Stepwise Unfolding of a β Barrel Protein by the AAA+ ClpXP Protease

In the AAA+ ClpXP protease, ClpX uses the energy of ATP binding and hydrolysis to unfold proteins before translocating them into ClpP for degradation. For proteins with C-terminal ssrA tags, ClpXP pulls on the tag to initiate unfolding and subsequent degradation. Here, we demonstrate that an initial step in ClpXP unfolding of the 11-stranded β barrel of superfolder GFP-ssrA involves extraction of the C-terminal β strand. The resulting 10-stranded intermediate is populated at low ATP concentrations, which stall ClpXP unfolding, and at high ATP concentrations, which support robust degradation. To determine if stable unfolding intermediates cause low-ATP stalling, we designed and characterized circularly permuted GFP variants. Notably, stalling was observed for a variant that formed a stable 10-stranded intermediate but not for one in which this intermediate was unstable. A stepwise degradation model in which the rates of terminal-strand extraction, strand refolding or recapture, and unfolding of the 10-stranded intermediate all depend on the rate of ATP hydrolysis by ClpXP accounts for the observed changes in degradation kinetics over a broad range of ATP concentrations. Our results suggest that the presence or absence of unfolding intermediates will play important roles in determining whether forced enzymatic unfolding requires a minimum rate of ATP hydrolysis.National Institutes of Health (U.S.) (Grant AI-15706

Structural variability of 4f and 5f thiocyanate complexes and dissociation of uranium(III)–thiocyanate bonds with increased ionicity

A series of complexes [Et4N][Ln(NCS)4(H2O)4] (Ln = Pr, Tb, Dy, Ho, Yb) have been structurally characterized, all showing the same structure, namely a distorted square antiprismatic coordination geometry, and the Ln–O and Ln–N bond lengths following the expected lanthanide contraction. When the counterion is Cs+, a different structural motif is observed and the eight-coordinate complex Cs5[Nd(NCS)8] isolated. The thorium compounds [Me4N]4[Th(NCS)7(NO3)] and [Me4N]4[Th(NCS)6(NO3)2] have been characterized, and high coordination numbers are also observed. Finally, attempts to synthesize a U(III) thiocyanate compound has been unsuccessful; from the reaction mixture, a heterocycle formed by condensation of five MeCN solvent molecules, possibly promoted by U(III), was isolated and structurally characterized. To rationalize the inability to isolate U(III) thiocyanate compounds, thin-layer cyclic voltammetry and IR spectroelectrochemistry have been utilized to explore the cathodic behavior of [Et4N]4[U(NCS)8] and [Et4N][U(NCS)5(bipy)2] along with a related uranyl compound [Et4N]3[UO2(NCS)5]. In all examples, the reduction triggers a rapid dissociation of [NCS]− ions and decomposition. Interestingly, the oxidation chemistry of [Et4N]3[UO2(NCS)5] in the presence of bipy gives the U(IV) compound [Et4N]4[U(NCS)8], an unusual example of a ligand-based oxidation triggering a metal-based reduction. The experimental results have been augmented by a computational investigation, concluding that the U(III)–NCS bond is more ionic than the U(IV)–NCS bond

An authoritative global database for active submarine hydrothermal vent fields

Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry, Geophysics, Geosystems 14 (2013): 4892–4905, doi:10.1002/2013GC004998.The InterRidge Vents Database is available online as the authoritative reference for locations of active submarine hydrothermal vent fields. Here we describe the revision of the database to an open source content management system and conduct a meta-analysis of the global distribution of known active vent fields. The number of known active vent fields has almost doubled in the past decade (521 as of year 2009), with about half visually confirmed and others inferred active from physical and chemical clues. Although previously known mainly from mid-ocean ridges (MORs), active vent fields at MORs now comprise only half of the total known, with about a quarter each now known at volcanic arcs and back-arc spreading centers. Discoveries in arc and back-arc settings resulted in an increase in known vent fields within exclusive economic zones, consequently reducing the proportion known in high seas to one third. The increase in known vent fields reflects a number of factors, including increased national and commercial interests in seafloor hydrothermal deposits as mineral resources. The purpose of the database now extends beyond academic research and education and into marine policy and management, with at least 18% of known vent fields in areas granted or pending applications for mineral prospecting and 8% in marine protected areas.For support to prepare this manuscript, we thank the National Science Foundation (OCE08-38923, GeoEd12-02977), the NOAA Vents (now Earth-Ocean Interactions) Program and the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA Cooperative Agreement NA10OAR4320148, and WHOI.2014-05-1

Turbo-discharging turbocharged internal combustion engines

Turbo-discharging is a novel approach that can better utilize the energy recoverable by a turbine (or series of turbines) mounted in the exhaust flow of internal combustion engines. The recovery of blowdown pulse energy in isolation of displacement pulse energy allows the discharging (depressurization) of the exhaust system to reduce engine pumping work and improve engine fuel economy. This is a novel approach to air system optimization that has previously been studied for naturally aspirated engines. However, to be successful, turbo-discharging should be applicable to turbocharged engines, as downsizing is a promising direction for future powertrain systems. This study uses one-dimensional gas dynamics modelling to explore the effect of turbo-discharging on a turbocharged gasoline engine, particularly focusing on the interaction with the turbocharging system. The results show that the peak engine torque is increased at low to mid speeds with high speed torque slightly reduced due to restrictions in engine breathing with low lift exhaust valves. The engine peak torque as a function of speed with a larger turbocharger and turbo-discharging was comparable to that of the smaller turbocharger without turbo-discharging. Fuel economy improvements were evident over most part-load regions of the engine map, with peak values varying from 2 to 7% depending on the baseline engine air system strategy. Hot trapped residual mass was consistently reduced across a large fraction of the engine map, with the exception of high power conditions, where the valve pressure drop effect dominated. This is expected to enable spark advance and further fuel economy benefit. The results from this study are promising and show that the use of some of the available exhaust gas energy for turbo-discharging in preference to turbocharging can have a positive effect on both part-load and full-load engine performance. There remains significant potential for further optimization with application of variable valve actuation and turbocharger control systems (for example, variable geometry turbines)

Formation of Uniaxial Molecular Films by Liquid-Crystal Imprinting in a Magnetic Field

Scanning tunneling microscopy was used to study molecular order in monolayer organic films formed by solution-phase growth from thermotropic liquid crystal solvents. The films develop macroscopically uniaxial alignment, with adlayer orientation controlled by an external magnetic field through interactions mediated by the liquid crystal. Results are presented for two films deposited from nematic and smectic- A solvents, along with a discussion of the alignment mechanism

A historical perspective of research on the biology of aging from Nathan W. Shock

This article describes some of the thoughts and the conceptual framework from which Nathan W. Shock prepared his last major presentation. This paper, written some 8 months following Dr. Shock's death on November 12, 1989, is based upon his extensive notes and discussions with one of the authors (George T. Baker). This presentation in no way is meant to encapsulate the long and distinguished career of Nathan Shock, but rather to provide a glimpse of his perspectives on the development of the field of aging. Furthermore, we believe that the scientific principles concerning aging research laid out by Dr. Shock in this publication are still valid today and may provide valuable insights for researchers in the field.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30332/1/0000734.pd

Revisiting Old Friends: Is CoDel Really Achieving What RED Cannot?

We use ns-2 simulations to compare RED's gentle mode to CoDel in terms of their ability to reduce the latency for various TCP variants. We use a common dumbbell topology with Pareto background traffic, and measure the packet delays and transmission time of a 10MB FTP transfer. In our scenarios, we find that CoDel reduces the latency by 87%, but RED still manages to reduce it by 75%. However, the use of CoDel results in a transmission time 42% longer than when using RED. In light of its maturity, we therefore argue that RED could be considered as a good candidate to tackle Bufferbloat

Lunar radiation environment and space weathering from the Cosmic Ray Telescope for the Effects of Radiation (CRaTER)

[1] The Cosmic Ray Telescope for the Effects of Radiation (CRaTER) measures linear energy transfer by Galactic Cosmic Rays (GCRs) and Solar Energetic Particles (SEPs) on the Lunar Reconnaissance Orbiter (LRO) Mission in a circular, polar lunar orbit. GCR fluxes remain at the highest levels ever observed during the space age. One of the largest SEP events observed by CRaTER during the LRO mission occurred on June 7, 2011. We compare model predictions by the Earth-Moon-Mars Radiation Environment Module (EMMREM) for both dose rates from GCRs and SEPs during this event with results from CRaTER. We find agreement between these models and the CRaTER dose rates, which together demonstrate the accuracy of EMMREM, and its suitability for a real-time space weather system. We utilize CRaTER to test forecasts made by the Relativistic Electron Alert System for Exploration (REleASE), which successfully predicts the June 7th event. At the maximum CRaTER-observed GCR dose rate (∼11.7 cGy/yr where Gy is a unit indicating energy deposition per unit mass, 1 Gy = 1 J/kg), GCRs deposit ∼88 eV/molecule in water over 4 billion years, causing significant change in molecular composition and physical structure (e.g., density, color, crystallinity) of water ice, loss of molecular hydrogen, and production of more complex molecules linking carbon and other elements in the irradiated ice. This shows that space weathering by GCRs may be extremely important for chemical evolution of ice on the Moon. Thus, we show comprehensive observations from the CRaTER instrument on the Lunar Reconnaissance Orbiter that characterizes the radiation environment and space weathering on the Moon

Luminous Infrared Galaxies with the Submillimeter Array: I. Survey Overview and the Central Gas to Dust Ratio

We present new data obtained with the Submillimeter Array for a sample of fourteen nearby luminous and ultraluminous infrared galaxies. The galaxies were selected to have luminosity distances D < 200 Mpc and far-infrared luminosities log(L_FIR) > 11.4. The galaxies were observed with spatial resolutions of order 1 kpc in the CO J=3-2, CO J=2-1, 13CO J=2-1, and HCO+ J=4-3 lines as well as the continuum at 880 microns and 1.3 mm. We have combined our CO and continuum data to measure an average gas-to-dust mass ratio of 120 +/- 28 (rms deviation 109) in the central regions of these galaxies, very similar to the value of 150 determined for the Milky Way. This similarity is interesting given the more intense heating from the starburst and possibly accretion activity in the luminous infrared galaxies compared to the Milky Way. We find that the peak H_2 surface density correlates with the far-infrared luminosity, which suggests that galaxies with higher gas surface densities inside the central kiloparsec have a higher star formation rate. The lack of a significant correlation between total H_2 mass and far-infrared luminosity in our sample suggests that the increased star formation rate is due to the increased availability of molecular gas as fuel for star formation in the central regions. In contrast to previous analyses by other authors, we do not find a significant correlation between central gas surface density and the star formation efficiency, as trace by the ratio of far-infrared luminosity to nuclear gas mass. Our data show that it is the star formation rate, not the star formation efficiency, that increases with increasing central gas surface density in these galaxies.Comment: 66 pages, 39 figures, aastex preprint format; to be published in ApJ Supplements. Version of paper with full resolution figures available at http://www.physics.mcmaster.ca/~wilson/www_xfer/ULIRGS_publi