Showing 41 - 50 of 67 Items
Discovery and characterization of novel crustin family antimicrobial peptides (AMPs) in the American lobster, Homarus americanus, using transcriptomics and peptidomics Access to this record is restricted to members of the Bowdoin community. Log in here to view.
- Restriction End Date: 2027-06-01
Date: 2022-01-01
Creator: Emily Yuan-ann Pan
Access: Access restricted to the Bowdoin Community
Photoacidic properties of 8-amino-2-naphthol in imidazolium salts Access to this record is restricted to members of the Bowdoin community. Log in here to view.
Date: 2023-01-01
Creator: Rachel E Nealon
Access: Access restricted to the Bowdoin Community
The Determination of the Aqueous Oxidation Potentials of Aniline and Sixteen of its Derivatives via Ultrafast Cyclic Voltammetry to Model the Photocatalyzed Degradation of Organic Pollutants in Natural Bodies of Water Access to this record is restricted to members of the Bowdoin community. Log in here to view.
Date: 2014-05-01
Creator: Joshua V Pondick
Access: Access restricted to the Bowdoin Community
MnNiO3 revisited with modern theoretical and experimental methods
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.
Glycans in pathogenic bacteria - potential for targeted covalent therapeutics and imaging agents
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.
Assessing the Accuracy of Quantum Monte Carlo Pseudopotentials for CO2 Capture in Metal Organic Frameworks
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.
Investigating the Effects of Mixed Solvents on the Excited State Proton Transfer Mechanisms of 8-Amino-2-naphthol This record is embargoed.
- Embargo End Date: 2027-05-19
Date: 2022-01-01
Creator: Alexander Avrom Kreines
Access: Embargoed
Ionic Liquids as Additives for Metal-Organic Framework Crystallization Access to this record is restricted to members of the Bowdoin community. Log in here to view.
- Restriction End Date: 2027-06-01
Date: 2024-01-01
Creator: Oliver Wang
Access: Access restricted to the Bowdoin Community
Multiple transcriptome mining coupled with tissue specific molecular cloning and mass spectrometry provide insights into agatoxin-like peptide conservation in decapod crustaceans
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.
SIFamide peptides modulate cardiac activity differently in two species of Cancer crab
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.