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Monotopic phosphoglycosyl transferase enzymes (MonoPGTs) initiate the assembly of prokaryotic glycoconjugates essential for bacterial survival and proliferation. MonoPGTs belong to an expansive superfamily with a diverse and richly annotated sequence space; however, the biochemical roles of most monoPGTs in glycoconjugate biosynthesis pathways remain elusive. To better understand these critical enzymes, we have implemented activity-based protein profiling (ABPP) probes as protein-centric, membrane-protein compatible tools that lay the groundwork for understanding the activity and regulation of the monoPGT superfamily from a cellular proteome. With straightforward gel-based read outs we demonstrate robust, covalent labeling at the active site of various representative monoPGTs from unfractionated cell membrane fractions using 3-phenyl-2H-azirine probes.

Laser depth profiling of laboratory-induced helium diffusion profiles in natural zircon confirms that helium diffusivity is crystallographically controlled and significantly anisotropic. Experiments on Mud Tank zircon with low degrees of alpha radiation damage (5.6 × 1016 to 1.3 × 1017 α/g) indicate that c ‖ diffusion is ∼400 to 700 times faster than a ‖ diffusion over the experimental temperature range investigated (400–600 °C). This magnitude of diffusive anisotropy implies that zircon crystals with different crystal morphologies record different helium closure temperatures. Zircon diffusion models commonly used in thermal-kinematic modeling programs do not properly account for diffusive anisotropy, and consequently, are likely to over- or underestimate helium closure temperatures in low-damage zircon. Additional experiments on pieces of a large Sri Lankan zircon crystal with strong radiation damage zoning demonstrate that both c ‖ and a ‖ diffusivity – as well as the magnitude of diffusive anisotropy – decrease with increasing radiation damage over an alpha dose range of ∼4.2 × 1017 to 8.5 × 1017 α/g. Decreases in diffusivity appear to reflect changes in the diffusion coefficient D0 and not the activation energy for diffusion. While we did not design our experiments to explore the effect of trace element geochemistry on helium diffusion in zircon in detail, our results suggest that such an effect may be significant.

Aspirin and Celebrex are well-known time-dependent inhibitors of the cyclooxygenases (COX). Molecular dynamics simulations suggest that Arg-513 and Leu-531 contribute to the structural mechanisms of COX inhibition. We used mutagenesis and functional analyses to characterize how substitutions at these positions influence time-dependent inhibition by aspirin and Celebrex. We show that substitutions of Leu-531 with asparagine and phenylalanine significantly attenuate time-dependent inhibition of COX-2 by these drugs. The introduction of side chain bulk, rigidity, and charge would disrupt the formation of the initial noncovalent complex, in the case of aspirin, and the "high-affinity" binding state, in the case of Celebrex. Substitution of Arg-513 with histidine (the equivalent residue in COX-1) resulted in a 2-fold potentiation of aspirin inhibition, in support of the hypothesis that the presence of histidine in COX-1 lowers the activation barrier associated with the formation of the initial noncovalent enzyme-inhibitor complex. As a corollary, we previously hypothesized that the flexibility associated with Leu-531 contributes to the binding of arachidonic acid (AA) to acetylated COX-2 to generate 15R-hydroxyeicosatetraenoic acid (15R-HETE). We determined the X-ray crystal structure of AA bound to Co3+-protoporphyrin IX-reconstituted V349I murine COX-2 (muCOX-2). V349I muCOX-2 was utilized as a surrogate to trap AA in a conformation leading to 15R-HETE. AA binds in a C-shaped pose, facilitated by the rotation of the Leu-531 side chain. Ile-349 is positioned to sterically shield antarafacial oxygen addition at carbon-15 in a manner similar to that proposed for the acetylated Ser-530 side chain.

In this study, we empirically evaluate the impact of radiation damage on zircon (U-Th)/He closure temperatures for a suite of zircon crystals from the slowly cooled McClure Mountain syenite of south-central Colorado, USA. We present new zircon, titanite, and apatite conventional (U-Th)/He dates, zircon laser ablation (U-Th)/He and U-Pb dates, and zircon Raman spectra for crystals from the syenite. Titanite and apatite (U-Th)/He dates range from 447 to 523 Ma and 88.0 to 138.9 Ma, respectively, and display no clear correlation between (U-Th)/He date and effective uranium concentration. Conventional zircon (U-Th)/He dates range from 230.3 to 474 Ma, while laser ablation zircon (U-Th)/He dates show even greater dispersion, ranging from 5.31 to 520 Ma. Dates from both zircon (U-Th)/He datasets decrease with increasing alpha dose, indicating that most of the dispersion can be attributed to radiation damage. Alpha dose values for the dated zircon crystals range from effectively zero to 2.15 × 1019 α /g, spanning the complete damage spectrum. We use an independently constrained thermal model to empirically assign a closure temperature to each dated zircon grain. If we assume that this thermal model is robust, the zircon radiation damage accumulation and annealing model of Guenthner et al. (2013) does not accurately predict closure temperatures for many of the analyzed zircon crystals. Raman maps of the zircons dated by laser ablation document complex radiation damage zoning, sometimes revealing crystalline zones in grains with alpha dose values suggestive of amorphous material. Such zoning likely resulted in heterogeneous intra-crystalline helium diffusion and may help explain some of the discrepancies between our empirical findings and the Guenthner et al. (2013) model predictions. Because U-Th zoning is a common feature in zircon, radiation damage zoning is likely to be a concern for most ancient, slowly cooled zircon (U-Th)/He datasets. Whenever possible, multiple mineral-isotopic systems should be employed to add additional, independent constraints to a sample’s thermal history.

Mispositioned nuclei are a hallmark of skeletal muscle disease. Many of the genes that are linked to Emery-Dreifuss muscular dystrophy (EDMD) encode proteins that are critical for nuclear movement in various cells, suggesting that disruptions in nuclear movement and position may contribute to disease progression. Yet how these genes are coordinated to move nuclei is not known. Here we focused on two different emerin proteins, Bocksbeutel and Otefin and their effects on nuclear movement. Although nuclear position was dependent on both, elimination of either Bocksbeutel or Otefin produced distinct phenotypes that were based in differential effects on the KASH-domain protein Klarsicht. Specifically, loss of Bocksbeutel reduced Klarsicht localization to the nucleus and resulted in a disruption in nuclear separation. Loss of Otefin increased the transcription of Klarsicht and led to premature separation of nuclei and their positioning closer to the edge of the muscle. Consistent with opposing functions, nuclear position is normal in otefin; bocksbeutel double mutants. These data indicate emerin-dependent regulation of Klarsicht levels in the nuclear envelope are a critical determinant of nuclear position.

Recent research has demonstrated the importance of understanding alpha radiation damage in zircon in order to effectively interpret the thermochronologic significance of (U-Th)/He dates and to appropriately select laser ablation U/Pb reference standards. Direct measurements of alpha radiation damage in zircon are most easily done by using Raman spectral response as a proxy. Current Raman microscopes provide the opportunity to quantify not just a crystal's bulk radiation damage, but to map intracrystalline variations in radiation damage related to radionuclide zoning. Here we illustrate the procedure through a detailed study of zoned Proterozoic zircon crystals from the Adirondack Mountains of New York state. Although previous Raman studies have focused on the response of the v3(SiO4) stretching band (1008 cm−1) to radiation damage, we demonstrate that the internal v2(SiO4) bending band (439 cm−1) and the external Eg band (357 cm−1) are in some cases more useful – and in the case of the Eg band more responsive – proxies. We present curves that permit α dose estimates to be made from Eg and v2 band widths over a range of ~2 × 1017 to 1.8 × 1018 α/g. We then illustrate how these radiation damage maps can be used to visualize and interrogate intracrystalline variations in any damage-dependent material property in zircon, using helium diffusivity as an example, and discuss the implications for (U-Th)/He and U/Pb chronology of ancient, zoned zircon.

Drosophila is used as a model system to show that the common phenotype of mispositioned nuclei occurs via distinct mechanisms in Emery–Dreifuss muscular dystrophy and centronuclear myopathy., Muscle cells are a syncytium in which the many nuclei are positioned to maximize the distance between adjacent nuclei. Although mispositioned nuclei are correlated with many muscle disorders, it is not known whether this common phenotype is the result of a common mechanism. To answer this question, we disrupted the expression of genes linked to Emery–Dreifuss muscular dystrophy (EDMD) and centronuclear myopathy (CNM) in Drosophila and evaluated the position of the nuclei. We found that the genes linked to EDMD and CNM were each necessary to properly position nuclei. However, the specific phenotypes were different. EDMD-linked genes were necessary for the initial separation of nuclei into distinct clusters, suggesting that these factors relieve interactions between nuclei. CNM-linked genes were necessary to maintain the nuclei within clusters as they moved toward the muscle ends, suggesting that these factors were necessary to maintain interactions between nuclei. Together these data suggest that nuclear position is disrupted by distinct mechanisms in EDMD and CNM.