The Lantern, 2013-2014

• Strikes • Pietro di Venezia • To the Lover of Small Things • Jim\u27s Big Day • Akademiks • Redamancy • A Love Poem for Arctia Caja • Mother River • The Lyrics to Your Song • Nerves • Gemini Season • White Interface • The Last Time I Played with Dolls • The Mechanic • My Goldfish • Put Down Your Hammer • Strip • Hollywood • Identity • The Grey Zone • Sophia • When I Became a Poet • Unbroken • The Veteran Aeronaut • I Have Running Water but They had the Stars • Not A Nigga • Mother, Adam, Eve • From Fragile Seeds: A Palindrome • Conspiring, The Spires • Finally Working Out What Goes Where (God, For Example, is in His Kingdom) • Identity Crisis • Affection • Patience • An Enchanting Lost Cause • False Starts • Soggy Rice, Lukewarm Water • The Glow • Heat • 9-14 • Filigree • Diane Arbus • Touched • Dying Alive • Just Another Drunkard on the Train • Dinner • The French Legionnaire • Conspiracy and Theory • 1249am • Colored Pencils • Sea Glass • Roundtrip • The Muse Heard Music • Lacrimosa • The Allegory of the Maze • The Stars on Stuart Road • To Isabella • For Want of a Potato Chip • Termite Nests • Saving a Rose • Today and Yesterday • A Foggy New York • Cat; Wurtzburg • Embrace • Faces • Geisha • Pacis Leo • Patterns • Te-Whanganui-a-Tara (The Dock)https://digitalcommons.ursinus.edu/lantern/1180/thumbnail.jp

Tailoring the catalytic properties and specificity of subtilisin B. lentus via a combined site-directed mutagenesis and chemical modification approach

grantor: University of TorontoChemically modified mutant enzymes (CMMs) of subtilisin 'Bacillus lentus' (SBL) were designed to alter its specificity and catalytic properties. Modification of S156C, which is located toward the bottom of the S1 pocket and whose side chain is solvated, effected only small changes in its catalytic properties. Conversely, modification of S166C, which is located at the bottom of the S1 pocket and points into the pocket, effected larger changes. The S166C-S-CH2CH2SO3 - CMM caused a 16-fold decrease in 'k cat'/'KM' with the standard suc-AAPF-pNA substrate, a 5-fold decrease in the binding of the 2,4-diclorophenylboronic acid inhibitor and a 0.93 unit increase in the pKa of His64. The restricted S1 pocket of S166C-CMMs was demonstrated by the precluded binding and covalent attachment of a 'p'-boronic acid benzophenone photoactivatable active-site directed inhibitor. SBL prefers large hydrophobic P1 substrate residues and the CMM strategy was exploited to confer a more universal P1 specificity on S1. A large cyclohexyl group was introduced at position S166C to fill up the S1 pocket, causing a 2-fold improvement in ' kcat'/'KM' for the small P 1 residue suc-AAPA-pNA substrate and a 51-fold improvement in suc-AAPA-pNA/suc-AAPF-pNA selectivity compared to WT. Negatively and positively charged groups were introduced at position S166C. A monotonic increase in 'kcat'/' KM' with the positively charged P1 residue containing substrate suc-AAPR-pNA was effected by increasing negative charge at position 166. This culminated in a 9-fold improvement in 'kcat'/' KM' for the tri-negatively charged S166C-S-CH2CH 2C(COO-)3 CMM and a 61-fold improvement in its suc-AAPR-pNA/suc-AAPF-pNA selectivity. The positively charged S166C-S-CH 2CH2NH3+ CMM showed a 19-fold improvement in 'kcat'/'KM' with the negatively charged P1 residue containing substrate, suc-AAPE-pNA and a 54-fold improvement in its suc-AAPE-pNA/suc-AAPF-pNA selectivity. Modification of the S2 pocket N62C residue resulted in seven of eleven CMMs, with higher than wild type (WT) levels of activity. A monotonic increase in activity with increasing side-chain size was observed culminating in a 3-fold improvement in 'kcat'/'K M' for N62C-S-'c'-CH2C6H 11. The indication from molecular modelling that this was due to increased acidity of the catalytic triad residue His64 was confirmed by pH-activity profile studies which revealed pKa decreases of up to 0.72 units. A linear correlation between the hydrophobicity of the introduced side chain and the observed pKa was apparent.Ph.D

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High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses

Two serious public health challenges have emerged in the current COVID-19 pandemic namely, deficits in SARS-CoV-2 variant monitoring and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent, and dynamics of the outbreak is required to understand the transmission of the virus. To address these challenges, we evaluated 533 samples using a high-throughput next-generation sequencing (NGS) respiratory viral panel (RVP) that includes 40 viral pathogens. The performance metrics revealed a PPA, NPA, and accuracy of 95.98%, 85.96%, and 94.4%, respectively. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF3a, and S84L in ORF8 covarying with the D614G spike protein mutation, were the most prevalent early in the pandemic in Georgia, USA. The isolates from the same county formed paraphyletic groups, indicating virus transmission between counties. The study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats and models that provide insights into viral transmission patterns and predict transmission/resurgence of regional outbreaks as well as providing critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden