Showing 51 - 59 of 59 Items

Probing mucin-type O-linked glycosylation in living animals

Date: 2006-03-28

Creator: Danielle H. Dube, Jennifer A. Prescher, Chi M. Quang, Carolyn R. Bertozzi

Access: Open access

Changes in O-linked protein glycosylation are known to correlate with disease states but are difficult to monitor in a physiological setting because of a lack of experimental tools. Here, we report a technique for rapid profiling of O-linked glycoproteins in living animals by metabolic labeling with N-azidoacetylgalactosamine (GalNAz) followed by Staudinger ligation with phosphine probes. After injection of mice with a peracetylated form of GalNAz, azide-labeled glycoproteins were observed in a variety of tissues, including liver, kidney, and heart, in serum, and on isolated splenocytes. B cell glycoproteins were robustly labeled with GalNAz but T cell glycoproteins were not, suggesting fundamental differences in glycosylation machinery or metabolism. Furthermore, GalNAz-labeled B cells could be selectively targeted with a phosphine probe by Staudinger ligation within the living animal. Metabolic labeling with GalNAz followed by Staudinger ligation provides a means for proteomic analysis of this posttranslational modification and for identifying O-linked glycoprotein fingerprints associated with disease. © 2006 by The National Academy of Sciences of the USA.


Quantitative estimation of localization errors of 3 d transition metal pseudopotentials in diffusion Monte Carlo

Date: 2017-07-14

Creator: Allison L. Dzubak, Jaron T. Krogel, Fernando A. Reboredo

Access: Open access

The necessarily approximate evaluation of non-local pseudopotentials in diffusion Monte Carlo (DMC) introduces localization errors. We estimate these errors for two families of non-local pseudopotentials for the first-row transition metal atoms Sc-Zn using an extrapolation scheme and multideterminant wavefunctions. Sensitivities of the error in the DMC energies to the Jastrow factor are used to estimate the quality of two sets of pseudopotentials with respect to locality error reduction. The locality approximation and T-moves scheme are also compared for accuracy of total energies. After estimating the removal of the locality and T-moves errors, we present the range of fixed-node energies between a single determinant description and a full valence multideterminant complete active space expansion. The results for these pseudopotentials agree with previous findings that the locality approximation is less sensitive to changes in the Jastrow than T-moves yielding more accurate total energies, however not necessarily more accurate energy differences. For both the locality approximation and T-moves, we find decreasing Jastrow sensitivity moving left to right across the series Sc-Zn. The recently generated pseudopotentials of Krogel et al. [Phys. Rev. B 93, 075143 (2016)] reduce the magnitude of the locality error compared with the pseudopotentials of Burkatzki et al. [J. Chem. Phys. 129, 164115 (2008)] by an average estimated 40% using the locality approximation. The estimated locality error is equivalent for both sets of pseudopotentials when T-moves is used. For the Sc-Zn atomic series with these pseudopotentials, and using up to three-body Jastrow factors, our results suggest that the fixed-node error is dominant over the locality error when a single determinant is used.


Recruiting the Host's Immune System to Target Helicobacter pylori's Surface Glycans

Date: 2013-04-01

Creator: Pornchai Kaewsapsak, Onyinyechi Esonu, Danielle H. Dube

Access: Open access

Due to the increased prevalence of bacterial strains that are resistant to existing antibiotics, there is an urgent need for new antibacterial strategies. Bacterial glycans are an attractive target for new treatments, as they are frequently linked to pathogenesis and contain distinctive structures that are absent in humans. We set out to develop a novel targeting strategy based on surface glycans present on the gastric pathogen Helicobacter pylori (Hp). In this study, metabolic labeling of bacterial glycans with an azide-containing sugar allowed selective delivery of immune stimulants to azide-covered Hp. We established that Hp's surface glycans are labeled by treatment with the metabolic substrate peracetylated N-azidoacetylglucosamine (Ac4GlcNAz). By contrast, mammalian cells treated with Ac4GlcNAz exhibited no incorporation of the chemical label within extracellular glycans. We further demonstrated that the Staudinger ligation between azides and phosphines proceeds under acidic conditions with only a small loss of efficiency. We then targeted azide-covered Hp with phosphines conjugated to the immune stimulant 2,4-dinitrophenyl (DNP), a compound capable of directing a host immune response against these cells. Finally, we report that immune effector cells catalyze selective damage in vitro to DNP-covered Hp in the presence of anti-DNP antibodies. The technology reported herein represents a novel strategy to target Hp based on its glycans. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Metabolic inhibitors of bacterial glycan biosynthesis

Date: 2020-02-21

Creator: Daniel A. Williams, Kabita Pradhan, Ankita Paul, Ilana R. Olin, Owen T., Tuck, Karen D. Moulton, Suvarn S. Kulkarni, Danielle H. Dube

Access: Open access

The bacterial cell wall is a quintessential drug target due to its critical role in colonization of the host, pathogen survival, and immune evasion. The dense cell wall glycocalyx contains distinctive monosaccharides that are absent from human cells, and proper assembly of monosaccharides into higher-order glycans is critical for bacterial fitness and pathogenesis. However, the systematic study and inhibition of bacterial glycosylation enzymes remains challenging. Bacteria produce glycans containing rare deoxy amino sugars refractory to traditional glycan analysis, complicating the study of bacterial glycans and the creation of glycosylation inhibitors. To ease the study of bacterial glycan function in the absence of detailed structural or enzyme information, we crafted metabolic inhibitors based on rare bacterial monosaccharide scaffolds. Metabolic inhibitors were assessed for their ability to interfere with glycan biosynthesis and fitness in pathogenic and symbiotic bacterial species. Three metabolic inhibitors led to dramatic structural and functional defects in Helicobacter pylori. Strikingly, these inhibitors acted in a bacteria-selective manner. These metabolic inhibitors will provide a platform for systematic study of bacterial glycosylation enzymes not currently possible with existing tools. Moreover, their selectivity will provide a pathway for the development of novel, narrow-spectrum antibiotics to treat infectious disease. Our inhibition approach is general and will expedite the identification of bacterial glycan biosynthesis inhibitors in a range of systems, expanding the glycochemistry toolkit.


Miniature of Synthesis and Metalation of a Bifunctional Ligand for Hydrogen Activation
Synthesis and Metalation of a Bifunctional Ligand for Hydrogen Activation
This record is embargoed.
    • Embargo End Date: 2028-05-18

    Date: 2023-01-01

    Creator: Eliana Roberts

    Access: Embargoed



      Miniature of Phenylisonitrile Ligand Synthesis and Coordination to Cobalt to Form a Catalyst for the Selective Dimerization of Linear Alpha Olefins
      Phenylisonitrile Ligand Synthesis and Coordination to Cobalt to Form a Catalyst for the Selective Dimerization of Linear Alpha Olefins
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      • Restriction End Date: 2026-06-01

        Date: 2023-01-01

        Creator: Colleen Hughes McAloon

        Access: Access restricted to the Bowdoin Community



          Miniature of An Exploration of the Room Temperature Growth and Tuning of Cobalt Hydroxide Carbonate Morphologies and Assemblies
          An Exploration of the Room Temperature Growth and Tuning of Cobalt Hydroxide Carbonate Morphologies and Assemblies
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          • Restriction End Date: 2026-06-01

            Date: 2023-01-01

            Creator: Zubin Jay Kenkare

            Access: Access restricted to the Bowdoin Community



              AMGSEFLamide, a member of a broadly conserved peptide family, modulates multiple neural networks in Homarus americanus

              Date: 2019-01-01

              Creator: Patsy S. Dickinson, Evyn S. Dickinson, Emily R. Oleisky, Cindy D. Rivera, Meredith E., Stanhope, Elizabeth A. Stemmler, J. Joe Hull, Andrew E. Christie

              Access: Open access

              Recent genomic/transcriptomic studies have identified a novel peptide family whose members share the carboxyl terminal sequence –GSEFLamide. However, the presence/identity of the predicted isoforms of this peptide group have yet to be confirmed biochemically, and no physiological function has yet been ascribed to any member of this peptide family. To determine the extent to which GSEFLamides are conserved within the Arthropoda, we searched publicly accessible databases for genomic/transcriptomic evidence of their presence. GSEFLamides appear to be highly conserved within the Arthropoda, with the possible exception of the Insecta, in which sequence evidence was limited to the more basal orders. One crustacean in which GSEFLamides have been predicted using transcriptomics is the lobster, Homarus americanus. Expression of the previously published transcriptome-derived sequences was confirmed by reverse transcription (RT)-PCR of brain and eyestalk ganglia cDNAs; mass spectral analyses confirmed the presence of all six of the predicted GSEFLamide isoforms – IGSEFLamide, MGSEFLamide, AMGSEFLamide, VMGSEFLamide, ALGSEFLamide and AVGSEFLamide – in H. americanus brain extracts. AMGSEFLamide, of which there are multiple copies in the cloned transcripts, was the most abundant isoform detected in the brain. Because the GSEFLamides are present in the lobster nervous system, we hypothesized that they might function as neuromodulators, as is common for neuropeptides. We thus asked whether AMGSEFLamide modulates the rhythmic outputs of the cardiac ganglion and the stomatogastric ganglion. Physiological recordings showed that AMGSEFLamide potently modulates the motor patterns produced by both ganglia, suggesting that the GSEFLamides may serve as important and conserved modulators of rhythmic motor activity in arthropods.


              Miniature of Evaluation of the Effectiveness of Probe Compounds at Predicting Anionic Pharmaceutical Sorption to Soils
              Evaluation of the Effectiveness of Probe Compounds at Predicting Anionic Pharmaceutical Sorption to Soils
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                  Date: 2021-01-01

                  Creator: Ben Cook

                  Access: Access restricted to the Bowdoin Community