Scientific Publications 2009
2009. "Adsorption of Amelogenin onto Self-Assembled and Fluoroapatite Surfaces." Journal of Physical Chemistry B 113(7):1833-1842. Abstract Abstract. The interactions of proteins at surfaces are of great importance to biomineralizaton processes and to the development and function of biomaterials. Amelogenin is a unique biomineralization protein because it self-assembles to form supramolecular structures called “nanospheres,” spherical aggregates of monomers that are 20-60 nm in diameter. Although the nanosphere quaternary structure has been observed in solution, the quaternary structure of amelogenin adsorbed onto surfaces is also of great interest because the surface structure is critical to its function. We report studies of the adsorption of the amelogenin onto self-assembled monolayers (SAMs) with COOH and CH3 end group functionality and single crystal fluoroapatite (FAP). Dynamic light scattering (DLS) experiments showed that the solutions contained nanospheres and aggregates of nanospheres. Protein adsorption onto the various substrates was evidenced by null ellipsometry, x-ray photoelectron spectroscopy (XPS), and external reflectance Fourier transform infrared spectroscopy (ERFTIR). Although only nanospheres were observed in solution, ellipsometry and atomic force microscopy (AFM) indicated that the protein adsorbates were much smaller structures than the original nanospheres, from monomers to small oligomers in size. Monomer adsorption was promoted onto the CH3 surfaces and small oligomer adsorption was promoted onto the COOH and FAP substrates. In some cases, remnants of the original nanospheres adsorbed as multilayers on top of the underlying subnanosphere layers. This work suggests that amelogenin can adsorb by the “shedding” or disassembling of substructures from the nanospheres onto substrates and indicates that amelogenin may have a range of possible quaternary structures depending on whether it is in solution or interacting with surfaces.
2009. "Changes in the quaternary structure of amelogenin when adsorbed onto surfaces." Biopolymers 91(2):103-107. doi:10.1002/bip.21095 Abstract The amelogenin protein is involved in the formation of highly controlled and anisotropic hydroxyapatite crystals in tooth enamel. Amelogenin is unique in that it self assembles to form supramolecular quaternary structures called “nanospheres,” spherical aggregates of amelogenin monomers typically 20-60 nm in diameter. Although nanospheres have been observed in solution, the quaternary structure of amelogenin adsorbed onto surfaces is not well known. A better understanding of the surface structure is of great importance, however, because the function of amelogenin depends on it. We report studies of the adsorption of amelogenin onto self-assembled monolayers (SAMs) containing COOH and CH3 end group functionality as well as single crystal fluoroapatite (FAP), a biologically relevant surface. The supramolecular structures of the protein in solution as determined by dynamic light scattering (DLS) were compared with the supramolecular structures of the protein physisorbed onto surfaces as studied by atomic force microscopy (AFM). We found that although our solutions contained only nanospheres of narrow size distribution, smaller structures such as monomers and dimers were observed onto both hydrophilic and hydrophobic surfaces. This suggests that amelogenin can adsorb onto surfaces as small structures that peel away or “shed” from the nanospheres that are present in solution.
2009. "EFFECTS OF INCOMPLETE MIXING ON MULTICOMPONENT REACTIVE TRANSPORT." Advances in Water Resources 32(11):1674-1679. Abstract Darcy scale description of multi-component reactive transport can significantly over-predict the extent of mixing-controlled reactions. In this letter we describe a systematic pore- and Darcy-scale study of multicomponent reactive transport for various Peclet ($Pe$) and Damkohler ($Da$) numbers. We used pore-scale models to parameterize and validate Darcy scale simulations. We found that for small $Pe$, the Darcy scale model of mixing-controlled reactions is accurate, but its accuracy deteriorates with increasing $Pe$. The dilution index was calculated based on the pore-scale simulations as a measure of the degree of true solute mixing (dilution) for different $Pe$. We found that true mixing decreases with increasing $Pe$. A strong correlation was found between the magnitude of the dilution index and the error in the Darcy scale model prediction. The error (over-prediction of the mass of a product of the mixing controlled reaction) increases with decreasing dilution index (reduced dilution).
2009. "A Seafloor Microbial Biome Hosted within Incipient Ferromanganese Crusts." Nature Geoscience 2(12):872-876. Abstract Unsedimented volcanic rocks exposed on the seafloor at ridge systems and Seamounts host complex, abundant and diverse microbial communities that are relatively cosmopolitan in distribution (Lysnes, Thorseth et al. 2004; Mason, Stingl et al. 2007; Santelli, Orcutt et al. 2008). The most commonly held hypothesis is that the energy released by the hydration, dissolution and oxidative alteration of volcanic glasses in seawater drives the formation of an ocean crust biosphere (Thorseth, Furnes et al. 1992; Fisk, Giovannoni et al. 1998; Furnes and Staudigel 1999). The combined thermodynamically favorable weathering reactions could theoretically support anywhere from 105 to 109 cells/gram of rock depending upon the metabolisms utilized and cellular growth rates and turnover (Bach and Edwards 2003; Santelli, Orcutt et al. 2008). Yet microbially-mediated basalt alteration and energy conservation has not been directly demonstrated on the seafloor. By using synchrotron-based x-ray microprobe mapping, x-ray absorption spectroscopy and high-resolution scanning and transmission electron microscopy observations of young volcanic glasses recovered from the outer flanks of Loihi Seamount, we intended to identify the initial rates and mechanisms of microbial basalt colonization and bioalteration. Instead, here we show that microbial biofilms are intimately associated with ferromanganese crusts precipitating onto basalt surfaces from cold seawater. Thus we hypothesize that microbial communities colonizing seafloor rocks are established and sustained by external inputs of potential energy sources, such as dissolved and particulate Fe(II), Mn(II) and organic matter, rather than rock dissolution.
2009. "A converse approach to the calculation of NMR shielding tensors." Journal of Chemical Physics 131(10):Article No.: 101101. doi:10.1063/1.3216028 Abstract We introduce an alternative approach to the first-principles calculation of NMR shielding tensors. These are obtained from the derivative of the orbital magnetization with respect to the application of a microscopic, localized magnetic dipole. The approach is simple, general, and can be applied to either isolated or periodic systems. Calculated results for simple hydrocarbons, crystalline diamond, and liquid water show very good agreement with established methods and experimental results.
2009. "NMR shifts for polycyclic aromatic hydrocarbons from first-principles." International Journal of Quantum Chemistry 109(14):3336-3342. doi:10.1002/qua.21941 Abstract We present first-principles, density-functional theory calculations of the NMR chemical shifts for polycyclic aromatic hydrocarbons, starting with benzene and increasing sizes up to the one- and two-dimensional infinite limits of graphene ribbons and sheets. Our calculations are performed using a combination of the recently developed theory of orbital magnetization in solids, and a novel approach to NMR calculations where chemical shifts are obtained from the derivative of the orbital magnetization with respect to a microscopic, localized magnetic dipole. Using these methods we study on equal footing the 1H and 13C shifts in benzene, pyrene, coronene, in naphthalene, anthracene, naphthacene, and pentacene, and finally in graphene, graphite, and an infinite graphene ribbon. Our results show very good agreement with experiments and allow us to characterize the trends for the chemical shifts as a function of system size.
2009. "N-15 NMR spectra of naturally abundant nitrogen in soil and aquatic natural organic matter samples of the International Humic Substances Society." Organic Geochemistry 40(4):484–499. doi:10.1016/j.orggeochem.2009.01.007 Abstract The naturally abundant nitrogen in soil and aquatic NOM samples from the International Humic Substances Society has been characterized by solid state CP/MAS ¹⁵N NMR. Soil samples include humic and fulvic acids from the Elliot soil, Minnesota Waskish peat and Florida Pahokee peat, as well as the Summit Hill soil humic acid and the Leonardite humic acid. Aquatic samples include Suwannee River humic, fulvic and reverse osmosis isolates, Nordic humic and fulvic acids and Pony Lake fulvic acid. Additionally, Nordic and Suwannee River XAD-4 acids and Suwannee River hydrophobic neutral fractions were analyzed. Similar to literature reports, amide/aminoquinone nitrogens comprised the major peaks in the solid state spectra of the soil humic and fulvic acids, along with heterocyclic and amino sugar/terminal amino acid nitrogens. Spectra of aquatic samples, including the XAD-4 acids, contain resolved heterocyclic nitrogen peaks in addition to the amide nitrogens. The spectrum of the nitrogen enriched, microbially derived Pony Lake, Antarctica fulvic acid, appeared to contain resonances in the region of pyrazine, imine and/or pyridine nitrogens, which have not been observed previously in soil or aquatic humic substances by ¹⁵N NMR. Liquid state ¹⁵N NMR experiments were also recorded on the Elliot soil humic acid and Pony Lake fulvic acid, both to examine the feasibility of the techniques, and to determine whether improvements in resolution over the solid state could be realized. For both samples, polarization transfer (DEPT) and indirect detection (¹H–¹⁵N gHSQC) spectra revealed greater resolution among nitrogens directly bonded to protons. The amide/aminoquinone nitrogens could also be observed by direct detection experiments.
2009. "Amorphous Molecular Organic Solids for Gas Adsorption." Angewandte Chemie International Edition 48(30):5492 –5495. Abstract We show that molecular organic compounds with large accessible internal cavities, as part of their rigid molecular structure, display exceptional ability for gas storage and separation in the amorphous solid state. This finding suggests for the first time that long-range molecular order is not a prerequisite for organic molecules to be engineered as porous materials
2009. "Transcriptional analysis of the unicellular, diazotrophic cyanobacterium Cyanothece sp. ATCC 51142 grown under short day/night cycles." Journal of Phycology 45(3):610-620. Abstract Cyanothece sp. strain ATCC 51142 is a unicellular, diazotrophic cyanobacterium that demonstrates extensive metabolic periodicities of photosynthesis, respiration and nitrogen fixation when grown under N2-fixing conditions. We have performed a global transcription analysis of this organism using 6 h light/dark cycles in order to determine the response of the cell to these conditions and to differentiate between diurnal and circadian regulated genes. In addition, we used a context-likelihood of relatedness (CLR) analysis with this data and those from two-day light/dark and light-dark plus continuous light experiments to better differentiate between diurnal and circadian regulated genes. Cyanothece sp. adapted in several ways to growth under short light/dark conditions. Nitrogen was fixed in every second dark period and only once in each 24 h period. Nitrogen fixation was strongly correlated to the energy status of the cells and glycogen breakdown and high respiration rates were necessary to provide appropriate energy and anoxic conditions for this process. We conclude that glycogen breakdown is a key regulatory step within these complex processes. Our results demonstrated that the main metabolic genes involved in photosynthesis, respiration, nitrogen fixation and central carbohydrate metabolism have strong (or total) circadian-regulated components. The short light/dark cycles enable us to identify transcriptional differences among the family of psbA genes, as well as the differing patterns of the hup genes, which follow the same pattern as nitrogenase genes, relative to the hox genes which displayed a diurnal, dark-dependent gene expression.
2009. "FT-ICR MS optimization for the analysis of intact proteins." International Journal of Mass Spectrometry 287(1-3 SP ISS):32-38. doi:10.1016/j.ijms.2008.10.010 Abstract Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) remains the technique of choice for the analysis of intact proteins from complex biological systems, i.e. top-down proteomics. Recently, we have implemented a compensated open cylindrical ion trapping cell into a 12 T FT-ICR mass spectrometer. This new cell has previously demonstrated improved sensitivity, dynamic range, and mass measurement accuracy for the analysis of relatively small tryptic peptides. These improvements are due to the improved trapping potential of the cell which is significantly closer to the ideal harmonic trapping potential. Here we report the instrument optimization for the analysis of large macro-molecular ions, such as proteins. Also, presented are first principle theoretical considerations to account for different optimum conditions for the analysis of large macro-molecules. The proposed high energy ion loss mechanism is further supported by experimental results of bovine ubiquitin and serum albumin. We find that the analysis of large macro-molecules can be significantly improved by the further reduction of pressure in the ion trapping cell. This will reduce the impact of the high energy ion loss mechanism and enable increased sensitivity and mass measurement accuracy to be realized without compromising resolution. Further, these results appear to be applicable to FTMS in general, and the high energy ion loss mechanism applies to Orbitrap mass analyzers as well.
2009. "Excitation, Ionization, and Desorption: How Sub-band gap Photons Modify the Structure of Oxide Nanoparticles." Journal of Physical Chemistry C 113(4):1274-1279. Abstract Nanoparticles of wide-band-gap materials MgO and CaO, subjected to low-intensity ultraviolet irradiation with 266 nm (4.66 eV) photons, emit hyperthermal oxygen atoms with kinetic energies up to ~ 0.4 eV. We use ab initio embedded cluster methods to study theoretically a variety of elementary photoinduced processes at both ideal and defect-containing surfaces of these nanoparticles and develop a mechanism for the desorption process. The proposed mechanism includes multiple local photoexcitations resulting in sequential formation of localized excitons, their ionization, and further excitations. It is suggested that judicious choice of sub-band-gap photon energies can be used to selectively modify surfaces of nanomaterials.
2009. "Analytical and computational approaches to define the Aspergillus niger secretome." Fungal Genetics and Biology : FG & B 46(1, Suppl. 1):S153-S160. doi:10.1016/j.fgb.2008.07.014 Abstract We used computational and mass spectrometric approaches to characterize the Aspergillus niger secretome. The 11,200 gene models predicted in the genome of A. niger strain ATCC 1015 were the data source for the analysis. Depending on the computational methods used, 691 to 881 proteins were predicted to be secreted proteins. We cultured A. niger in six different media and analyzed the extracellular proteins produced using mass spectrometry. A total of 222 proteins were identified, with 39 proteins expressed under all six conditions and 74 proteins expressed under only one condition. The secreted proteins identified by mass spectrometry were used to guide the correction of about 20 gene models. Additional analysis focused on extracellular enzymes of interest for biomass processing. Of the 63 glycoside hydrolases predicted to be capable of hydrolyzing cellulose, hemicellulose or pectin, 94% of the exo-acting enzymes and only 18% of the endo-acting enzymes were experimentally detected.