The global colour model of QCD and its relationship to the NJL model, chiral perturbation theory and other models

The Global Colour Model (GCM) of QCD is a very successful model. Not only is it formally derivable from QCD but under various conditions it reduces to the NJL model and also to Chiral Perturbation Theory, and to other models. Results presented include the effective gluon propagator, the difference between constituent and exact quark propagators, various meson and nucleon observables, a new mass formula for the Nambu-Goldstone mesons of QCD, and the change in the MIT bag constant in nuclei

Toward understanding the S2-S3 transition in the Kok cycle of Photosystem II:Lessons from Sr-substituted structure

Understanding the water oxidation mechanism in Photosystem II (PSII) stimulates the design of biomimetic artificial systems that can convert solar energy into hydrogen fuel efficiently. The Sr2+-substituted PSII is active but slower than with the native Ca2+ containing PSII as an oxygen evolving catalyst. Here, we use Density Functional Theory (DFT) to compare the energetics of the S2 to S3 transition in the Mn4O5Ca2+ and Mn4O5Sr2+ clusters. The calculations show that deprotonation of the water bound to Ca2+ (W3), required for the S2 to S3 transition, is energetically more favorable in Mn4O5Ca2+ than Mn4O5Sr2+. In addition, we have calculated the pKa of the water that bridges Mn4 and the Ca2+/Sr2+ in the S2 state using continuum electrostatics. The calculations show that the pKa is higher by 4 pH units in the Mn4O5Sr2+cluster

TruncTrimmer: A First Step Towards Automating Standard Bioinformatic Analysis

Bioinformatic analysis is a time-consuming process for labs performing research on various microbiomes. Researchers use tools like Qiime2 to help standardize the bioinformatic analysis methods, but even large, extensible platforms like Qiime2 have drawbacks due to the attention required by researchers. In this project, we propose to automate additional standard lab bioinformatic procedures by eliminating the existing manual process of determining the trim and truncate locations for paired end 2 sequences. We introduce a new Qiime2 plugin called TruncTrimmer to automate the process that usually requires the researcher to make a decision on where to trim and truncate manually after importing and demultiplexing sequences in the Qiime2 pipeline. By automating this process and removing the need for manual interaction by the researcher, this plugin provides another opportunity to automate another standard bioinformatic analysis procedure

Studies in the Geochronology and Geochemistry of the Transantarctic Mountains

This is the third annual progress report submitted by Institute of Polar Studies researchers to the National Science Foundation (Grant No. GA-898X) on the geochronology and geochemistry of rocks from the Transantarctic Mountains, Antarctica. The results reported in this report are preliminary in nature.National Science Foundation Grant GA-898

Rapid Prenatal Diagnosis and Exclusion of Epidermolysis Bullosa Using Novel Antibody Probes

Prenatal diagnosis of recessive dystrophic epidermolysis bullosa was successfully achieved at 19 weeks' gestation by indirect immunofluorescence examination of a fetal skin biopsy sample using the monoclonal antibody LH 7:2. The abortus displayed marked blistering and the diagnosis was confirmed by transmission electron microscopy (TEM). In 3 further pregnancies at risk for lethal junctional epidermolysis bullosa the diagnosis was excluded using the polyclonal antibody AA3. In all these studies the results were available within 4h of receiving the samples. These new techniques offer a quick and simple alternative to TEM for midtrimester prenatal diagnosis of 2 severe recessive forms of epidermolysis bullosa

Photosystem II oxygen-evolving complex photoassembly displays an inverse H/D solvent isotope effect under chloride-limiting conditions

© 2019 National Academy of Sciences. All rights reserved. Photosystem II (PSII) performs the solar-driven oxidation of water used to fuel oxygenic photosynthesis. The active site of water oxidation is the oxygen-evolving complex (OEC), a Mn4CaO5 cluster. PSII requires degradation of key subunits and reassembly of the OEC as frequently as every 20 to 40 min. The metals for the OEC are assembled within the PSII protein environment via a series of binding events and photochemically induced oxidation events, but the full mechanism is unknown. A role of proton release in this mechanism is suggested here by the observation that the yield of in vitro OEC photoassembly is higher in deuterated water, D2O, compared with H2O when chloride is limiting. In kinetic studies, OEC photoassembly shows a significant lag phase in H2O at limiting chloride concentrations with an apparent H/D solvent isotope effect of 0.14 ± 0.05. The growth phase of OEC photoassembly shows an H/D solvent isotope effect of 1.5 ± 0.2. We analyzed the protonation states of the OEC protein environment using classical Multiconformer Continuum Electrostatics. Combining experiments and simulations leads to a model in which protons are lost from amino acid that will serve as OEC ligands as metals are bound. Chloride and D2O increase the proton affinities of key amino acid residues. These residues tune the binding affinity of Mn2+/3+ and facilitate the deprotonation of water to form a proposed μ-hydroxo bridged Mn2+Mn3+ intermediate