Substrate Specificity and Structural Characteristics of the Novel Rieske Nonheme Iron Aromatic Ring-Hydroxylating Oxygenases NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1

The Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs) NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1 have been implicated in the initial oxidation of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs), forming cis-dihydrodiols. To clarify how these two RHOs are functionally different with respect to the degradation of HMW PAHs, we investigated their substrate specificities to 13 representative aromatic substrates (toluene, m-xylene, phthalate, biphenyl, naphthalene, phenanthrene, anthracene, fluoranthene, pyrene, benz[a]anthracene, benzo[a]pyrene, carbazole, and dibenzothiophene) by enzyme reconstitution studies of Escherichia coli. Both Nid systems were identified to be compatible with type V electron transport chain (ETC) components, consisting of a [3Fe-4S]-type ferredoxin and a glutathione reductase (GR)-type reductase. Metabolite profiles indicated that the Nid systems oxidize a wide range of aromatic hydrocarbon compounds, producing various isomeric dihydrodiol and phenolic compounds. NidAB and NidA3B3 showed the highest conversion rates for pyrene and fluoranthene, respectively, with high product regiospecificity, whereas other aromatic substrates were converted at relatively low regiospecificity. Structural characteristics of the active sites of the Nid systems were investigated and compared to those of other RHOs. The NidAB and NidA3B3 systems showed the largest substrate-binding pockets in the active sites, which satisfies spatial requirements for accepting HMW PAHs. Spatially conserved aromatic amino acids, Phe-Phe-Phe, in the substrate-binding pockets of the Nid systems appeared to play an important role in keeping aromatic substrates within the reactive distance from the iron atom, which allows each oxygen to attack the neighboring carbons

Commissioning of the electron injector for the AWAKE experiment

The advanced wakefield experiment (AWAKE) at CERN is the first proton beam-driven plasma wakefield acceleration experiment. The main goal of AWAKE RUN 1 was to demonstrate seeded self-modulation (SSM) of the proton beam and electron witness beam acceleration in the plasma wakefield. For the AWAKE experiment, a 10-meter-long Rubidium-vapor cell together with a high-power laser for ionization was used to generate the plasma. The plasma wakefield is driven by a 400 GeV/c proton beam extracted from the super proton synchrotron (SPS), which undergoes a seeded self-modulation process in the plasma. The electron witness beam used to probe the wakefields is generated from an S-band RF photo-cathode gun and then accelerated by a booster structure up to energies between 16 and 20 MeV. The first run of the AWAKE experiment revealed that the maximum energy gain after the plasma cell is 2 GeV, and the SSM mechanism of the proton beam was verified. In this paper, we will present the details of the AWAKE electron injector. A comparison of the measured electron beam parameters, such as beam size, energy, and normalized emittance, with the simulation results was performed

Cloud optical depth retrievals from the Aerosol Robotic Network (AERONET) cloud mode observations

Cloud optical depth is one of the most poorly observed climate variables. The new “cloud mode” capability in the Aerosol Robotic Network (AERONET) will inexpensively yet dramatically increase cloud optical depth observations in both number and accuracy. Cloud mode optical depth retrievals from AERONET were evaluated at the Atmospheric Radiation Measurement program’s Oklahoma site in sky conditions ranging from broken clouds to overcast. For overcast cases, the 1.5 min average AERONET cloud mode optical depths agreed to within 15% of those from a standard ground‐based flux method. For broken cloud cases, AERONET retrievals also captured rapid variations detected by the microwave radiometer. For 3 year climatology derived from all nonprecipitating clouds, AERONET monthly mean cloud optical depths are generally larger than cloud radar retrievals because of the current cloud mode observation strategy that is biased toward measurements of optically thick clouds. This study has demonstrated a new way to enhance the existing AERONET infrastructure to observe cloud optical properties on a global scale

Hyb:A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

Peer reviewedPublisher PD

Advancing Learning in the Communication BA through ePortfolios

In 2018, the Communication program in the School of Communications conducted a program assessment of undergraduate senior capstone ePortfolios to evaluate the evidence of quality learning within the Communication major. The poster presents our assessment results and pre- and post- evaluation activities toward curriculum improvement

Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations

Hairpin loops belong to the most important structural motifs in folded nucleic acids. The d(GNA) sequence in DNA can form very stable trinucleotide hairpin loops depending, however, strongly on the closing base pair. Replica-exchange molecular dynamics (REMD) were employed to study hairpin folding of two DNA sequences, d(gcGCAgc) and d(cgGCAcg), with the same central loop motif but different closing base pairs starting from single-stranded structures. In both cases, conformations of the most populated conformational cluster at the lowest temperature showed close agreement with available experimental structures. For the loop sequence with the less stable G:C closing base pair, an alternative loop topology accumulated as second most populated conformational state indicating a possible loop structural heterogeneity. Comparative-free energy simulations on induced loop unfolding indicated higher stability of the loop with a C:G closing base pair by ~3 kcal mol−1 (compared to a G:C closing base pair) in very good agreement with experiment. The comparative energetic analysis of sampled unfolded, intermediate and folded conformational states identified electrostatic and packing interactions as the main contributions to the closing base pair dependence of the d(GCA) loop stability

This Is Just A Test: Overcoming High-Stakes Test Anxiety through Relaxation and Gum Chewing When Preparing for the ACT

This study was a replication of a previous study (in which) participants were given relaxation and deep breathing training to help manage test anxiety. The study examined the correlations between relaxation strategies, gum chewing and variables including socioeconomic status, class rank, GPA, and importance of going to college. Participants included 96 high school students (36 males, 60 females), preparing for the ACT (American College Testing). Results indicated that the relaxation intervention had a significant effect in reducing test anxiety

This Is Just A Test: Overcoming High-Stakes Test Anxiety through Relaxation and Gum Chewing When Preparing for the ACT

This study was a replication of a previous study (in which) participants were given relaxation and deep breathing training to help manage test anxiety. The study examined the correlations between relaxation strategies, gum chewing and variables including socioeconomic status, class rank, GPA, and importance of going to college. Participants included 96 high school students (36 males, 60 females), preparing for the ACT (American College Testing). Results indicated that the relaxation intervention had a significant effect in reducing test anxiety