, with enrichment factor (EF) values (calculated using Sc) in the range 107 to 1081 for Ag, As, Bi, Cd, Cu, Mo, Pb, Sb, Te, and Zn. Relative to M/Sc ratios in snow, water samples collected at two artesian flows in this area are significantly depleted in Ag, Al, Be, Bi, Cd, Cr, Cu, Ni, Pb, Sb, Tl, V, and Zn at both sites, and in Co, Th and Tl at one of the sites. The removal from the waters of these elements is presumably due to such processes as physical retention (filtration) of metal-bearing atmospheric aerosols by organic and mineral soil components as well as adsorption and surface complexation of ionic species onto organic, metal oxyhydroxide and clay mineral surfaces. In the case of Pb, the removal processes are so effective that apparently ''natural'' ratios of Pb to Sc are found in the groundwaters. Tritium measurements show that the groundwater at one of the sites is modern (ie not more than 30 years old) meaning that the inputs of Pb and other trace elements to the groundwaters may originally have been much higher than they are today; the M/Sc ratios measured in the groundwaters today, therefore, represent a conservative estimate of the extent of metal removal along the flow path. Lithogenic elements significantly enriched in the groundwaters at both sites include Ba, Ca, Li, Mg, Mn, Na, Rb, S, Si, Sr, and Ti. The abundance of these elements can largely be explained in terms of weathering of the dominant silicate (plagioclase, potassium feldspar, amphibole and biotite) and carbonate minerals (calcite, dolomite and ankerite) in the soils and sediments of the watershed. Arsenic, Mo, Te, and especially U are also highly enriched in the groundwaters, due to chemical weathering: these could easily be explained if there are small amounts of sulfides (As, Mo, Te) and apatite (U) in the soils of the source area. Elements neither significantly enriched nor depleted at both sites include Fe, Ga, Ge, and P.

BLOCK COPOLYMERS CONTAINING A LOW-SURFACE-ENERGY BLOCK AND THEIR APPLICATIONS

This thesis reports the synthesis and/or applications of three types of block copolymers that each bear a low-surface-energy block. First, poly(dimethylsiloxane)-block-poly(2-cinnamoyloxyethyl acrylate) (PDMS-b-PCEA) was synthesized and characterized. Cotton coating using a micellar solution of this block copolymer yielded superhydrophobic cotton fabrics. X-ray photoelectron spectroscopy (XPS) and surface property analyses indicated that the PDMS block topped the polymer coating. Photocuring the cotton swatches crosslinked the underlying PCEA layer and yielded permanent coatings. More interestingly, hydrophilically patterned superhydrophobic cotton fabrics were produced using photolithography that allowed the crosslinking of the coating around irradiated fibers but the removal, by solvent extraction, of the coating on fibers that were not irradiated. Since water-based ink only permeated the uncoated regions, such patterned fabric was further used to print ink patterns onto substrates such as fabrics, cardboard, paper, wood, and aluminum foil. Then, another PDMS-based diblock copolymer poly(dimethylsiloxane)-block-poly(glycidyl methacrylate) (PDMS-b-PGMA) was prepared. Different from PCEA that photocrosslinked around cotton fibers, PGMA reacted with hydroxyl groups on cotton fiber surfaces to get covalently attached. Further, different PGMA chains crosslinked with each other. PDMS-b-PGMA-coated cotton fabrics have been used for oil-water separations. In addition, polymeric nanoparticles were grafted onto cotton fiber surface before PDMS-b-PGMA was used to cover the surfaces of the grafted spheres and the residual surfaces of the cotton fibers. These two types of fabrics, coated by the block copolymer alone or by the polymer nanospheres and then the copolymer, were characterized by scanning electron microscope (SEM), Fourier transform infrared spectroscopy (FT-IR), and water repellency analyses. A comprehensive comparative study was made of their performances in oil-water separation. Finally, a fluorinated ABC triblock copolymer poly(acrylic acid)-block-poly(2-cinnamoyloxyethyl methacrylate)-block-poly(2-perfluorooctylethyl methacrylate) (PAA-b-PCEMA-b-PFOEMA) was used to iii encapsulate air nanobubbles. The produced air nanobubbles were thermodynamically stable in water and were some 100 times more stable than commercially available perfluorocarbon-filled microbubbles under ultrasound. These nanobubbles, due to their small sizes and thus ability to permeate the capillary networks of organs and to reach tumors, may expand the applications of microbubbles in diagnostic ultrasonography and find new applications in ultrasound-regulated drug delivery.

Gravimetric and density profiling using the combination of surface acoustic waves and neutron reflectivity

A new approach is described herein, where neutron reflectivity measurements that probe changes in the density profile of thin films as they absorb material from the gas phase have been combined with a Love wave based gravimetric assay that measures the mass of absorbed material. This combination of techniques not only determines the spatial distribution of absorbed molecules, but also reveals the amount of void space within the thin film (a quantity that can be difficult to assess using neutron reflectivity measurements alone). The uptake of organic solvent vapours into spun cast films of polystyrene has been used as a model system with a view to this method having the potential for extension to the study of other systems. These could include, for example, humidity sensors, hydrogel swelling, biomolecule adsorption or transformations of electroactive and chemically reactive thin films. This is the first ever demonstration of combined neutron reflectivity and Love wave-based gravimetry and the experimental caveats, limitations and scope of the method are explored and discussed in detail.

Modifying the band gap and optical properties of Germanium nanowires by surface termination

Semiconductor nanowires, based on silicon (Si) or germanium (Ge) are leading candidates for many ICT applications, including next generation transistors, optoelectronics, gas and biosensing and photovoltaics. Key to these applications is the possibility to tune the band gap by changing the diameter of the nanowire. Ge nanowires of different diameter have been studied with H termination, but, using ideas from chemistry, changing the surface terminating group can be used to modulate the band gap. In this paper we apply the generalised gradient approximation of density functional theory (GGA-DFT) and hybrid DFT to study the effect of diameter and surface termination using –H, –NH2 and –OH groups on the band gap of (001), (110) and (111) oriented germanium nanowires. We show that the surface terminating group allows both the magnitude and the nature of the band gap to be changed. We further show that the absorption edge shifts to longer wavelength with the –NH2 and –OH terminations compared to the –H termination and we trace the origin of this effect to valence band modifications upon modifying the nanowire with –NH2 or –OH. These results show that it is possible to tune the band gap of small diameter Ge nanowires over a range of ca. 1.1 eV by simple surface chemistry.

Graphene Oxide: A Carrier For Pharmaceuticals And A Scaffold For Cell Interactions.

During the last ten years, graphene oxide has been explored in many applications due to its remarkable electroconductivity, thermal properties and mobility of charge carriers, among other properties. As discussed in this review, the literature suggests that a total characterization of graphene oxide must be conducted because oxidation debris (synthesis impurities) present in the graphene oxides could act as a graphene oxide surfactant, stabilizing aqueous dispersions. It is also important to note that the structure models of graphene oxide need to be revisited because of significant implications for its chemical composition and its direct covalent functionalization. Another aspect that is discussed is the need to consider graphene oxide surface chemistry. The hemolysis assay is recommended as a reliable test for the preliminary assessment of graphene oxide toxicity, biocompatibility and cell membrane interaction. More recently, graphene oxide has been extensively explored for drug delivery applications. An important increase in research efforts in this emerging field is clearly represented by the hundreds of related publications per year, including some reviews. Many studies have been performed to explore the graphene oxide properties that enable it to deliver more than one activity simultaneously and to combine multidrug systems with photothermal therapy, indicating that graphene oxide is an attractive tool to overcome hurdles in cancer therapies. Some strategic aspects of the application of these materials in cancer treatment are also discussed. In vitro studies have indicated that graphene oxide can also promote stem cell adhesion, growth and differentiation, and this review discusses the recent and pertinent findings regarding graphene oxide as a valuable nanomaterial for stem cell research in medicine. The protein corona is a key concept in nanomedicine and nanotoxicology because it provides a biomolecular identity for nanomaterials in a biological environment. Understanding protein corona-nanomaterial interactions and their influence on cellular responses is a challenging task at the nanobiointerface. New aspects and developments in this area are discussed.

The Coupled Aerosol and Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CATT-BRAMS) - Part 1: Model description and evaluation

We introduce the Coupled Aerosol and Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CATT-BRAMS). CATT-BRAMS is an on-line transport model fully consistent with the simulated atmospheric dynamics. Emission sources from biomass burning and urban-industrial-vehicular activities for trace gases and from biomass burning aerosol particles are obtained from several published datasets and remote sensing information. The tracer and aerosol mass concentration prognostics include the effects of sub-grid scale turbulence in the planetary boundary layer, convective transport by shallow and deep moist convection, wet and dry deposition, and plume rise associated with vegetation fires in addition to the grid scale transport. The radiation parameterization takes into account the interaction between the simulated biomass burning aerosol particles and short and long wave radiation. The atmospheric model BRAMS is based on the Regional Atmospheric Modeling System (RAMS), with several improvements associated with cumulus convection representation, soil moisture initialization and surface scheme tuned for the tropics, among others. In this paper the CATT-BRAMS model is used to simulate carbon monoxide and particulate material (PM(2.5)) surface fluxes and atmospheric transport during the 2002 LBA field campaigns, conducted during the transition from the dry to wet season in the southwest Amazon Basin. Model evaluation is addressed with comparisons between model results and near surface, radiosondes and airborne measurements performed during the field campaign, as well as remote sensing derived products. We show the matching of emissions strengths to observed carbon monoxide in the LBA campaign. A relatively good comparison to the MOPITT data, in spite of the fact that MOPITT a priori assumptions imply several difficulties, is also obtained.

Hybrid layer-by-layer assembly based on animal and vegetable structural materials: multilayered films of collagen and cellulose nanowhiskers

Layer-by-layer (LBL) assembly was used to combine crystalline rod-like nanoparticles obtained from a vegetable source, cellulose nanowhiskers (CNWs), with collagen, the main component of skin and connective tissue found exclusively in animals. The film growth of the multilayered collagen/CNW was monitored by UV-Vis spectroscopy and ellipsometry measurements, whereas the film morphology and surface roughness were characterized by SEM and AFM. UV-Vis spectra showed the deposition of the same amount of collagen, 5 mg m(-2), in each dipping cycle. Ellipsometry data showed an increment in thickness with the number of layers, and the average thickness of each bilayer was found to be 8.6 nm. The multilayered bio-based nanocomposites were formed by single layers of densely packed CNWs adsorbed on top of each thin collagen layer where the hydrogen bonding between collagen amide groups and OH groups of the CNWs plays a mandatory role in the build-up of the thin films. The approach used in this work represents a potential strategy to mimic the characteristics of natural extracellular matrix (ECM) which can be used for applications in the biomedical field.

Chromic materials for responsive surface-enhanced resonance Raman scattering systems: a nanometric pH sensor

The use of chromic materials for responsive surface-enhanced resonance Raman scattering (SERRS) based nanosensors is reported. The potential of nano-chromic SERRS is demonstrated with the use of the halochrome methyl yellow to fabricate an ultrasensitive pH optical sensor. Some of the challenges of the incorporation of chromic materials with metal nanostructures are addressed through the use of computational calculations and a comparison to measured SERRS and surface-enhanced Raman scattering (SERS) spectra is presented. A strong correlation between the measured SERRS and the medium's proton concentration is demonstrated for the pH range 2-6. The high sensitivity achieved by the use of resonance Raman conditions is shown through responsive SERRS measurements from only femtolitres of volume and with the concentration of the reporting molecules approaching the single molecule regime.

Relevance of leaf surface contamination for assessing chemical composition of bromeliads in a restinga forest

Resuspended soil and other airborne particles adhered to the leaf surface affect the chemical composition of the plant. A well-defined cleaning procedure is necessary to avoid this problem, providing a correct assessment of the inherent chemical composition of bromeliads. To evaluate the influence of a washing procedure, INAA was applied for determining chemical elements in the leaves of bromeliads from Vriesea carinata species, both non-washed and washed with Alconox, EDTA and bi-distilled water. Br, Ce, Hg, La, Sc, Se, Sm and Th showed higher mass fractions in non-washed leaves. The washing procedure removed the exogenous material without leaching chemical elements from inside the tissues.