Draft crystal structure of the vault shell at 9-A resolution.

Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized. The best crystals thus far were formed from empty vaults built from a cysteine-tag construct of major vault protein (termed cpMVP vaults), diffracting to about 9-A resolution. The asymmetric unit contains a half vault of molecular mass 4.65 MDa. X-ray phasing was initiated by molecular replacement, using density from cryo-electron microscopy (cryo-EM). Phases were improved by density modification, including concentric 24- and 48-fold rotational symmetry averaging. From this, the continuous cryo-EM electron density separated into domain-like blocks. A draft atomic model of cpMVP was fit to this improved density from 15 domain models. Three domains were adapted from a nuclear magnetic resonance substructure. Nine domain models originated in ab initio tertiary structure prediction. Three C-terminal domains were built by fitting poly-alanine to the electron density. Locations of loops in this model provide sites to test vault functions and to exploit vaults as nanocapsules

The Mitospecific Domain of Mrp7 (bL27) Supports Mitochondrial Translation during Fermentation and is Required for Effective Adaptation to Respiration

We demonstrate here that mitoribosomal protein synthesis, responsible for the synthesis of oxidative phosphorylation (OXPHOS) subunits encoded by the mitochondrial genome, occurs at high levels during glycolysis fermentation and in a manner uncoupled from OXPHOS complex assembly regulation. Furthermore, we provide evidence that the mitospecific domain of Mrp7 (bL27), a mitoribosomal component, is required to maintain mitochondrial protein synthesis during fermentation but is not required under respiration growth conditions. Maintaining mitotranslation under high-glucose-fermentation conditions also involves Mam33 (p32/gC1qR homologue), a binding partner of Mrp7’s mitospecific domain, and together they confer a competitive advantage for a cell’s ability to adapt to respiration-based metabolism when glucose becomes limiting. Furthermore, our findings support that the mitoribosome, and specifically the central protuberance region, may be differentially regulated and/or assembled, under the different metabolic conditions of fermentation and respiration. On the basis of our findings, we propose that the purpose of mitotranslation is not limited to the assembly of OXPHOS complexes, but also plays a role in mitochondrial signaling critical for switching cellular metabolism from a glycolysis- to a respiration-based state

The ultrafast ground and excited state dynamics of cis-hexatriene in cyclohexane

One- and two-color kinetics have been combined with broadband ultraviolet transient absorption spectroscopy in the 265–300 nm region to elucidate the photophysics of cis-hexatriene in cyclohexane solvent. The lowest singlet excited state, the 2 1A121A1 state, is observed to have a lifetime of 200±50 fs. The ground-state hexatriene is produced vibrationally hot. The excess vibrational energy permits ultrafast isomerization around the C–C single bonds in hexatriene. This results in a dynamic equilibrium of the three cis-hexatriene rotamers, which then relaxes multiexponentially to the room-temperature distribution in which the di-s-trans-Z-hexatriene form predominates. The peak of the mono-s-trans (cZt-HT) population is estimated to be ∼50%. Vibrational cooling results in trapping of a small amount, ∼8%, of cZt-HT that relaxes on a much longer time scale as the barrier to isomerization becomes important. An estimate of the absorption spectrum of cZt-HT is deduced from analysis of the spectral data at 50 ps. © 1997 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70051/2/JCPSA6-107-13-4985-1.pd

The ultrafast photochemical ring-opening reaction of 1,3-cyclohexadiene in cyclohexane

The ring-opening reaction of 1,3-cyclohexadiene in cyclohexane solution and the subsequent photoproduct cooling dynamics have been investigated by using two-color transient absorption kinetic measurements and novel time-resolved absorption spectroscopy in the 260–300 nm spectral region. The initial photoproduct in this reaction, s-cis,Z,s-cis-1,3,5-hexatrienes-cis,Z,s-cis-1,3,5-hexatriene (cZc-HT) is formed on a ∼ 250 fs∼250fs time scale. Spectra deduced for time delays very close to zero, as well as calculated Rice–Ramsperger–Kassel–Marcus unimolecular reaction rates, provide strong evidence that the quantum yield for the reaction is determined before any relaxation occurs on the ground state. Upon formation, the vibrationally excited hexatriene photoproduct is able to isomerize around C–C single bonds freely. As a result, the evolution observed in the transient absorption measurements represents a combination of rotamer population dynamics and thermalization due to energy transfer to the solvent. Three distinct time scales for relaxation are observed. These time scales correspond approximately to the development of an evolving equilibrium of Z-HT rotamers (1–5 ps), vibrational cooling and thermal equilibration with the surroundings (10–20 ps), and activated isomerization of trapped cZt-HT to tZt-HT (≫100 ps).(≫100ps). © 1998 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70793/2/JCPSA6-108-2-556-1.pd

Physical Processes Dictate Early Biogeochemical Dynamics of Soil Pyrogenic Organic Matter in a Subtropical Forest Ecosystem

Quantifying links between pyOM dynamics, environmental factors and processes is central to predicting ecosystem function and response to future perturbations. In this study, changes in carbon (TC), nitrogen (TN), pH, and relative recalcitrance (R50) for pineand cordgrass-derived pyOM were measured at 3–6 weeks intervals throughout the first year of burial in the soil. Objectives were to (1) identify key environmental factors and processes driving early-stage pyOM dynamics, and (2) develop quantitative relationships between environmental factors and observed changes in pyOM properties. The study was conducted in sandy soils of a forested ecosystem within the Longleaf pine range of the United States with a focus on links between changes in pyOM properties, fire history (FH), cumulative precipitation (Pcum), average temperature (Tavg) and soil residence time (SRT). Pcum, SRT and Tavg were the main factors controlling TC and TN accounting for 77–91% and 64–96% of their respective variability. Fire history, along with Pcum, SRT and Tavg, exhibited significant controlling effects on pyOM pH and R50—accounting for 48–91% and 88–93% of respective variability. Volatilization of volatiles and leaching of water-soluble components (in summer) and the sorption of exogenous organic matter (fall through spring) were most plausibly controlling pyOM dynamics in this study. Overall, our results point to climatic and land management factors and physicochemical process as the main drivers of pyOM dynamics in the pine ecosystems of the Southeastern U

BOSS-LDG: A Novel Computational Framework that Brings Together Blue Waters, Open Science Grid, Shifter and the LIGO Data Grid to Accelerate Gravitational Wave Discovery

We present a novel computational framework that connects Blue Waters, the NSF-supported, leadership-class supercomputer operated by NCSA, to the Laser Interferometer Gravitational-Wave Observatory (LIGO) Data Grid via Open Science Grid technology. To enable this computational infrastructure, we configured, for the first time, a LIGO Data Grid Tier-1 Center that can submit heterogeneous LIGO workflows using Open Science Grid facilities. In order to enable a seamless connection between the LIGO Data Grid and Blue Waters via Open Science Grid, we utilize Shifter to containerize LIGO's workflow software. This work represents the first time Open Science Grid, Shifter, and Blue Waters are unified to tackle a scientific problem and, in particular, it is the first time a framework of this nature is used in the context of large scale gravitational wave data analysis. This new framework has been used in the last several weeks of LIGO's second discovery campaign to run the most computationally demanding gravitational wave search workflows on Blue Waters, and accelerate discovery in the emergent field of gravitational wave astrophysics. We discuss the implications of this novel framework for a wider ecosystem of Higher Performance Computing users.Comment: 10 pages, 10 figures. Accepted as a Full Research Paper to the 13th IEEE International Conference on eScienc

The impact of confounding on the associations of different adiposity measures with the incidence of cardiovascular disease: a cohort study of 296 535 adults of white European descent

Aims: The data regarding the associations of body mass index (BMI) with cardiovascular (CVD) risk, especially for those at the low categories of BMI, are conflicting. The aim of our study was to examine the associations of body composition (assessed by five different measures) with incident CVD outcomes in healthy individuals. Methods and results: A total of 296 535 participants (57.8% women) of white European descent without CVD at baseline from the UK biobank were included. Exposures were five different measures of adiposity. Fatal and non-fatal CVD events were the primary outcome. Low BMI (≤18.5 kg m−2) was associated with higher incidence of CVD and the lowest CVD risk was exhibited at BMI of 22–23 kg m−2 beyond, which the risk of CVD increased. This J-shaped association attenuated substantially in subgroup analyses, when we excluded participants with comorbidities. In contrast, the associations for the remaining adiposity measures were more linear; 1 SD increase in waist circumference was associated with a hazard ratio of 1.16 [95% confidence interval (CI) 1.13–1.19] for women and 1.10 (95% CI 1.08–1.13) for men with similar magnitude of associations for 1 SD increase in waist-to-hip ratio, waist-to-height ratio, and percentage body fat mass. Conclusion: Increasing adiposity has a detrimental association with CVD health in middle-aged men and women. The association of BMI with CVD appears more susceptible to confounding due to pre-existing comorbidities when compared with other adiposity measures. Any public misconception of a potential ‘protective’ effect of fat on CVD risk should be challenged

Leaf Growth and Senescence Rates in Brown-Back Wallaby Grass, \u3cem\u3eRytidosperma duttonianum\u3c/em\u3e

Knowledge of leaf turnover in grasses is necessary to model curing (the accumulation of dead material in the sward), which is not well represented in current pasture growth models, nor for many Australian native species. Leaf turnover begins with the appearance of successive leaves, which elongate until typically, a leaf ligule develops to indicate a mature, fully expanded length. Green leaf life span extends from appearance to the beginning of senescence, which ultimately leads to death (Fig. 1). Here, the individual rates of leaf growth and senescence for the Australian native brown-back wallaby grass, Rytidosperma duttonianum (Cashmore) Connor & Edgar, over the whole life cycle, are reported

A Plant-Physiology Approach to a Fire-y Problem

As vegetation dies, it dries and becomes more flammable. Fire agencies require accurate and timely assessments of curing (the percentage of dead material in the sward) to model grass fire behaviour and calculate fire danger ratings (Cheney and Sullivan 2008). Visual observation is commonplace and the more objective use of the Levy Rod is recommended, although both have drawbacks (Anderson et al. 2011). There is great potential for pasture growth models to provide curing estimates to assist with the management of wild grass fires (Gill et al. 2010). This PhD project focused on plant physiological characters to populate models that could be used to predict curing assessments for fire management purposes