Transition State Analysis of the Reaction Catalyzed by the Phosphotriesterase from Sphingiobium sp. TCM1

Organophosphorus flame retardants are stable toxic compounds used in nearly all durable plastic products and are considered major emerging pollutants. The phosphotriesterase from Sphingobium sp. TCM1 (Sb-PTE) is one of the few enzymes known to be able to hydrolyze organophosphorus flame retardants such as triphenyl phosphate and tris(2-chloroethyl) phosphate. The effectiveness of Sb-PTE for the hydrolysis of these organophosphates appears to arise from its ability to hydrolyze unactivated alkyl and phenolic esters from the central phosphorus core. How Sb-PTE is able to catalyze the hydrolysis of the unactivated substituents is not known. To interrogate the catalytic hydrolysis mechanism of Sb-PTE, the pH dependence of the reaction and the effects of changing the solvent viscosity were determined. These experiments were complemented by measurement of the primary and secondary 18-oxygen isotope effects on substrate hydrolysis and a determination of the effects of changing the pKa of the leaving group on the magnitude of the rate constants for hydrolysis. Collectively, the results indicated that a single group must be ionized for nucleophilic attack and that a separate general acid is not involved in protonation of the leaving group. The Brønsted analysis and the heavy atom kinetic isotope effects are consistent with an early associative transition state with subsequent proton transfers not being rate limiting. A novel binding mode of the substrate to the binuclear metal center and a catalytic mechanism are proposed to explain the unusual ability of Sb-PTE to hydrolyze unactivated esters from a wide range of organophosphate substrates

Development of an Online General Biology Open Educational Resource (OER) Laboratory Manual

Currently, many academic institutions are using one or more variations of online modalities due to the COVID-19 pandemic, and science educators face a unique challenge with distance-learning laboratories. Many resources to engage students in virtual, interactive laboratory activities exist, but we found that high costs and/or overlooked content left gaps for several topics typically taught in a general, introductory biology course for undergraduate biology majors (e.g., organismal biology). Additionally, resources for an online lab must be identified and curated from multiple sources, requiring intense demands on the instructors’ time. To meet this need and to overcome the financial burden of high-cost lab manuals or software, we developed, piloted, and revised a series of online general biology lab exercises. We have published these exercises as an Open Educational Resource (OER) digital laboratory manual under the Creative Commons License Agreement, and they are accessible online via Manifold, Creative Commons, and the CUNY Academic Works portal

General Biology 2 Laboratory Manual

Currently, many academic institutions are using one or more variations of online modalities due to the Covid-19 pandemic, and science educators face a unique challenge with distance-learning laboratories. Many resources to engage students in virtual, interactive laboratory activities exist, but we found that high costs and/or overlooked content left gaps for several topics typically taught in a general, introductory biology course for undergraduate biology majors (e.g., organismal biology). Additionally, resources for an online lab must be identified and curated from multiple sources, requiring intense demands on the instructors’ time. To meet this need and to overcome the financial burden of high-cost lab manuals or software, we developed, piloted, and revised a series of online general biology lab exercises. We have published these exercises as an Open Educational Resource (OER) digital laboratory manual under the Creative Commons License Agreement, and they are accessible online via Manifold, Creative Commons, and the CUNY Academic Works portal

KP line solitons and Tamari lattices

The KP-II equation possesses a class of line soliton solutions which can be qualitatively described via a tropical approximation as a chain of rooted binary trees, except at "critical" events where a transition to a different rooted binary tree takes place. We prove that these correspond to maximal chains in Tamari lattices (which are poset structures on associahedra). We further derive results that allow to compute details of the evolution, including the critical events. Moreover, we present some insights into the structure of the more general line soliton solutions. All this yields a characterization of possible evolutions of line soliton patterns on a shallow fluid surface (provided that the KP-II approximation applies).Comment: 49 pages, 36 figures, second version: section 4 expande