Showing 1 - 50 of 67 Items

• Restriction End Date: 2025-06-01

Date: 2020-01-01

Creator: Katharine Toll

Access: Access restricted to the Bowdoin Community

Date: 2013-09-01

Creator: Kanokwan Champasa, Scott A. Longwell, Aimee M. Eldridge, Elizabeth A. Stemmler, Danielle H., Dube

Access: Open access

Virulence of the gastric pathogen Helicobacter pylori (Hp) is directly linked to the pathogen's ability to glycosylate proteins; for example, Hp flagellin proteins are heavily glycosylated with the unusual nine-carbon sugar pseudaminic acid, and this modification is absolutely essential for Hp to synthesize functional flagella and colonize the host's stomach. Although Hp's glycans are linked to pathogenesis, Hp's glycome remains poorly understood; only the two flagellin glycoproteins have been firmly characterized in Hp. Evidence from our laboratory suggests that Hp synthesizes a large number of as-yet unidentified glycoproteins. Here we set out to discover Hp's glycoproteins by coupling glycan metabolic labeling with mass spectrometry analysis. An assessment of the subcellular distribution of azide-labeled proteins by Western blot analysis indicated that glycoproteins are present throughout Hp and may therefore serve diverse functions. To identify these species, Hp's azide-labeled glycoproteins were tagged via Staudinger ligation, enriched by tandem affinity chromatography, and analyzed by multidimensional protein identification technology. Direct comparison of enriched azide-labeled glycoproteins with a mock-enriched control by both SDS-PAGE and mass spectrometry-based analyses confirmed the selective enrichment of azide-labeled glycoproteins. We identified 125 candidate glycoproteins with diverse biological functions, including those linked with pathogenesis. Mass spectrometry analyses of enriched azide-labeled glycoproteins before and after cleavage of O-linked glycans revealed the presence of Staudinger ligation-glycan adducts in samples only after beta-elimination, confirming the synthesis of O-linked glycoproteins in Hp. Finally, the secreted colonization factors urease alpha and urease beta were biochemically validated as glycosylated proteins via Western blot analysis as well as by mass spectrometry analysis of cleaved glycan products. These data set the stage for the development of glycosylation-based therapeutic strategies, such as new vaccines based on natively glycosylated Hp proteins, to eradicate Hp infection. Broadly, this report validates metabolic labeling as an effective and efficient approach for the identification of bacterial glycoproteins. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.

Date: 2009-04-15

Creator: Patsy S. Dickinson, Teerawat Wiwatpanit, Emily R. Gabranski, Rachel J. Ackerman, Jake S., Stevens, Christopher R. Cashman, Elizabeth A. Stemmler, Andrew E. Christie

Access: Open access

The allatostatins comprise three structurally distinct peptide families that regulate juvenile hormone production by the insect corpora allata. A-type family members contain the C-terminal motif -YXFGLamide and have been found in species from numerous arthropod taxa. Members of the B-type family exhibit a -WX6Wamide C-terminus and, like the A-type peptides, appear to be broadly conserved within the Arthropoda. By contrast, members of the C-type family, typified by the unblocked C-terminus -PISCF, a pyroglutamine blocked N-terminus, and a disulfide bridge between two internal Cys residues, have only been found in holometabolous insects, i.e. lepidopterans and dipterans. Here, using transcriptomics, we have identified SYWKQCAFNAVSCFamide (disulfide bridging predicted between the two Cys residues), a known honeybee and water flea C-typelike peptide, from the American lobster Homarus americanus (infraorder Astacidea). Using matrix assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS), a mass corresponding to that of SYWKQCAFNAVSCFamide was detected in the H. americanus brain, supporting the existence of this peptide and its theorized structure. Furthermore, SYWKQCAFNAVSCFamide was detected by MALDI-FTMS in neural tissues from five additional astacideans as well as 19 members of four other decapod infraorders (i.e. Achelata, Anomura, Brachyura and Thalassinidea), suggesting that it is a broadly conserved decapod peptide. In H. americanus, SYWKQCAFNAVSCFamide is capable of modulating the output of both the pyloric circuit of the stomatogastric nervous system and the heart. This is the first demonstration of bioactivity for this peptide in any species.

Date: 2010-07-21

Creator: Pamela V. Chang, Danielle H. Dube, Ellen M. Sletten, Carolyn R. Bertozzi

Access: Open access

Glycans can be imaged by metabolic labeling with azidosugars followed by chemical reaction with imaging probes; however, tissue-specific labeling is difficult to achieve. Here we describe a strategy for the use of a caged metabolic precursor that is activated for cellular metabolism by enzymatic cleavage. An N-azidoacetylmannosamine derivative caged with a peptide substrate for the prostate-specific antigen (PSA) protease was converted to cell-surface azido sialic acids in a PSA-dependent manner. The approach has applications in tissue-selective imaging of glycans for clinical and basic research purposes. © 2010 American Chemical Society.

Date: 2015-06-15

Creator: Bess Vlaisavljevich, Samuel O. Odoh, Sondre K. Schnell, Allison L. Dzubak, Kyuho, Lee, Nora Planas, Jeffrey B. Neaton, Laura Gagliardi, Berend Smit

Access: Open access

Using a combination of density functional theory and lattice models, we study the effect of CO2 adsorption in an amine functionalized metal-organic framework. These materials exhibit a step in the adsorption isotherm indicative of a phase change. The pressure at which this step occurs is not only temperature dependent but is also metal center dependent. Likewise, the heats of adsorption vary depending on the metal center. Herein we demonstrate via quantum chemical calculations that the amines should not be considered firmly anchored to the framework and we explore the mechanism for CO2 adsorption. An ammonium carbamate species is formed via the insertion of CO2 into the M-Namine bonds. Furthermore, we translate the quantum chemical results into isotherms using a coarse grained Monte Carlo simulation technique and show that this adsorption mechanism can explain the characteristic step observed in the experimental isotherm while a previously proposed mechanism cannot. Furthermore, metal analogues have been explored and the CO2 binding energies show a strong metal dependence corresponding to the M-Namine bond strength. We show that this difference can be exploited to tune the pressure at which the step in the isotherm occurs. Additionally, the mmen-Ni2(dobpdc) framework shows Langmuir like behavior, and our simulations show how this can be explained by competitive adsorption between the new model and a previously proposed model.

Date: 2010-08-01

Creator: Sedat H. Beis, Saikrishna Mukkamala, Nathan Hill, Jincy Joseph, Cirila, Baker, Bruce Jensen, Elizabeth A. Stemmler, M. Clayton Wheeler, Brian G. Frederick

Access: Open access

Three lignins: Indulin AT, Lignoboost™, and Acetocell lignin, were characterized and pyrolyzed in a continuous-fed fast pyrolysis process. The physical and chemical properties of the lignins included chemical composition, heat content, ash, and water content. The distributed activation energy model (DAEM) was used to describe the pyrolysis of each lignin. Activation energy distributions of each lignin were quite different and generally covered a broad range of energies, typically found in lignins. Process yields for initial continuous-fed fast pyrolysis experiments are reported. Bio-oil yield was low, ranging from 16 to 22%. Under the fast pyrolysis conditions used, the Indulin AT and Lignoboost™ lignin yielded slightly more liquid product than the Acetocell lignin. Lignin kinetic parameters and chemical composition vary considerably and fast pyrolysis processes must be specified for each type of lignin.

Date: 2013-02-01

Creator: Scott A. Longwell, Danielle H. Dube

Access: Open access

Bacterial glycoproteins represent an attractive target for new antibacterial treatments, as they are frequently linked to pathogenesis and contain distinctive glycans that are absent in humans. Despite their potential therapeutic importance, many bacterial glycoproteins remain uncharacterized. This review focuses on recent advances in deciphering the bacterial glycocode, including metabolic glycan labeling to discover and characterize bacterial glycoproteins, lectin-based microarrays to monitor bacterial glycoprotein dynamics, crosslinking sugars to assess the roles of bacterial glycoproteins, and harnessing bacterial glycosylation systems for the efficient production of industrially important glycoproteins. © 2012 Elsevier Ltd.

Date: 2014-05-01

Creator: Peyton C Morss

Access: Access restricted to the Bowdoin Community

Date: 2023-01-01

Creator: Jack R Callahan

Access: Access restricted to the Bowdoin Community

Date: 2023-01-01

Creator: Mariah McKenzie

Access: Access restricted to the Bowdoin Community

Date: 2021-06-01

Creator: Tom Ichibha, Allison L. Dzubak, Jaron T. Krogel, Valentino R. Cooper, Fernando A., Reboredo

Access: Open access

CrI3 has recently been shown to exhibit low-dimensional, long-range magnetic ordering from few layers to single layers of CrI3. The properties of CrI3 bulk and few-layered systems are uniquely defined by a combination of short-range intralayer and long-range interlayer interactions, including strong correlations, exchange, and spin-orbit coupling. Unfortunately, both the long-range van der Waals interactions, which are driven by dynamic, many-body electronic correlations, and the competing strong intralayer correlations, present a formidable challenge for the local or semilocal mean-field approximations employed in workhorse electronic structure approaches like density-functional theory. In this paper we employ a sophisticated many-body approach that can simultaneously describe long- and short-range correlations. We establish that the fixed-node diffusion Monte Carlo (FNDMC) method reproduces the experimental interlayer separation distance of bulk CrI3 for the high-temperature monoclinic phase with a reliable prediction of the interlayer binding energy. We subsequently employed the FNDMC results to benchmark the accuracy of several density-functional theory exchange-correlation approximations.

Date: 2019-06-18

Creator: Peter Schwerdtfeger, Jeffrey K. Nagle

Access: Open access

A 2018 update of the most accurate calculated and experimental static dipole polarizabilities of the neutral atoms in the Periodic Table from nuclear charge Z = 1 to 120 is given. Periodic trends are analyzed and discussed.

Date: 2007-06-01

Creator: Elizabeth A. Stemmler, Braulio Peguero, Emily A. Bruns, Patsy S. Dickinson, Andrew E., Christie

Access: Open access

In most invertebrates, multiple species-specific isoforms of tachykinin-related peptide (TRP) are common. In contrast, only a single conserved TRP isoform, APSGFLGMRamide, has been documented in decapod crustaceans, leading to the hypothesis that it is the sole TRP present in this arthropod order. Previous studies of crustacean TRPs have focused on neuronal tissue, but the recent demonstration of TRPs in midgut epithelial cells in Cancer species led us to question whether other TRPs are present in the gut, as is the case in insects. Using direct tissue matrix assisted laser desorption/ionization Fourier transform mass spectrometry, in combination with sustained off-resonance irradiation collision-induced dissociation, we found that at least one additional TRP is present in Cancer irroratus, Cancer borealis, Cancer magister, and Cancer productus. The novel TRP isoform, TPSGFLGMRamide, was present not only in the midgut, but also in the stomatogastric nervous system (STNS). In addition, we identified an unprocessed TRP precursor APSGFLGMRG, which was detected in midgut tissues only. TRP immunohistochemistry, in combination with preadsorption studies, suggests that APSGFLGMRamide and TPSGFLGMRamide are co-localized in the stomatogastric ganglion (STG), which is contained within the STNS. Exogenous application of TPSGFLGMRamide to the STG elicited a pyloric motor pattern that was identical to that elicited by APSGFLGMRamide, whereas APSGFLGMRG did not alter the pyloric motor pattern. © 2007 The Authors.

Date: 2020-01-01

Creator: Julia Hazlitt Morris

Access: Access restricted to the Bowdoin Community

Date: 2021-01-01

Creator: Gabrielle Vandendries

Access: Open access

Photoacids, compounds that undergo excited state proton transfer (ESPT), have been utilized in different solar energy and lithographic applications.1, 2 The addition of functional groups and solvent can both change the ESPT mechanism of photoacids. In this study, the effect of solvent on the ESPT mechanism was explored using a model diprotic photoacid, 8-amino-2-naphthol (8N2OH). The photochemistry of 8N2OH in water and common nonaqueous solvents, acetonitrile, tetrahydrofuran (THF), and methanol, were studied using UV/Vis absorption, steady-state emission, and time-correlated single photon counting (TCPSC) emission spectroscopy. The results were analyzed using the Kamlet-Taft parameters. It was found that the ESPT mechanism of the cation in water is different from the mechanism in acetonitrile and THF. In water the excited cation forms the zwitterion, i.e. the OH site undergoes ESPT, while in acetonitrile and THF, the excited cation forms the neutral species, i.e. the NH3+ site undergoes ESPT. No ESPT was observed for 8N2OH in methanol. The effect of solvent mixtures on photoacidity was also investigated using acetonitrile and water mixtures. The solvent effects were more subtle; the time-resolved emission measurements showed the greatest stabilization of the excited neutral 8N2OH species at 20/80% acetonitrile-water mixtures. Finally, the ability to extend the solvent studies to ionic liquids, 1-ethyl-3-methylimidazolium (Im) trifluromethanesulfonate (OTF), was demonstrated. The combined studies reveal that solvent plays a large role in determining the ESPT mechanism and stabilization of 8N2OH.

Date: 2014-05-01

Creator: Nathan D Ricke

Access: Access restricted to the Bowdoin Community

• Embargo End Date: 2027-05-19

Date: 2022-01-01

Creator: Oliver M. Nix

Access: Embargoed

Date: 2016-05-01

Creator: Kasidet Trerayapiwat

Access: Open access

Understanding the changes in molecular electronic structure following the absorption of light is a fundamental challenge for the goal of predicting photochemical rates and mechanisms. Proposed here is a systematic benchmarking method to evaluate accuracy of a model to quantitatively predict photo-degradation of small organic molecules in aquatic environments. An overview of underlying com- putational theories relevant to understanding sunlight-driven electronic processes in organic pollutants is presented. To evaluate the optimum size of solvent sphere, molecular Dynamics and Time Dependent Density Functional Theory (MD-TD-DFT) calculations of an aniline molecule in di↵erent numbers of water molecules using CAM-B3LYP functional yielded excited state energy and oscillator strength values, which were compared with data from experimental absorption spectra. For the first time, a statistical method of comparing experimental and theoretical data is proposed. Underlying Gaussian functions of absorption spectra were deconvoluted and integrated to calculate experimental oscillator strengths. A Matlab code written by Soren Eustis was utilized to decluster MD-TD-DFT results. The model with 256 water molecules was decided to give the most accurate results with optimized com- putational cost and accuracy. MD-TD-DFT calculations were then performed on aniline, 3-F-aniline, 4-F-aniline, 3-Cl-aniline, 4-MeOacetophenone, and (1,3)-dimethoxybenzophenone with CAM-B3LYP, PBE0, M06-2X, LCBLYP, and BP86 functionals. BP86 functional was determined to be the best functional. Github repository: https://github.com/eustislab/MD_Scripts

Date: 2025-01-01

Creator: Nadia E. Puente

Access: Access restricted to the Bowdoin Community

Date: 2010-12-01

Creator: Danielle H. Dube, Bin Li, Ethan J. Greenblatt, Sadeieh Nimer, Amanda K., Raymond, Jennifer J. Kohler

Access: Open access

Interactions of transcriptional activators are difficult to study using transcription-based two-hybrid assays due to potent activation resulting in false positives. Here we report the development of the Golgi two-hybrid (G2H), a method that interrogates protein interactions within the Golgi, where transcriptional activators can be assayed with negligible background. The G2H relies on cell surface glycosylation to report extracellularly on protein-protein interactions occurring within the secretory pathway. In the G2H, protein pairs are fused to modular domains of the reporter glycosyltransferase, Och1p, and proper cell wall formation due to Och1p activity is observed only when a pair of proteins interacts. Cells containing interacting protein pairs are identified by selectable phenotypes associated with Och1p activity and proper cell wall formation: cells that have interacting proteins grow under selective conditions and display weak wheat germ agglutinin (WGA) binding by flow cytometry, whereas cells that lack interacting proteins display stunted growth and strong WGA binding. Using this assay, we detected the interaction between transcription factor MyoD and its binding partner Id2. Interfering mutations along the MyoD:Id2 interaction interface ablated signal in the G2H assay. Furthermore, we used the G2H to detect interactions of the activation domain of Gal4p with a variety of binding partners. Finally, selective conditions were used to enrich for cells encoding interacting partners. The G2H detects protein-protein interactions that cannot be identified via traditional two-hybrid methods and should be broadly useful for probing previously inaccessible subsets of the interactome, including transcriptional activators and proteins that traffic through the secretory pathway. © 2010 Dube et al.

Date: 2020-12-11

Creator: Karen D. Moulton, Adedunmola P. Adewale, Hallie A. Carol, Sage A. Mikami, Danielle H., Dube

Access: Open access

Bacterial cell surface glycans are quintessential drug targets due to their critical role in colonization of the host, pathogen survival, and immune evasion. The dense cell envelope glycocalyx contains distinctive monosaccharides that are stitched together into higher order glycans to yield exclusively bacterial structures that are critical for strain fitness and pathogenesis. However, the systematic study and inhibition of bacterial glycosylation enzymes remains challenging. Bacteria produce glycans containing rare sugars refractory to traditional glycan analysis, complicating the study of bacterial glycans and the identification of their biosynthesis machinery. To ease the study of bacterial glycans in the absence of detailed structural information, we used metabolic glycan labeling to detect changes in glycan biosynthesis. Here, we screened wild-type versus mutant strains of the gastric pathogen Helicobacter pylori, ultimately permitting the identification of genes involved in glycoprotein and lipopolysaccharide biosynthesis. Our findings provide the first evidence that H. pylori protein glycosylation proceeds via a lipid carrier-mediated pathway that overlaps with lipopolysaccharide biosynthesis. Protein glycosylation mutants displayed fitness defects consistent with those induced by small molecule glycosylation inhibitors. Broadly, our results suggest a facile approach to screen for bacterial glycosylation genes and gain insight into their biosynthesis and functional importance, even in the absence of glycan structural information.

Date: 2016-12-16

Creator: Emily L. Clark, Madhu Emmadi, Katharine L. Krupp, Ananda R. Podilapu, Jennifer D., Helble, Suvarn S. Kulkarni, Danielle H. Dube

Access: Open access

Bacterial glycans contain rare, exclusively bacterial monosaccharides that are frequently linked to pathogenesis and essentially absent from human cells. Therefore, bacterial glycans are intriguing molecular targets. However, systematic discovery of bacterial glycoproteins is hampered by the presence of rare deoxy amino sugars, which are refractory to traditional glycan-binding reagents. Thus, the development of chemical tools that label bacterial glycans is a crucial step toward discovering and targeting these biomolecules. Here, we explore the extent to which metabolic glycan labeling facilitates the studying and targeting of glycoproteins in a range of pathogenic and symbiotic bacterial strains. We began with an azide-containing analog of the naturally abundant monosaccharide N-acetylglucosamine and discovered that it is not broadly incorporated into bacterial glycans, thus revealing a need for additional azidosugar substrates to broaden the utility of metabolic glycan labeling in bacteria. Therefore, we designed and synthesized analogs of the rare deoxy amino d-sugars N-acetylfucosamine, bacillosamine, and 2,4-diacetamido-2,4,6-trideoxygalactose and established that these analogs are differentially incorporated into glycan-containing structures in a range of pathogenic and symbiotic bacterial species. Further application of these analogs will refine our knowledge of the glycan repertoire in diverse bacteria and may find utility in treating a variety of infectious diseases with selectivity.

Date: 2018-07-01

Creator: Danielle H. Dube

Access: Open access

“Drug Discovery” is a 13-week lecture and laboratory-based course that was developed to introduce non-science majors to foundational chemistry and biochemistry concepts as they relate to the unifying theme of drug discovery. The first part of this course strives to build students' understanding of molecules, their properties, the differences that enable them to be separated from one another, and their abilities to bind to biological receptors and elicit physiological effects. After building students' molecular worldview, the course then focuses on four classes of drugs: antimicrobials, drugs that affect the mind, steroid-based drugs, and anti-cancer drugs. During each of these modules, an emphasis is placed on how understanding the basis of disease and molecular-level interactions empowers us to identify novel medicinal compounds. Periodic in class discussions based on articles pertinent to class topics ranging from the spread of antibiotic resistance, to the molecular basis of addiction, to rational drug design, are held to enable students to relate course material to pressing problems of national and daily concern. In addition to class time, weekly inquiry-based laboratories allow students to critically analyze data related to course concepts, and later in the semester give students an opportunity to design and implement their own experiments to screen for antimicrobial activity. This course provides students with an understanding of the importance of chemistry and biochemistry to human health while emphasizing the process, strategies, and challenges related to drug discovery. © 2018 by The International Union of Biochemistry and Molecular Biology, 46:327–335, 2018.

Date: 2020-01-01

Creator: Michael Harris

Access: Open access

A significant market share of modern plastics is held by long-chain hydrocarbon polymers, such as polyethylene and polypropylene, properties of which can be dramatically changed by addition of linear α-olefins. Production of linear α-olefins involves the creation of many unwanted byproducts, representing significant quantities of both economic and ecological waste. While catalysts have been designed to selectively produce industrially useful olefins, these catalysts often encounter challenges such as synthesis of other unwanted byproducts, slow reaction times, and difficulty of synthesis. Based on one such prior catalyst, we report here synthetic work towards a cobalt catalyst with a constrained N-heterocyclic carbene supporting ligand predicted to allow for more favorable product distributions. Synthesis of two precursors to a sterically unhindered N-heterocyclic carbene, as well as development of a synthetic protocol for the coordination of N,N’- dimethylimidazolium-2-carboxylate to Cp*Co(ethene)2 was completed. Activation of the precatalyst and preliminary catalytic experiments were performed, though abbreviated research periods made complete analysis impossible. Finally, we report evidence of the formation of a novel cobalt-NHC dimer as a temperature controlled byproduct of the desired catalyst synthesis.

• Restriction End Date: 2028-06-01

Date: 2023-01-01

Creator: Kevin Jairre Fleshman

Access: Access restricted to the Bowdoin Community

Date: 2013-09-01

Creator: Kanokwan Champasa, Scott A. Longwell, Aimee M. Eldridge, Elizabeth A. Stemmler, Danielle H., Dube

Access: Open access

Virulence of the gastric pathogen Helicobacter pylori (Hp) is directly linked to the pathogen's ability to glycosylate proteins; for example, Hp flagellin proteins are heavily glycosylated with the unusual nine-carbon sugar pseudaminic acid, and this modification is absolutely essential for Hp to synthesize functional flagella and colonize the host's stomach. Although Hp's glycans are linked to pathogenesis, Hp's glycome remains poorly understood; only the two flagellin glycoproteins have been firmly characterized in Hp. Evidence from our laboratory suggests that Hp synthesizes a large number of as-yet unidentified glycoproteins. Here we set out to discover Hp's glycoproteins by coupling glycan metabolic labeling with mass spectrometry analysis. An assessment of the subcellular distribution of azide-labeled proteins by Western blot analysis indicated that glycoproteins are present throughout Hp and may therefore serve diverse functions. To identify these species, Hp's azide-labeled glycoproteins were tagged via Staudinger ligation, enriched by tandem affinity chromatography, and analyzed by multidimensional protein identification technology. Direct comparison of enriched azide-labeled glycoproteins with a mock-enriched control by both SDS-PAGE and mass spectrometry-based analyses confirmed the selective enrichment of azide-labeled glycoproteins. We identified 125 candidate glycoproteins with diverse biological functions, including those linked with pathogenesis. Mass spectrometry analyses of enriched azide-labeled glycoproteins before and after cleavage of O-linked glycans revealed the presence of Staudinger ligation-glycan adducts in samples only after beta-elimination, confirming the synthesis of O-linked glycoproteins in Hp. Finally, the secreted colonization factors urease alpha and urease beta were biochemically validated as glycosylated proteins via Western blot analysis as well as by mass spectrometry analysis of cleaved glycan products. These data set the stage for the development of glycosylation-based therapeutic strategies, such as new vaccines based on natively glycosylated Hp proteins, to eradicate Hp infection. Broadly, this report validates metabolic labeling as an effective and efficient approach for the identification of bacterial glycoproteins. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.

Date: 2025-01-01

Creator: Brendan J. Hill

Access: Access restricted to the Bowdoin Community

Date: 2017-11-07

Creator: Allison L. Dzubak, Chandrima Mitra, Michael Chance, Stephen Kuhn, Gerald E., Jellison, Athena S. Sefat, Jaron T. Krogel, Fernando A. Reboredo

Access: Open access

MnNiO3 is a strongly correlated transition metal oxide that has recently been investigated theoretically for its potential application as an oxygen-evolution photocatalyst. However, there is no experimental report on critical quantities such as the band gap or bulk modulus. Recent theoretical predictions with standard functionals such as LDA+U and HSE show large discrepancies in the band gaps (about 1.23 eV), depending on the nature of the functional used. Hence there is clearly a need for an accurate quantitative prediction of the band gap to gauge its utility as a photocatalyst. In this work, we present a diffusion quantum Monte Carlo study of the bulk properties of MnNiO3 and revisit the synthesis and experimental properties of the compound. We predict quasiparticle band gaps of 2.0(5) eV and 3.8(6) eV for the majority and minority spin channels, respectively, and an equilibrium volume of 92.8 Å3, which compares well to the experimental value of 94.4 Å3. A bulk modulus of 217 GPa is predicted for MnNiO3. We rationalize the difficulty for the formation of ordered ilmenite-type structure with specific sites for Ni and Mn to be potentially due to the formation of antisite defects that form during synthesis, which ultimately affects the physical properties of MnNiO3.

Date: 2014-04-08

Creator: Van N. Tra, Danielle H. Dube

Access: Open access

A substantial obstacle to the existing treatment of bacterial diseases is the lack of specific probes that can be used to diagnose and treat pathogenic bacteria in a selective manner while leaving the microbiome largely intact. To tackle this problem, there is an urgent need to develop pathogen-specific therapeutics and diagnostics. Here, we describe recent evidence that indicates distinctive glycans found exclusively on pathogenic bacteria could form the basis of targeted therapeutic and diagnostic strategies. In particular, we highlight the use of metabolic oligosaccharide engineering to covalently deliver therapeutics and imaging agents to bacterial glycans. © 2014 The Partner Organisations.

Date: 2021-01-01

Creator: Chloe Renfro

Access: Open access

As global emissions of CO2 and other greenhouse gases rises, global warming persists as an imminent threat to the environment and every day lives. To reduce greenhouse gas emissions in the atmosphere, there is a need to design materials to separate and capture the different gasses. Current gas capturing technologies lack efficiency and have extensive energy costs. A class of materials for CO2 capture is Molecular Organic Frameworks (MOFs). In order for a MOF to be efficient for this type of separation, the MOF needs to be able to selectively bind to the gas, while also not suffering a high energy cost to remove the gas and reuse the material. Computationally calculated binding energies are used to determine the usefulness of a MOF at capture and separation of a certain gas. Each computational method has its advantages and limitations. In this work, diffusion quantum Monte Carlo is being explored. This paper focuses on the accuracy of recently developed pseudopotentials for DMC use. These pseudopotentials have been tested on smaller molecules but have not been systematically tested for systems such as MOFs. Results from a DMC calculation of Zn-MOF-74 show a binding energy of -18.02 kJ/mol with an error bound of 16.74 kJ/mol. In order to assess the accuracy of the DMC results for binding energies of this magnitude the uncertainty need to be reduced, a subject of ongoing work.

• Embargo End Date: 2027-05-19

Date: 2022-01-01

Creator: Alexander Avrom Kreines

Access: Embargoed

• Restriction End Date: 2027-06-01

Date: 2024-01-01

Creator: Oliver Wang

Access: Access restricted to the Bowdoin Community

Date: 2020-12-01

Creator: Andrew E. Christie, Cindy D. Rivera, Catherine M. Call, Patsy S. Dickinson, Elizabeth A., Stemmler, J. Joe Hull

Access: Open access

Over the past decade, in silico genome and transcriptome mining has led to the identification of many new crustacean peptide families, including the agatoxin-like peptides (ALPs), a group named for their structural similarity to agatoxin, a spider venom component. Here, analysis of publicly accessible transcriptomes was used to expand our understanding of crustacean ALPs. Specifically, transcriptome mining was used to investigate the phylogenetic/structural conservation, tissue localization, and putative functions of ALPs in decapod species. Transcripts encoding putative ALP precursors were identified from one or more members of the Penaeoidea (penaeid shrimp), Sergestoidea (sergestid shrimps), Caridea (caridean shrimp), Astacidea (clawed lobsters and freshwater crayfish), Achelata (spiny/slipper lobsters), and Brachyura (true crabs), suggesting a broad, and perhaps ubiquitous, conservation of ALPs in decapods. Comparison of the predicted mature structures of decapod ALPs revealed high levels of amino acid conservation, including eight identically conserved cysteine residues that presumably allow for the formation of four identically positioned disulfide bridges. All decapod ALPs are predicted to have amidated carboxyl-terminals. Two isoforms of ALP appear to be present in most decapod species, one 44 amino acids long and the other 42 amino acids in length, both likely generated by alternative splicing of a single gene. In carideans, a gene or terminal exon duplication appears to have occurred, with alternative splicing producing four ALPs, two 44 and two 42 amino acid isoforms. The identification of ALP precursor-encoding transcripts in nervous system-specific transcriptomes (e.g., Homarus americanus brain, eyestalk ganglia, and cardiac ganglion assemblies, finding confirmed using RT-PCR) suggests that members of this peptide family may serve as locally-released and/or hormonally-delivered neuromodulators in decapods. Their detection in testis- and hepatopancreas-specific transcriptomes suggests that members of the ALP family may also play roles in male reproduction and innate immunity/detoxification.

Date: 2019-10-01

Creator: Patsy S. Dickinson, Heidi M. Samuel, Elizabeth A. Stemmler, Andrew E. Christie

Access: Open access

The SIFamides are a broadly conserved arthropod peptide family characterized by the C-terminal motif –SIFamide. In decapod crustaceans, two isoforms of SIFamide are known, GYRKPPFNGSIFamide (Gly1-SIFamide), which is nearly ubiquitously conserved in the order, and VYRKPPFNGSIFamide (Val1-SIFamide), known only from members of the astacidean genus Homarus. While much work has focused on the identification of SIFamide isoforms in decapods, there are few direct demonstrations of physiological function for members of the peptide family in this taxon. Here, we assessed the effects of Gly1- and Val1-SIFamide on the cardiac neuromuscular system of two closely related species of Cancer crab, Cancer borealis and Cancer irroratus. In each species, both peptides were cardioactive, with identical, dose-dependent effects elicited by both isoforms in a given species. Threshold concentrations for bioactivity are in the range typically associated with hormonal delivery, i.e., 10−9 to 10−8 M. Interestingly, and quite surprisingly, while the predicted effects of SIFamide on cardiac output are similar in both C. borealis and C. irroratus, frequency effects predominate in C. borealis, while amplitude effects predominate in C. irroratus. These findings suggest that, while SIFamide is likely to increase cardiac output in both crabs, the mechanism through which this is achieved is different in the two species. Immunohistochemical/mass spectrometric data suggest that SIFamide is delivered to the heart hormonally rather than locally, with the source of hormonal release being midgut epithelial endocrine cells in both Cancer species. If so, midgut-derived SIFamide may function as a regulator of cardiac output during the process of digestion.

Date: 2007-05-15

Creator: Elizabeth A. Stemmler, Emily A. Bruns, Noah P. Gardner, Patsy S. Dickinson, Andrew E., Christie

Access: Open access

In invertebrates, peptides possessing the carboxy (C)-terminal motif -RXRFamide have been proposed as the homologs of vertebrate neuropeptide Y (NPY). Using matrix assisted laser desorption/ionization mass spectrometry, in combination with sustained off-resonance irradiation collision-induced dissociation and chemical and enzymatic reactions, we have identified the peptide pEGFYSQRYamide from the neuroendocrine pericardial organ (PO) of the crab Pugettia producta. This peptide is likely the same as that previously reported, but misidentified, as PAFYSQRYamide in several earlier reports (e.g. [Li, L., Kelley, W.P., Billimoria, C.P., Christie, A.E., Pulver, S.R., Sweedler, J.V., Marder, E. 2003. Mass spectrometric investigation of the neuropeptide complement and release in the pericardial organs of the crab, Cancer borealis. J. Neurochem. 87, 642-656; Fu, Q., Kutz, K.K., Schmidt, J.J., Hsu, Y.W., Messinger, D.I., Cain, S.D., de la Iglesia, H.O., Christie, A.E., Li, L. 2005. Hormone complement of the Cancer productus sinus gland and pericardial organ: an anatomical and mass spectrometric investigation. J. Comp. Neurol. 493, 607-626.]). The -QRYamide motif contained in pEGFYSQRYamide is identical to that present in many vertebrate members of the NPY superfamily. Mass spectrometric analysis conducted on the POs of several other decapods showed that pEGFYSQRYamide is present in three other brachyurans (Cancer borealis, Cancer irroratus and Cancer productus) as well as in one species from another decapod infraorder (Lithodes maja, an anomuran). Thus, our findings show that at least some invertebrates possess NPY-like peptides in addition to those exhibiting an -RXRFamide C-terminus, and raise the question as to whether the invertebrate -QRYamides are functionally and/or evolutionarily related to the NPY superfamily. © 2007 Elsevier Inc. All rights reserved.

Date: 2025-01-01

Creator: Rhys Edwards

Access: Access restricted to the Bowdoin Community

Date: 2025-01-01

Creator: Philip Spyrou

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Date: 2025-01-01

Creator: Runqin Chen

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Date: 2022-01-01

Creator: Francesca Ann Cawley

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• Restriction End Date: 2027-06-01

Date: 2022-01-01

Creator: Jeffrey Charles Price

Access: Access restricted to the Bowdoin Community

Date: 2015-05-01

Creator: Amanda Howard

Access: Open access

Neuropeptides are small signaling molecules found throughout the nervous system that influence animal behavior. Using the American lobster, Homarus americanus, as a model system, this research focused on an allatostatin type-C (AST-C) peptide, pQIRYHQCYFNPISCF (disulfide bond between underlined cysteine residues), and a structurally similar crustacean peptide, SYWKQCAFNAVSCFamide. These neuropeptides influence cardiac muscle contraction patterns and stomatogastric nervous system activity in the lobster. To understand their roles, this study sought to develop a method to quantify peptides in the pericardial organ (PO) and other crustacean tissues. Overall analysis involved microdissection to isolate tissues, tissue extraction, extract purification and concentration, and analysis by chip-based nano-electrospray ionization-liquid chromatography-mass spectrometry (nanoESI-LC-MS). In the present study, pQIRYHQCYFNPISCF was identified in the PO. To quantify target peptides, internal standards were tested as recovery and calibration references. However, experiments with pQIRYHQCYFNPISCF and other peptides showed evidence of adsorptive losses during sample preparation and analysis, with improvements in recovery resulting from the use of isopropanol-prewashed polypropylene vials. Preliminary results also suggested that introducing polyethylene glycol (PEG) in solution reduced adsorptive losses for hydrophobic peptides, but may have compromised hydrophilic peptide detection. Future directions include characterizing other sources of analyte loss and developing techniques to recover these signals. Since both target peptides as detected in the lobster are post-translationally modified, other directions include identifying modified and unmodified forms of these peptides in H. americanus. Ultimately, quantifying AST-C peptides and viii identifying their modified and unmodified forms will help explain how neuropeptides regulate behavior within the lobster and more complex systems.

• Restriction End Date: 2028-06-01

Date: 2023-01-01

Creator: Emily Grace Herndon

Access: Access restricted to the Bowdoin Community

• Restriction End Date: 2027-06-01

Date: 2022-01-01

Creator: Emily Yuan-ann Pan

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Date: 2023-01-01

Creator: Rachel E Nealon

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Date: 2014-05-01

Creator: Joshua V Pondick

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Date: 2021-07-15

Creator: Phuong Luong, Danielle H. Dube

Access: Open access

The bacterial glycocalyx is a quintessential drug target comprised of structurally distinct glycans. Bacterial glycans bear unusual monosaccharide building blocks whose proper construction is critical for bacterial fitness, survival, and colonization in the human host. Despite their appeal as therapeutic targets, bacterial glycans are difficult to study due to the presence of rare bacterial monosaccharides that are linked and modified in atypical manners. Their structural complexity ultimately hampers their analytical characterization. This review highlights recent advances in bacterial chemical glycobiology and focuses on the development of chemical tools to probe, perturb, and image bacterial glycans and their biosynthesis. Current technologies have enabled the study of bacterial glycosylation machinery even in the absence of detailed structural information.

Date: 2015-09-01

Creator: Kate R. Farnham, Danielle H. Dube

Access: Open access

Here we present the development of a 13 week project-oriented biochemistry laboratory designed to introduce students to foundational biochemical techniques and then enable students to perform original research projects once they have mastered these techniques. In particular, we describe a semester-long laboratory that focuses on a biomedically relevant enzyme-Helicobacter pylori (Hp) urease-the activity of which is absolutely required for the gastric pathogen Hp to colonize the human stomach. Over the course of the semester, students undertake a biochemical purification of Hp urease, assess the success of their purification, and investigate the activity of their purified enzyme. In the final weeks of the semester, students design and implement their own experiments to study Hp urease. This laboratory provides students with an understanding of the importance of biochemistry in human health while empowering them to engage in an active area of research.

Date: 2001-06-09

Creator: D. J. Sutton, Z. J. Kabala, A. Francisco, D. Vasudevan

Access: Open access

We conducted chemical characterization, batch, column, and modeling studies to elucidate the sorption and transport of rhodamine WT (RWT) in the subsurface. The sand-pack material from the Lizzie field site near Greenville, North Carolina, served as our porous media. Our study confirms earlier results that RWT consists of two isomers with different sorption properties. It also shows that the two isomers have distinct emission spectra and are equally distributed in the RWT solution. The presence of the two isomers with different sorption properties and distinct emission spectra introduces an error in measuring the RWT concentration with fluorometers during porous media tracer studies. The two isomers become chromatographically separated during transport and thus arrive in a different concentration ratio than that of the RWT solutions used for fluorometer calibration and test injection. We found that this groundwater tracer chromatographic error could be as high as 7.8%. We fit six different reactive-solute transport models of varying complexity to our four column experiments. A two-solute, two-site sorption transport model that accounts for nonequilibrium sorption accurately describes the breakthrough curves of the shorter-timescale column experiments. However, possibly due to the groundwater tracer chromatographic error we discovered, this model, or a similar one that accounts for a Freundlich isotherm for one of the solutes, fails to describe the RWT transport in the longer-timescale column experiments. The presence of the two RWT isomers may complicate the interpretation of field tracer tests because a shoulder, or any two peaks in a breakthrough curve, could result from either aquifer heterogeneity or the different arrival times of the two isomers. In cases where isomer 2 sorbs to such an extent that its breakthrough is not recorded during a test, only isomer 1 is measured, and therefore only 50% of the injected mass is recorded. Isomer 1 of RWT can be accurately modeled with a one-solute, two-site, nonequilibrium sorption model. This conclusion and the results from our batch studies suggest that RWT isomer 1 is an effective groundwater tracer but that the presence of isomer 2 hampers its effectiveness.

Date: 2022-01-01

Creator: William J. Rackear

Access: Access restricted to the Bowdoin Community

Date: 2020-01-01

Creator: Thomas Regan

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