Aminoacyl-tRNA Synthetase Complexes: Molecular Multitasking Revealed

The accurate synthesis of proteins, dictated by the corresponding nucleotide sequence encoded in mRNA, is essential for cell growth and survival. Central to this process are the aminoacyl-tRNA synthetases (aaRSs), which provide amino acid substrates for the growing polypeptide chain in the form of aminoacyl-tRNAs. The aaRSs are essential for coupling the correct amino acid and tRNA molecules, but are also known to associate in higher order complexes with proteins involved in processes beyond translation. Multiprotein complexes containing aaRSs are found in all three domains of life playing roles in splicing, apoptosis, viral assembly, and regulation of transcription and translation. An overview of the complexes aaRSs form in all domains of life is presented, demonstrating the extensive network of connections between the translational machinery and cellular components involved in a myriad of essential processes beyond protein synthesis

Putting hydrodynamic interactions to work: tagged particle separation

Separation of magnetically tagged cells is performed by attaching markers to a subset of cells in suspension and applying fields to pull from them in a variety of ways. The magnetic force is proportional to the field gradient, and the hydrodynamic interactions play only a passive, adverse role. Here we propose using a homogeneous rotating magnetic field only to make tagged particles rotate, and then performing the actual separation by means of hydrodynamic interactions, which thus play an active role. The method, which we explore here theoretically and by means of numerical simulations, lends itself naturally to sorting on large scales.Comment: Version accepted for publication - Europhysics Letter

Structural and Functional Mapping of the Archaeal Multi-aminoacyl-tRNA Synthetase Complex

Methanothermobacter thermautotrophicus contains a multi-aminoacyl-tRNA synthetase complex (MSC) of LysRS, LeuRS and ProRS. Elongation factor (EF) 1A also associates to the MSC, with LeuRS possibly acting as a core protein. Analysis of the MSC revealed that LysRS and ProRS specifically interact with the idiosyncratic N- and C- termini of LeuRS, respectively. EF-1A instead interacts with the inserted CP1 proofreading domain, consistent with models for post-transfer editing by class I synthetases such as LeuRS. Together with previous genetic data, these findings show that LeuRS plays a central role in mediating interactions within the archaeal MSC by acting as a core scaffolding protein

Controlled placement of enzymes on carbon nanotubes using comb-branched DNA

pre-printImmobilization is not only useful for preserving enzyme activity, but also to adhere an enzyme to a surface, such as an electrode, so that the enzyme does not leach into solution during testing. Current immobilization approaches do not readily allow for adjustments to the distance between the enzyme and the electrode or other enzymes. The ability to control the distance of enzymes relative to each other on an electrode can allow for optimal placement and improved current responses. In this report, we investigate the use of comb-branched DNA for enzyme immobilization. A DNA foundation strand was covalently attached to multiwalled carbon nanotubes on a glassy carbon electrode. Comb-branched DNA was then successfully formed using a previously-identified deoxyribozyme to attach DNA strands at specific locations on this foundation strand. By changing the foundation strands, the placement of the DNA strands can be adjusted, allowing for distance changes between the enzyme and the electrode surface. Using standard bioconjugation methods, alcohol dehydrogenase and glucose dehydrogenase were attached to these comb-branched DNA structures, resulting in enzyme immobilization on electrode surfaces. Amperometric analysis revealed both distance and DNA foundation strand length dependence for current response of these enzymes in the presence of their appropriate substrates

Contribution of oil and natural gas production to renewed increase of atmospheric methane (2007-2014): top-down estimate from ethane and methane column observations

Abstract. Harmonized time series of column-averaged mole fractions of atmospheric methane and ethane over the period 1999–2014 are derived from solar Fourier transform infrared (FTIR) measurements at the Zugspitze summit (47° N, 11° E; 2964 m a.s.l.) and at Lauder (45° S, 170° E; 370 m a.s.l.). Long-term trend analysis reveals a consistent renewed methane increase since 2007 of 6.2 [5.6, 6.9] ppb yr−1 (parts-per-billion per year) at the Zugspitze and 6.0 [5.3, 6.7] ppb yr−1 at Lauder (95 % confidence intervals). Several recent studies provide pieces of evidence that the renewed methane increase is most likely driven by two main factors: (i) increased methane emissions from tropical wetlands, followed by (ii) increased thermogenic methane emissions due to growing oil and natural gas production. Here, we quantify the magnitude of the second class of sources, using long-term measurements of atmospheric ethane as a tracer for thermogenic methane emissions. In 2007, after years of weak decline, the Zugspitze ethane time series shows the sudden onset of a significant positive trend (2.3 [1.8, 2.8]  ×  10−2 ppb yr−1 for 2007–2014), while a negative trend persists at Lauder after 2007 (−0.4 [−0.6, −0.1]  ×  10−2 ppb yr−1). Zugspitze methane and ethane time series are significantly correlated for the period 2007–2014 and can be assigned to thermogenic methane emissions with an ethane-to-methane ratio (EMR) of 12–19 %. We present optimized emission scenarios for 2007–2014 derived from an atmospheric two-box model. From our trend observations we infer a total ethane emission increase over the period 2007–2014 from oil and natural gas sources of 1–11 Tg yr−1 along with an overall methane emission increase of 24–45 Tg yr−1. Based on these results, the oil and natural gas emission contribution (C) to the renewed methane increase is deduced using three different emission scenarios with dedicated EMR ranges. Reference scenario 1 assumes an oil and gas emission combination with EMR  =  7.0–16.2 %, which results in a minimum contribution C  >  39 % (given as lower bound of 95 % confidence interval). Beside this most plausible scenario 1, we consider two less realistic limiting cases of pure oil-related emissions (scenario 2 with EMR  =  16.2–31.4 %) and pure natural gas sources (scenario 3 with EMR  =  4.4–7.0  %), which result in C  >  18 % and C  >  73 %, respectively. Our results suggest that long-term observations of column-averaged ethane provide a valuable constraint on the source attribution of methane emission changes and provide basic knowledge for developing effective climate change mitigation strategies

Effect of Control Mode and Test Rate on the Measured Fracture Toughness of Advanced Ceramics

The effects of control mode and test rate on the measured fracture toughness of ceramics were evaluated by using chevron-notched flexure specimens in accordance with ASTM C1421. The use of stroke control gave consistent results with about 2% (statistically insignificant) variation in measured fracture toughness for a very wide range of rates (0.005 to 0.5 mm/min). Use of strain or crack mouth opening displacement (CMOD) control gave approx. 5% (statistically significant) variation over a very wide range of rates (1 to 80 m/m/s), with the measurements being a function of rate. However, the rate effect was eliminated by use of dry nitrogen, implying a stress corrosion effect rather than a stability effect. With the use of a nitrogen environment during strain controlled tests, fracture toughness values were within about 1% over a wide range of rates (1 to 80 micons/m/s). CMOD or strain control did allow stable crack extension well past maximum force, and thus is preferred for energy calculations. The effort is being used to confirm recommendations in ASTM Test Method C1421 on fracture toughness measurement

Effects of Aqueous Solutions on the Slow Crack Growth of Soda-Lime-Silicate Glass

The slow crack growth (SCG) parameters of soda-lime-silicate were measured in distilled and saltwater of various concentrations in order to determine if the presence of salt and the contaminate formation of a weak sodium film affects stress corrosion susceptibility. Past research indicates that solvents affect the rate of crack growth; however, the effects of salt have not been studied. The results indicate a small but statistically significant effect on the SCG parameters A and n at high concentrations; however, for typical engineering purposes, the effect can be ignored

Effect of Control Mode and Test Rate on Fracture Toughness of Advanced Ceramics

The effects of control mode and rate on the fracture toughness of ceramics were measured by using chevron-notched flexure specimen in accordance with ASTM C1421. The use of stroke control gave consistent results with about 2% variation in measured fracture toughness for a very wide range of rates (0.005 to 0.5 mm/min). Use of strain or CMOD control gave ~5% variation over a very wide range of rates, with the measurements being a function of rate. However, the effect was eliminated by use of dry nitrogen, implying a stress corrosion effect rather than a stability effect. With the use of nitrogen for strain control, fracture toughness values were within about 1% over a wide range of rates (1 to 80 /s). CMOD or strain control did allow stable crack extension well past maximum load, and thus is preferred for energy calculations. The effort is being used to confirm recommendations in ASTM International standard C1421 on fracture toughness measurement

Investigating routes toward atomic layer deposition of silicon carbide: Ab initio screening of potential silicon and carbon precursors

Silicon carbide (SiC) is a promising material for electronics due to its hardness, and ability to carry high currents and high operating temperature. SiC films are currently deposited using chemical vapor deposition (CVD) at high temperatures 1500–1600 °C. However, there is a need to deposit SiC-based films on the surface of high aspect ratio features at low temperatures. One of the most precise thin film deposition techniques on high-aspect-ratio surfaces that operates at low temperatures is atomic layer deposition (ALD). However, there are currently no known methods for ALD of SiC. Herein, the authors present a first-principles thermodynamic analysis so as to screen different precursor combinations for SiC thin films. The authors do this by calculating the Gibbs energy ΔGΔG of the reaction using density functional theory and including the effects of pressure and temperature. This theoretical model was validated for existing chemical reactions in CVD of SiC at 1000 °C. The precursors disilane (Si2H6), silane (SiH4), or monochlorosilane (SiH3Cl) with ethyne (C2H2), carbontetrachloride (CCl4), or trichloromethane (CHCl3) were predicted to be the most promising for ALD of SiC at 400 °C