Scientific Publications 2010
2010. "Constraint of DNA on Functionalized Graphene Improves Its Biostability and Specificity." Small 6(11):1205-1209. doi:10.1002/smll.201000024 Abstract The single-stranded DNA constrained on graphene surface is effectively protected from enzymatic cleavage by DNase I. The anisotropy, fluorescence, NMR, and CD studies suggest that the single-stranded DNA is promptly adsorbed onto graphene forming strong molecular interactions. Furthermore, the constraint of DNA probe on graphene improves the specificity of its response to complementary DNA. These findings will promote the further application of graphene in biotechnology and biomedical fields.
2010. "Sensitive Immunoassays of Nitrated Fibrinogen in Human Biofluids." Talanta 81(4-5):1662-1669. Abstract Three new sandwich immunoassays for detection of nitrated biomarker have been established with potential applications in biomedical studies and clinical practice. In this study, nitrated human fibrinogen, a potential oxidative stress biomarker for several pathologies, was chosen as the target. To improve the sensitivity and overcome the interference caused by the complexity of human biofluids, we developed three sandwich strategies using various combinations of primary antibody and secondary antibody. All three strategies demonstrated high sensitivity and selectivity towards nitrated forms of fibrinogen in buffer, but their performances were dramatically reduced when tested with human plasma and serum samples. Systematically optimizations were carried out to investigate the effects of numerous factors, including sampling, coating, blocking, and immunoreactions. Our final optimization results indicate that two of these strategies retain sufficient sensitivity and selectivity for use as assays in human physiological samples. Specifically, detection limits reached the pM level and the linear response ranges were up to nM level with a correlation coefficient > 0.99. To our best knowledge, this is the first example of using an electrochemical immunoassay for a nitrated biomarker in a physiological fluid. This novel approach provides a rapid, sensitive, selective, cost efficient and robust bioassay for detection of oxidative stress in pathology and for clinical applications. Moreover, the sandwich strategies developed in this paper can be readily used to establish effective methods targeting other nitration biomarkers.
2010. "The leucine rich amelogenin protein (LRAP) adsorbs as monomers or dimers onto surfaces." Journal of Structural Biology 169(3):266-276 . Abstract Amelogenin and amelogenin splice variants are believed to be involved in controlling the formation of the highly anisotropic and ordered hydroxyapatite crystallites that form enamel. The adsorption behavior of amelogenin proteins onto substrates is very important because protein-surface interactions are critical to it’s function. We have studied the adsorption of LRAP, a splice variant of amelogenin which may also contribute to enamel function, onto model self-assembled monolayers on gold containing of COOH, CH3, and NH2 end groups. Dynamic light scattering (DLS) experiments indicated that LRAP in phosphate buffered saline (PBS) and solutions at saturation with calcium phosphate contained aggregates of nanospheres. Null ellipsometry and atomic force microscopy (AFM) were used to study protein adsorption amounts and structures. Relatively high amounts of adsorption occurred onto the CH3 and NH2 surfaces from both calcium phosphate and PBS solutions. Adsorption was also promoted onto COOH surfaces when calcium was present in the solutions suggesting an interaction that involves calcium bridging with the negatively charged C-terminus. The ellipsometry and AFM studies suggested that the protein adsorbed onto all surfaces as LRAP monomers. We propose that the monomers adsorb onto the surfaces by disassembling or “shedding” from the nanospheres that are present in solution. This work reveals the importance of small subnanosphere-sized structures of LRAP at interfaces, structures that may be important in the biomineralization of tooth enamel.
2010. "Langevin Model for Reactive Transport in Porous Media." Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 82(2 PT 2):Art. No. 026302. Abstract A meso-scale stochastic Lagrangian particle model is presented and used to simulate conservative and reactive transport in porous media. In the stochastic model, the fluid flow in a porous continuum is governed by a combination of a Langevin equation and continuity equation. Pore-scale velocity fluctuations, the source of mechanical dispersion, are represented by the white noise. Molecular diffusion and sub-pore-scale Taylor-type dispersion is modeled by effective stochastic advection-diffusion equation.In the meso-scale stochastic model the molecular and sub-pore-scale Taylor type dispersion is modeled by stochastic advection-diffusion equation. The advective velocity (the solution of langevin flow equation) causes the mechanical dispersion of a solute. A smoothed particle hydrodynamics method was used to solve the meso-scale transport equations. The comparison of the meso-scale model with pore-scale and Darcy-scale models shows that: 1) for a wide range of Peclet numbers the meso-scale model predicts the mass of reaction product more accurately than the macro-scale model; 2) for small Peclet numbers predictions of both the meso-scale and the macro-scale models agree well with a prediction of the pore-scale model; 3)the accuracy of the meso-scale model deteriorates with the increasing Peclet number but more slowly than the accuracy of the macro-scale model. These results show that the separate treatment of advective and diffusive mixing in the stochastic transport model is more accurate than the classical advection-dispersion theory, which uses a single effective diffusion coefficient (the dispersion coefficient) to describe both types of mixing.
2010. "Micro and Mesoporous Metal Organic Frameworks for Catalysis Applications." Dalton Transactions 39(7):1692 - 1694. doi:10.1039/b921118g Abstract Micro and mesoporous metal-organic frameworks were synthesized using a single tetrahedral building block and their catalytic properties towards alkylation of toluene and biphenyl were demonstrated.
2010. "Two-dimensional liquid chromatography system for online top-down mass spectrometry." Proteomics 10(20):3610-3620. doi:10.1002/pmic.201000367 Abstract An online metal-free weak cation exchange-hydrophilic interaction liquid chromatography/reversed phase liquid chromatography (WCX-HILIC/RPLC) system has been developed for sensitive high-throughput top-down mass spectrometry. Analyzing posttranslational modifications (PTMs) of core histones, with focus on histone H4, tested the system. Using ~24 μg of core histones (H4, H2B, H2A and H3) purified from human fibroblasts, 41 H4 isoforms were identified, with the type and locations of PTMs unambiguously mapped for 20 of these variants. Compared to corresponding offline studies reported previously, online WCXHILIC/ RPLC platform offers significant improvement in sensitivity, with several orders of magnitude reduction in sample requirements and reduction in the overall analysis time. To the best of our knowledge, this study represents the first online two-dimensional (2D) LC-MS/MS characterization of core histone mixture at the intact protein level.
2010. "Metal-Organic Charge Transfer Can Produce BiradicalStates and is Mediated by Conical Intersections." Proceedings of the National Academy of Sciences of the United States of America 107(45):19139-19145. doi:10.1073/pnas.1010287107 Abstract The present paper illustrates key features of charge transfer between calcium atoms and prototype conjugated hydrocarbons (ethylene, benzene, and coronene) as elucidated by electronic structure calculations. One- and two-electron charge transfer is controlled by two sequential conical intersections. The two lowest electronic states that undergo a conical intersection have closedshell and open-shell dominant configurations correlating with the 4s2 and 4s13d1 states of Ca, respectively. Unlike the neutralionic state crossing in, for example, hydrogen halides or alkali halides, the path from separated reactants to the conical intersection region is uphill and the charge-transferred state is a biradical. The lowest-energy adiabatic singlet state shows at least two minima along a single approach path of Ca to the π system: (i) a van der Waals complex with a doubly occupied highest molecular orbital, denoted ϕ21 , and a small negative charge on Ca and (ii) an open-shell singlet (biradical) at intermediate approach (Ca⋯C distance ≈2.5–2.7 Å) with molecular orbital structure ϕ1ϕ2, where ϕ2 is an orbital showing significant charge transfer form Ca to the π-system, leading to a one-electron multicentered bond. A third minimum (iii) at shorter distances along the same path corresponding to a closed-shell state with molecular orbital structure ϕ22 has also been found; however, it does not necessarily represent the ground state at a given Ca⋯C distance in all three systems. The topography of the lowest adiabatic singlet potential energy surface is due to the one- and two-electron bonding patterns in Ca-π complexes.
2010. "Scanning Probe Direct-Write of Germanium Nanostructures." Advanced Materials 22(41):4639–4642. doi:10.1002/adma.201001987 Abstract Bottom-up nanostructure synthesis has played a pivotal role in the advancement of nanoscale science. This approach is typically less labor and energy intensive than its topdown counterpart because only the required amount of material is grown from a chosen precursor, rather than a macroscopic object being chiseled down to the desired size. However, device integration often requires complex manipulation steps for placing the synthesized nano-object in the appropriate location.
2010. "CD90/THY1 is over-expressed in prostate cancer-associated fibroblasts and could serve as a cancer biomarker." Modern Pathology 23(10):1346-1356. Abstract A by-product in the processing of prostate tissue for cell sorting by collagenase digestion is the media supernatant that remains after the cells are harvested. These supernatants contain proteins made by the cells within the tissue. Quantitative proteomic analysis of Nglycosylated proteins detected an increased amount of CD90/THY1 in cancer supernatants compared to non-cancer supernatants. Immunohistochemistry showed that in all carcinomas, regardless of Gleason grade, a layer of CD90-positive stromal fibroblastic cells, approximately 5-to-10 cells deep, was localized to tumor glands. In contrast, a no more than 1-cell wide girth of CD90-positive stromal cells was found around benign glands. The increased number of CD90-positive stromal cells in cancer correlated with overexpression of CD90 mRNA detected by gene expression analysis of stromal cells obtained by laser-capture microdissection. There is increasing evidence that cancer-associated stroma plays a role in both tumor progression and carcinogenesis. Most experiments to identify cancer biomarkers have focused on the cancer cells. CD90, being a marker for prostate cancer-associated stroma, might be a potential biomarker for this cancer. A non-invasive test could be provided by a urine test. Proteomic analysis of urine from patients with prostate cancer identified CD90; conversely, CD90 was not detected in the urine of post-prostatectomy patients. Furthermore, this urinary CD90 protein was a variant CD90 protein not known to be expressed by such cells as lymphocytes that express CD90. These CD90 results were obtained from ~90 cases consisting of proteomic analysis of tissue and urine, immunohistochemistry, Western blot analysis of tissue media, flow cytometry of cells from digested tissue, and reverse transcriptase polymerase chain reaction analysis of isolated stromal cells.
2010. "An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences." PLoS One 5(11):Article No.: e13968. doi:10.1371/journal.pone.0013968 Abstract Current methods in proteomics are dependent on the availability of sequenced genomes to identify proteins. However, genomic sequences are not always available for bacteria or microbial communities, even with high throughput sequencing technology becoming more readily available. Nevertheless, the homology that exists between related bacteria makes possible the extraction of meaningful biological information from an organism’s, or community’s proteome using the genomic sequence of a near neighbor. Here, a cross-organism search strategy was used to look at the amount of proteomics information obtainable with relative genetic distance from a near neighbor organism and to identify proteins in the proteome of minimally characterized environmental isolates. We conclude that closely related organisms with sequenced genomes, can be used to characterize proteomes of organisms with unsequenced genomes. In general, a cross-organism search strategy demonstrates the first step to use of sequences genomes to evaluate the proteomes of environmental bacteria and microbial communities that have no sequenced genome