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  1. Well–Tempered Gaussian Basis Sets [Download]

    Title: Well–Tempered Gaussian Basis Sets
    Creator: Mariusz Klobukowski
    Description: These basis sets were prepared using the new well-tempered formula introduced by S. Huzinaga and B. Miguel (Chem. Phys. Lett., 175 (1990) 289-291): ζ(N) = α ζ(N−k+1) = ζ(N−k+2) * β * [ 1+ γ (k/N)^δ ] , k = 2, ... ,N where α, β, γ, and δ are parameters (common for the radial functions of all angular symmetries) and N is the total number of exponential parameters generated by the formula. The parameters were optimized by minimizing the ground-state energy of an atom. The additional parameter of the well-tempered basis sets, that is, the pattern in which of the primitives are shared between the s-, p-, d-, and f-spaces, can be deduced from the Tables. The Tables are numbered by the atomic number; for the atoms for which more than one basis set was prepared, the Table number is appended with the running basis set index.
    Subjects: computational chemistry, Gaussian basis sets, well-tempered Gaussian basis sets
    Date Created: Tue 18 Apr 2017 12:08:23 MDT
  2. Protecting group-free immobilization of glycans for affinity chromatography using glycosylsulfonohydrazide donors [Download]

    Title: Protecting group-free immobilization of glycans for affinity chromatography using glycosylsulfonohydrazide donors
    Creator: Heranadez Armada, Daniel
    Description: A variety of applications in glycobiology exploit affinity chromatography through the immobilization of glycans to a solid support. Although several strategies are known, they may provide certain advantages or disadvantages in how the sugar is attached to the affinity matrix. Additionally, the products of some methods may be hard to characterize chemically due to non-specific reactions. The lack of specificity in standard immobilization reactions makes affinity chromatography with expensive oligosaccharides challenging. As a result, methods for specific and efficient immobilization of oligosaccharides remain of interest. Herein, we present a method for the immobilization of saccharides using N'-glycosylsulfonohydrazide (GSH) carbohydrate donors. We have compared GSH immobilization to known strategies, including the use of divinyl sulfone (DVS) and cyanuric chloride (CC), for the generation of affinity matrices. We compared immobilization methods by determining their immobilization efficiency, based on a comparison of the mass of immobilized carbohydrate and the concentration of active binding sites (determined using lectins). Our results indicate that immobilization using GSH donors can provide comparable amounts of carbohydrate epitopes on solid support while consuming almost half of the material required for DVS immobilization. The lectin binding capacity observed for these two methods suggests that GSH immobilization is more efficient. We propose that this method of oligosaccharide immobilization will be an important tool for glycobiologists working with precious glycan samples purified from biological sources.
    Subjects: carbohydrate chemistry, affinity chromatography, glycosidation
    Date Created: 2015-09-16
  3. Integrin-mediated cell migration is blocked by inhibitors of human neuraminidase [Download]

    Title: Integrin-mediated cell migration is blocked by inhibitors of human neuraminidase
    Creator: Jia, Feng
    Description: Integrins are critical receptors in cell migration and adhesion. A number of mechanisms are known to regulate the function of integrins, including phosphorylation, conformational change, and cytoskeletal anchoring. We investigated whether native neuraminidase (Neu, or sialidase) enzymes which modify glycolipids could play a role in regulating integrin-mediated cell migration. Using a scratch assay, we found that exogenously added Neu3 and Neu4 activity altered rates of cell migration. We observed that Neu4 increased the rate of migration in two cell lines (HeLa, A549); while Neu3 only increased migration in HeLa cells. A bacterial neuraminidase was able to increase the rate of migration in HeLa, but not in A549 cells. Treatment of cells with complex gangliosides (GM1, GD1a, GD1b, and GT1b) resulted in decreased cell migration rates, while LacCer was able to increase rates of migration in both lines. Importantly, our results show that treatment of cells with inhibitors of native Neu enzymes had a dramatic effect on the rates of cell migration. The most potent compound tested targeted the human Neu4 isoenzyme, and was able to substantially reduce the rate of cell migration. We found that the lateral mobility of integrins was reduced by treatment of cells with Neu3, suggesting that Neu3 enzyme activity resulted in changes to integrin–co-receptor or integrin–cytoskeleton interactions. Finally, our results support the hypothesis that inhibitors of human Neu can be used to investigate mechanisms of cell migration and for the development of anti-adhesive therapies.
    Subjects: biochemistry, cell biology, glycolipid, glycobiology, neuraminidase
    Date Created: 2016/06/22
  4. Application of chemometrics to the interpretation of analytical separations data [Download]

    Title: Application of chemometrics to the interpretation of analytical separations data
    Creator: Harynuk, J. J.
    Description: Interesting real-world samples are almost always present as mixtures containing the analyte(s) of interest and a matrix of components that are irrelevant to answering the analytical question at hand. Additionally, the compounds comprising the matrix are usually present in far greater abundance (both number and concentration) than the analytes of interest, making quantification or even detection of these analytes difficult if not impossible. When tasked with these types of samples, analysts turn to some form of separations technique such as gas or liquid chromatography (GC or LC) or capillary electrophoresis (CE) so that individual components in each sample may be quantified. More recently, more complex analytical questions are being probed, for example profiling blood or urine to identify a disease state or ascertaining the geographic origin of a food/beverage sample. These tasks often go beyond the simple quantification of one or two analytes in a sample. For these and other similar questions, separations scientists are turning more often to chemometric tools as a means of visualizing and interpreting the rich data that they obtain from their separations systems. Here we present a brief overview of separations approaches, with a focus on the data that are derived from different methods and on phenomena in the separations approach that lead to challenges in data interpretation. This is followed by a discussion of approaches that exist for the chemometric interpretation of separations data, specific challenges that arise in the chemometric treatment of these data, and solutions that have been implemented to deal with these challenges.
    Subjects: chemistry methodologies, chemometrics, separations data, analytics
    Date Created: 2012
  5. SEM Images of Block Copolymer Templated Patterns from PS-b-P2VP on Silicon with Platinum for Testing with ADAblock [Download]

    Title: SEM Images of Block Copolymer Templated Patterns from PS-b-P2VP on Silicon with Platinum for Testing with ADAblock
    Creator: Murphy, Jeffrey N.
    Description: Scanning electron microscope (SEM) images of patterns derived from polystyrene-block-poly(2-vinylpyridine), where the poly(2-vinylpyridine) domains replaced with platinum metal. All samples were annealed for 20 minutes at 200 degrees celsius. Polymers used include PS(23.6k)-b-P2VP(10.4k), PS(32.5k)-b-P2VP(12k), PS(34k)-b-P2VP(18k), PS(44k)-b-P2VP(18.5k), PS(50k)-b-P2VP(16.5k).
    Subjects: poly(2-vinylpyridine), nanomaterial, polymer, image, polystyrene, silicon, materials, surface, chemistry, electron micrograph, Buriak Lab, Block copolymer, SEM, self-assembly, pattern
    Date Created: 2014/07/05
  6. Epitope Specificities of the Groups Y and W-135 Polysaccharides of Neisseria meningitides. [Download]

    Title: Epitope Specificities of the Groups Y and W-135 Polysaccharides of Neisseria meningitides.
    Creator: Moore, S. L.
    Description: Previous studies have identified the length dependency of several polysaccharide (PS) protective epitopes. We have investigated whether meningococcal polysaccharides Y and W-135 possess such epitopes. Oligosaccharides (OSs) consisting of one or more disaccharide repeating units (RU) were derived from the capsular PSs of group Y and W-135 meningococci (GYMP and GWMP, respectively) by mild acid hydrolysis. The relative affinities of anticapsular antibodies binding to derivative OSs of different chain lengths were measured in inhibition enzyme-linked immunosorbent assays. As OS size increased from two to three RU, there was a notable increase in binding inhibition of rabbit anti-group Y antiserum. This pattern of antibody binding inhibition was also observed for rabbit antiserum to group W-135, though the inhibition increase was much more pronounced. In the cases of both OS species, the concentration of inhibiting antigen required to achieve 50% inhibition of rabbit immunoglobulin binding increased progressively as the inhibiting disaccharide chain length increased from 1 RU through greater than 50 RU. These data suggest that antibodies directed against both of these meningococcal PSs recognize conformational epitopes only fully expressed in higher-molecularweight forms of these antigens.
    Subjects: epitopes, bacterial immunology, polysaccharides, antigens
    Date Created: 2007
  7. Impact of the nature and size of the polymeric backbone on the ability of heterobifunctional ligands to mediate Shiga toxin and serum amyloid P component ternary complex formation. [Download]

    Title: Impact of the nature and size of the polymeric backbone on the ability of heterobifunctional ligands to mediate Shiga toxin and serum amyloid P component ternary complex formation.
    Creator: Kitov, P. I.
    Description: Inhibition of AB(5)-type bacterial toxins can be achieved by heterobifunctional ligands (BAITs) that mediate assembly of supramolecular complexes involving the toxin's pentameric cell membrane-binding subunit and an endogenous protein, serum amyloid P component, of the innate immune system. Effective in vivo protection from Shiga toxin Type 1 (Stx1) is achieved by polymer-bound, heterobifunctional inhibitors-adaptors (PolyBAITs), which exhibit prolonged half-life in circulation and by mediating formation of face-to-face SAP-AB(5) complexes, block receptor recognition sites and redirect toxins to the spleen and liver for degradation. Direct correlation between solid-phase activity and protective dose of PolyBAITs both in the cytotoxicity assay and in vivo indicate that the mechanism of protection from intoxication is inhibition of toxin binding to the host cell membrane. The polymeric scaffold influences the activity not only by clustering active binding fragments but also by sterically interfering with the supramolecular complex assembly. Thus, inhibitors based on N-(2-hydroxypropyl) methacrylamide (HPMA) show significantly lower activity than polyacrylamide-based analogs. The detrimental steric effect can partially be alleviated by extending the length of the spacer, which separates pendant ligand from the backbone, as well as extending the spacer, which spans the distance between binding moieties within each heterobifunctional ligand. Herein we report that polymer size and payload of the active ligand had moderate effects on the inhibitor's activity.
    Subjects: E. coli O157:H7, Pk-trisaccharide, receptors, multivalent inhibitors, ligands, toxins, cell-mediated cytotoxicity, Gb3
    Date Created: 2011
  8. Self -adjuvanting Glycopeptide Conjugate Vaccine against Disseminated Candidiasis. [Download]

    Title: Self -adjuvanting Glycopeptide Conjugate Vaccine against Disseminated Candidiasis.
    Creator: Xin, H.
    Description: Our research on pathogenesis of disseminated candidiasis led to the discovery that antibodies specific for Candida albicans cell surface b-1, 2–mannotriose [b-(Man)3] protect mice. A 14 mer peptide Fba, which derived from the N-terminal portion of the C. albicans cytosolic/cell surface protein fructose-bisphosphate aldolase, was used as the glycan carrier and resulted in a novel synthetic glycopeptide vaccine b-(Man)3-Fba. By a dendritic cell-based immunization approach, this conjugate induced protective antibody responses against both the glycan and peptide parts of the vaccine. In this report, we modified the b-(Man)3-Fba conjugate by coupling it to tetanus toxoid (TT) in order to improve immunogenicity and allow for use of an adjuvant suitable for human use. By new immunization procedures entirely compatible with human use, the modified b- (Man)3-Fba-TT was administered either alone or as a mixture made with alum or monophosphoryl lipid A (MPL) adjuvants and given to mice by a subcutaneous (s.c.) route. Mice vaccinated with or, surprisingly, without adjuvant responded well by making robust antibody responses. The immunized groups showed a high degree of protection against a lethal challenge with C. albicans as evidenced by increased survival times and reduced kidney fungal burden as compared to control groups that received only adjuvant or DPBS buffer prior to challenge. To confirm that induced antibodies were protective, sera from mice immunized against the b-(Man)3-Fba-TT conjugate transferred protection against disseminated candidiasis to naı¨ve mice, whereas C. albicans-absorbed immune sera did not. Similar antibody responses and protection induced by the b- (Man)3-Fba-TT vaccine was observed in inbred BALB/c and outbred Swiss Webster mice. We conclude that addition of TT to the glycopeptide conjugate results in a self-adjuvanting vaccine that promotes robust antibody responses without the need for additional adjuvant, which is novel and represents a major step forward in vaccine design against disseminated candidiasis.
    Subjects: Candidiasis, glycopeptides, immunizaton, vaccination
    Date Created: 2012
  9. Density Doubling Image Equalization Macro for ImageJ [Download]

    Title: Density Doubling Image Equalization Macro for ImageJ
    Creator: Murphy, Jeffrey N.
    Description: In order to adapt images of patterns templated using block copolymers, acquired using a scanning electron microscope, for publication, an algorithm was developed to process the images, enhancing the darker features in a consistent and easily reproducible manner. This was done using ImageJ, a free and open source scientific image processing program. In order to maintain transparency in this process, the macro code is made available for inspection and use by others. Image equalization process description: SEM images of the double layer structures were enhanced to aid visualization of the darker structures templated by the lower-layer of cylinders by a process designed to “equalize” the image histogram as shown in Figure S8. A median filter with a 2-pixel radius was first applied over the image to reduce noise. It should be noted that good SEM images of double layer templated line structures ideally possess a trimodal histogram due to the varying intensities of structures templated from the upper and lower layers of cylinders, as contrasted with the substrate; using a median filter has the additional advantage of enhancing the separation of the three ranges of values (peaks in the histogram). Next, the brightness and contrast were automatically adjusted to expand the range of the histogram over the entire range of values (from 0 to 255 for these 8-bit images). Consequently, the bright lines (templated by the upper-layer cylinders) will have values near 255; the spaces between the lines having values near 0; and the darker lines (templated by the lower-layer cylinders) will have some intermediate value (in the case of Figure S8, the values are around 74). For increased contrast between the darker lines, templated by the lower layer, and the substrate, these intermediate pixel values were adjusted to have their intensity centered at approximately 128 by mapping the pixels to redistribute the intensity values using bi-linear interpolation based on the initial value found and selected for the darker lines.
    Subjects: image processing, scanning electron microscope, ImageJ, SEM, macro code, Block copolymer, Buriak Lab
    Date Created: 2011/11/30