The importance of lattice defects in katanin-mediated microtubule severing in vitro

The microtubule-severing enzyme katanin uses ATP hydrolysis to disrupt noncovalent bonds between tubulin dimers within the microtubule lattice. Although its microtubule severing activity is likely important for fundamental processes including mitosis and axonal outgrowth, its mechanism of action is poorly understood. To better understand this activity, an in vitro assay was developed to enable the real-time observation of katanin-mediated severing of individual, mechanically unconstrained microtubules. To interpret the experimental observations, a number of theoretical models were developed and compared quantitatively to the experimental data via Monte Carlo simulation. Models that assumed that katanin acts on a uniform microtubule lattice were incompatible with the in vitro data, whereas a model that assumed that katanin acts preferentially on spatially infrequent microtubule lattice defects was found to correctly predict the experimentally observed breaking rates, number and spatial frequency of severing events, final levels of severing, and sensitivity to katanin concentration over the range 6-300 nM. As a result of our analysis, we propose that defects in the microtubule lattice, which are known to exist but previously not known to have any biological function, serve as sites for katanin activity.     

Interactive effects of disturbance and nitrogen availability on phosphorus dynamics of southern Appalachian forests

Understanding the main and interactive effects of chronically altered resource availability and disturbance on phosphorus (P) availability is increasingly important in light of the rapid pace at which human activities are altering these processes and potentially introducing P limitation. We measured P pools and fluxes in eighteen mixed forest stands at three elevations (low, mid, high) subjected to increasing atmospheric N deposition, where hemlock (Tsuga canadensis) was absent or declining due to infestation by the exotic hemlock woolly adelgid (Adelges tsugae). While total soil P was similar across the study area, phosphorus fractionation revealed distinct differences in the distribution of soil P fractions as elevation and N availability increased. Soils from high elevation plots where N availability was greatest had 139 % larger organic P pools and 55 % smaller residual and refractory P pools than soils from low elevation plots with less N availability, suggesting that increased N availability has driven the depletion of recalcitrant P pools by stimulating biotic demand and sequestration. These differences in P distribution among fractions influenced how tree mortality affected P dynamics. At high elevations, plots containing declining hemlocks had significantly greater foliar P concentrations and fluxes of P from the forest floor than reference plots at similar elevations, whereas at low and mid-elevations there were no consistent differences between plots. Across all elevation classes, hardwood foliar N:P ratios were lower in plots with declining hemlocks. Collectively, these results suggest that increased N availability enhances bioavailable P, which is sequestered in vegetation until disturbances liberate it.     

N-Alkyldeoxynojirimycin derivatives with novel terminal tertiary amide substitution for treatment of bovine viral diarrhea virus (BVDV), Dengue,and Tacaribe virus infections

Novel N-alkyldeoxynojirimycins (NADNJs) with two hydrophobic groups attached to a nitrogen linker on the alkyl chain were designed. A novel NADNJ containing a terminal tertiary carboxamide moiety was discovered that was a potent inhibitor against BVDV. Further optimization resulted in a structurally more stable lead compound 24 with a submicromolar EC₅₀ against BVDV, Dengue, and Tacaribe; and low cytotoxicity.     

Single-molecule studies of riboswitch folding

The folding dynamics of riboswitches are central to their ability to modulate gene expression in response to environmental cues. In most cases, a structural competition between the formation of a ligand-binding aptamer and an expression platform (or some other competing off-state) determines the regulatory outcome. Here, we review single-molecule studies of riboswitch folding and function, predominantly carried out using single-molecule FRET or optical trapping approaches. Recent results have supplied new insights into riboswitch folding energy landscapes, the mechanisms of ligand binding, the roles played by divalent ions, the applicability of hierarchical folding models, and kinetic vs. thermodynamic control schemes. We anticipate that future work, based on improved data sets and potentially combining multiple experimental techniques, will enable the development of more complete models for complex RNA folding processes. This article is part of a Special Issue entitled: Riboswitches.     

Results of satellite tagging of Atlantic bluefin tuna, <Emphasis Type="Italic">Thunnus thynnus</Emphasis>, off the coast of Ireland

Pop-up satellite archival tags were attached to six Atlantic bluefin tuna (Thunnus thynnus) off the west coast of Ireland in autumn 2003 and 2004. The satellite tags measured pressure, ambient temperature and light for the term of deployment. Radio pop-up satellite endpoint positions, light and sea surface temperature estimations of geolocation indicate that two fish tagged minutes apart off the coast of County Donegal, migrated to the eastern and western Atlantic Ocean over the following 8 months. The two fish were 5218 km apart at the termination of the experiment. After tagging in September and popping up the following March and April, one fish had traveled to the western Atlantic while the other was located in the waters off the southwest coast of Portugal. A third fish tagged off the coast of County Donegal in October 2004 moved into the Mediterranean Sea and was caught by a fishing vessel southeast of Malta on 11 June 2005. The results link bluefin tuna feeding on European foraging grounds with known eastern breeding regions and western Atlantic waters.     

Isolation and Characterization of a Cytosolic Phospholipase A2 from Bovine Adrenal Medulla

Abstract: We have recently demonstrated that bovine adrenal medulla contains a soluble phospholipase A₂ (PLA₂), which is localized in the cytosol. In the present study, this PLA₂ was purified 1,097-fold using sequential concanavalin A, hydrophobic interaction, anion exchange, gel filtration, and an additional anion exchange chromatography. The enzyme is activated over the range of 20–1,000 µ M Ca²⁺ and has a pH optimum near 8.0. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the protein has a molecular mass of 26 kDa and an isoelectric point of 4.6 as revealed by isoelectric focusing. The cytosolic PLA₂ is not inhibited by NaCl, and the enzymatic activity is stimulated at low concentrations of Triton X-100 (0.01%) and deoxycholate (1 m M ) but inhibited at higher concentrations (0.1% and 3 m M , respectively) of these detergents. Furthermore, heat treatment (57°C, 5 min) reduced the enzymatic activity by 80%, whereas glycerol (30%) increased the activity. p -Bromophenacylbromide, a frequently used irreversible inhibitor of type II PLA₂, has little effect until 100 µ M , and 2–10 m M dithiothreitol totally inactivated the enzyme. The purified PLA₂ displays a preference for phosphatidylcholine as a substrate but hydrolyzes phospholipid substrates with arachidonic acid or linoleic acid esterified at the sn -2 position to the same extent. It is concluded that the chromaffin cell cytosolic PLA₂, which was isolated and characterized in this study, represents a type of PLA₂ that has not been formerly reported in chromaffin cells. Additional research on the chromaffin cell cytosolic PLA₂ will help to reveal whether the enzyme is important for exocytosis.     

Transient electric birefringence of the bacteriophages T3 and T7

Electric birefringence measurements of suspensions of T3 and T7 bacteriophages in 10^?2 M phosphate buffer, pH 6.9, show that there is a difference in their rotational diffusion coefficient. The values corrected to 25°C and water viscosity are D_25,w = 4630 ± 130 sec^?1 and D_25,w = 5290 ± 260 sec^?1 for T3 and T7, respectively. The value obtained from shell model calculations (according to Filson and Bloomfield) is D_25,w = 4500 ± 600 sec^?1. The apparent permanent dipole moments are 4.5 × 10^?26 C·m and 1.7 × 10^?26 C·m for T3 and T7, respectively. For both phage particles the intrinsic optical anisotropy is +7.2 × 10^?3. It is shown that this anisotropy is mainly due to the DNA molecule inside the head of the phage. Its positive value means that there exists an excess orientation of the DNA helix perpendicular to the symmetry axis of the particle. For T7 an unexpectedly large increase of Δn_s and K_sp occurs at a glycerol concentration of about 30% (v/v). This increase is interpreted as being caused by a change of the shape of the particle and/or a change in the secondary structure of the DNA inside the head of the bacteriophage.