Unexpected Accumulation of ncm\u3csup\u3e5\u3c/sup\u3eU and ncm\u3csup\u3e5\u3c/sup\u3es\u3csup\u3e2\u3c/sup\u3eU in a \u3cem\u3etrm9\u3c/em\u3e Mutant Suggests an Additional Step in the Synthesis of mcm\u3csup\u3e5\u3c/sup\u3eU and mcm\u3csup\u3e5\u3c/sup\u3es\u3csup\u3e2\u3c/sup\u3eU

Background Transfer RNAs are synthesized as a primary transcript that is processed to produce a mature tRNA. As part of the maturation process, a subset of the nucleosides are modified. Modifications in the anticodon region often modulate the decoding ability of the tRNA. At position 34, the majority of yeast cytosolic tRNA species that have a uridine are modified to 5-carbamoylmethyluridine (ncm5U), 5-carbamoylmethyl-2′-O-methyluridine (ncm5Um), 5-methoxycarbonylmethyl-uridine (mcm5U) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U). The formation of mcm5 and ncm5 side chains involves a complex pathway, where the last step in formation of mcm5 is a methyl esterification of cm5 dependent on the Trm9 and Trm112 proteins. Methodology and Principal Findings Both Trm9 and Trm112 are required for the last step in formation of mcm5 side chains at wobble uridines. By co-expressing a histidine-tagged Trm9p together with a native Trm112p in E. coli, these two proteins purified as a complex. The presence of Trm112p dramatically improves the methyltransferase activity of Trm9p in vitro. Single tRNA species that normally contain mcm5U or mcm5s2U nucleosides were isolated from trm9Δ or trm112Δ mutants and the presence of modified nucleosides was analyzed by HPLC. In both mutants, mcm5U and mcm5s2U nucleosides are absent in tRNAs and the major intermediates accumulating were ncm5U and ncm5s2U, not the expected cm5U and cm5s2U. Conclusions Trm9p and Trm112p function together at the final step in formation of mcm5U in tRNA by using the intermediate cm5U as a substrate. In tRNA isolated from trm9Δ and trm112Δ strains, ncm5U and ncm5s2U nucleosides accumulate, questioning the order of nucleoside intermediate formation of the mcm5 side chain. We propose two alternative explanations for this observation. One is that the intermediate cm5U is generated from ncm5U by a yet unknown mechanism and the other is that cm5U is formed before ncm5U and mcm5U

Electronic Tuning of Mixed Quinoidal‐Aromatic Conjugated Polyelectrolytes: Direct Ionic Substitution on Polymer Main‐Chains

The synthesis of conjugated polymers with ionic substituents directly bound to their main chain repeat units is a strategy for generating strongly electron-accepting conjugated polyelectrolytes, as demonstrated through the synthesis of a series of ionic azaquinodimethane (iAQM) compounds. The introduction of cationic substituents onto the quinoidal para-azaquinodimethane (AQM) core gives rise to a strongly electron-accepting building block, which can be employed in the synthesis of ionic small molecules and conjugated polyelectrolytes (CPEs). Electrochemical measurements alongside theoretical calculations indicate notably low-lying LUMO values for the iAQMs. The optical band gaps measured for these compounds are highly tunable based on structure, ranging from 2.30 eV in small molecules down to 1.22 eV in polymers. The iAQM small molecules and CPEs showcase the band gap reduction effects of combining the donor-acceptor strategy with the bond-length alternation reduction strategy. As a demonstration of their utility, the iAQM CPEs so generated were used as active agents in photothermal therapy

Algebraic Bethe ansatz for the supersymmetric t−Jt-J model with reflecting boundary conditions

In the framework of the graded quantum inverse scattering method (QISM), we obtain the eigenvalues and eigenvectors of the supersymmetric $t-J$ model with reflecting boundary conditions in FFB background. The corresponding Bethe ansatz equations are obtained.Comment: Latex file, 23 Page

Compressibility of titanosilicate melts

The effect of composition on the relaxed adiabatic bulk modulus (K0) of a range of alkali- and alkaline earth-titanosilicate [X 2 n/n+ TiSiO5 (X=Li, Na, K, Rb, Cs, Ca, Sr, Ba)] melts has been investigated. The relaxed bulk moduli of these melts have been measured using ultrasonic interferometric methods at frequencies of 3, 5 and 7 MHz in the temperature range of 950 to 1600°C (0.02 Pa s < s < 5 Pa s). The bulk moduli of these melts decrease with increasing cation size from Li to Cs and Ca to Ba, and with increasing temperature. The bulk moduli of the Li-, Na-, Ca- and Ba-bearing metasilicate melts decrease with the addition of both TiO2 and SiO2 whereas those of the K-, Rb- and Cs-bearing melts increase. Linear fits to the bulk modulus versus volume fraction of TiO2 do not converge to a common compressibility of the TiO2 component, indicating that the structural role of TiO2 in these melts is dependent on the identity of the cation. This proposition is supported by a number of other property data for these and related melt compositions including heat capacity and density, as well as structural inferences from X-ray absorption spectroscopy (XANES). The compositional dependence of the compressibility of the TiO2 component in these melts explains the difficulty incurred in previous attempts to incorporate TiO2 in calculation schemes for melt compressibility. The empirical relationship KV-4/3 for isostructural materials has been used to evaluate the compressibility-related structural changes occurring in these melts. The alkali metasilicate and disilicate melts are isostructural, independent of the cation. The addition of Ti to the metasilicate composition (i.e. X2TiSiO5), however, results in a series of melts which are not isostructural. The alkaline-earth metasilicate and disilicate compositions are not isostructural, but the addition of Ti to the metasilicate compositions (i.e. XTiSiO5) would appear, on the basis of modulus-volume systematics, to result in the melts becoming isostructural with respect to compressibility

The imaginary part of the gap function in color superconductivity

We clarify general properties of the energy gap regarding its functional dependence on the energy-momentum dictated by the invariance under a space inversion or a time reversal. Then we derive perturbatively the equation of the imaginary part of the gap function for dense QCD in weak coupling and generalize our results from 2SC case to CFL case. We confirm that the imaginary part is down by $g$ relative to the real part in weak coupling. The numerical results show that, up to the leading order, the imaginary part is no larger than one MeV at extremely large densities and can be as large as several MeV the densities are of physical interest.Comment: 15 pages, 2 figures, typos corrected, a figure replaced. The version to be appeared in Nucl.Phys.

DNA end resection by Dna2–Sgs1–RPA and its stimulation by Top3–Rmi1 and Mre11–Rad50–Xrs2

The repair of DNA double-strand breaks (DSBs) by homologous recombination requires processing of broken ends. For repair to start, the DSB must first be resected to generate a 3′-single-stranded DNA (ssDNA) overhang, which becomes a substrate for the DNA strand exchange protein, Rad51 (ref. 1). Genetic studies have implicated a multitude of proteins in the process, including helicases, nucleases and topoisomerases. Here we biochemically reconstitute elements of the resection process and reveal that it requires the nuclease Dna2, the RecQ-family helicase Sgs1 and the ssDNA-binding protein replication protein-A (RPA). We establish that Dna2, Sgs1 and RPA constitute a minimal protein complex capable of DNA resection in vitro. Sgs1 helicase unwinds the DNA to produce an intermediate that is digested by Dna2, and RPA stimulates DNA unwinding by Sgs1 in a species-specific manner. Interestingly, RPA is also required both to direct Dna2 nucleolytic activity to the 5′-terminated strand of the DNA break and to inhibit 3′ to 5′ degradation by Dna2, actions that generate and protect the 3′-ssDNA overhang, respectively. In addition to this core machinery, we establish that both the topoisomerase 3 (Top3) and Rmi1 complex and the Mre11–Rad50–Xrs2 complex (MRX) have important roles as stimulatory components. Stimulation of end resection by the Top3–Rmi1 heterodimer and the MRX proteins is by complex formation with Sgs1 (refs 5, 6), which unexpectedly stimulates DNA unwinding. We suggest that Top3–Rmi1 and MRX are important for recruitment of the Sgs1–Dna2 complex to DSBs. Our experiments provide a mechanistic framework for understanding the initial steps of recombinational DNA repair in eukaryotes

E‐ARK Dissemination Information Package (DIP) Final Specification

The primary aim of this report is to present the final version of the E-ARK Dissemination Information Package (DIP) formats. The secondary aim is to describe the access scenarios in which these DIP formats will be rendered for use

Fatigue evaluation in maintenance and assembly operations by digital human simulation

Virtual human techniques have been used a lot in industrial design in order to consider human factors and ergonomics as early as possible. The physical status (the physical capacity of virtual human) has been mostly treated as invariable in the current available human simulation tools, while indeed the physical capacity varies along time in an operation and the change of the physical capacity depends on the history of the work as well. Virtual Human Status is proposed in this paper in order to assess the difficulty of manual handling operations, especially from the physical perspective. The decrease of the physical capacity before and after an operation is used as an index to indicate the work difficulty. The reduction of physical strength is simulated in a theoretical approach on the basis of a fatigue model in which fatigue resistances of different muscle groups were regressed from 24 existing maximum endurance time (MET) models. A framework based on digital human modeling technique is established to realize the comparison of physical status. An assembly case in airplane assembly is simulated and analyzed under the framework. The endurance time and the decrease of the joint moment strengths are simulated. The experimental result in simulated operations under laboratory conditions confirms the feasibility of the theoretical approach

Neutron Scattering and Its Application to Strongly Correlated Systems

Neutron scattering is a powerful probe of strongly correlated systems. It can directly detect common phenomena such as magnetic order, and can be used to determine the coupling between magnetic moments through measurements of the spin-wave dispersions. In the absence of magnetic order, one can detect diffuse scattering and dynamic correlations. Neutrons are also sensitive to the arrangement of atoms in a solid (crystal structure) and lattice dynamics (phonons). In this chapter, we provide an introduction to neutrons and neutron sources. The neutron scattering cross section is described and formulas are given for nuclear diffraction, phonon scattering, magnetic diffraction, and magnon scattering. As an experimental example, we describe measurements of antiferromagnetic order, spin dynamics, and their evolution in the La(2-x)Ba(x)CuO(4) family of high-temperature superconductors.Comment: 31 pages, chapter for "Strongly Correlated Systems: Experimental Techniques", edited by A. Avella and F. Mancin