Impact of template backbone heterogeneity on RNA polymerase II transcription.

Variations in the sugar component (ribose or deoxyribose) and the nature of the phosphodiester linkage (3'-5' or 2'-5' orientation) have been a challenge for genetic information transfer from the very beginning of evolution. RNA polymerase II (pol II) governs the transcription of DNA into precursor mRNA in all eukaryotic cells. How pol II recognizes DNA template backbone (phosphodiester linkage and sugar) and whether it tolerates the backbone heterogeneity remain elusive. Such knowledge is not only important for elucidating the chemical basis of transcriptional fidelity but also provides new insights into molecular evolution. In this study, we systematically and quantitatively investigated pol II transcriptional behaviors through different template backbone variants. We revealed that pol II can well tolerate and bypass sugar heterogeneity sites at the template but stalls at phosphodiester linkage heterogeneity sites. The distinct impacts of these two backbone components on pol II transcription reveal the molecular basis of template recognition during pol II transcription and provide the evolutionary insight from the RNA world to the contemporary 'imperfect' DNA world. In addition, our results also reveal the transcriptional consequences from ribose-containing genomic DNA

Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution.

RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous 'synthetic nucleic acid substitution' strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of substrate influences the rate of P-O bond cleavage and formation during nucleotide incorporation is still unclear. Here, by employing β,γ-bridging atom-'substituted' NTPs, we elucidate how the methylene substitution in the pyrophosphate leaving group affects cognate and non-cognate nucleotide incorporation. Intriguingly, the effect of the β,γ-methylene substitution on the non-cognate UTP/dT scaffold (∼3-fold decrease in kpol) is significantly different from that of the cognate ATP/dT scaffold (∼130-fold decrease in kpol). Removal of the wobble hydrogen bonds in U:dT recovers a strong response to methylene substitution of UTP. Our kinetic and modeling studies are consistent with a unique altered transition state for bond formation and cleavage for UTP/dT incorporation compared with ATP/dT incorporation. Collectively, our data reveals the functional interplay between NTP triphosphate moiety and base pair hydrogen bonding recognition during nucleotide incorporation

Effects of annual flow characteristics on the freshwater life history of Chinese sturgeon: concern inferred from the number of seaward migrating juveniles

Abstract Since 2003, the flow characteristics of the Yangtze River, currently the only river where the protected Chinese sturgeon, Acipenser sinensis, spawns and where the young grows to the 6 to 8 month juvenile stage, has been regulated by the operation of the Three Gorges Project. The number of seaward migrating juveniles captured (NSMJC) in the Yangtze estuary from 2002 to 2010 was significantly positively related (Pearson correlation, P (two tailed) &lt;0.01; Lg (NSMJC) = 0.870 + 3.930 × AASC, R = 0.940, P = 0.000) to the annual sediment load and annual average sediment concentration (AASC) of the previous year, when adults entered the river and migrated upstream, used refuge areas, and spawned, and when early life stages were reared. This suggests that silt content may have a major effect on adult spawning success and rearing of early life stages. Based on the correlation between numbers of juveniles captured and numbers of adults in the spawning areas in the previous year (Pearson correlation, R = 0.965, P (two tailed) = 0.008), we speculated that the sediment characteristics affected the migration and gonad development of mature individuals and, indirectly, the number of juveniles reaching the Yangtze estuary during the following year. Decreased silt levels in the Yangtze River following installation of the Three Gorges Project may be having a deleterious effect on Chinese sturgeon reproduction and needs further research.</jats:p

Phenomenological study on the significance of the scalar potential and Lamb shift

We indicated in our previous work that for QED the contributions of the scalar potential which appears at the loop level is much smaller than that of the vector potential and in fact negligible. But the situation may be different for QCD, one reason is that the loop effects are more significant because $\alpha_s$ is much larger than $\alpha$, and secondly the non-perturbative QCD effects may induce the scalar potential. In this work, we phenomenologically study the contribution of the scalar potential to the spectra of charmonia. Taking into account both vector and scalar potentials, by fitting the well measured charmonia spectra, we re-fix the relevant parameters and test them by calculating other states of the charmonia family. We also consider the role of the Lamb shift and present the numerical results with and without involving the Lamb shift

Revealing of the Activation Pathway and Cathode Electrolyte Interphase Evolution of Li-Rich 0.5Li2MnO3·0.5LiNi0.3Co0.3Mn0.4O2 Cathode by in Situ Electrochemical Quartz Crystal Microbalance.

The first-cycle behavior of layered Li-rich oxides, including Li2MnO3 activation and cathode electrolyte interphase (CEI) formation, significantly influences their electrochemical performance. However, the Li2MnO3 activation pathway and the CEI formation process are still controversial. Here, the first-cycle properties of xLi2MnO3·(1- x) LiNi0.3Co0.3Mn0.4O2 ( x = 0, 0.5, 1) cathode materials were studied with an in situ electrochemical quartz crystal microbalance (EQCM). The results demonstrate that a synergistic effect between the layered Li2MnO3 and LiNi0.3Co0.3Mn0.4O2 structures can significantly affect the activation pathway of Li1.2Ni0.12Co0.12Mn0.56O2, leading to an extra-high capacity. It is demonstrated that Li2MnO3 activation in Li-rich materials is dominated by electrochemical decomposition (oxygen redox), which is different from the activation process of pure Li2MnO3 governed by chemical decomposition (Li2O evolution). CEI evolution is closely related to Li+ extraction/insertion. The valence state variation of the metal ions (Ni, Co, Mn) in Li-rich materials can promote CEI formation. This study is of significance for understanding and designing Li-rich cathode-based batteries

2-Hy­droxy-3-oct­yloxy-N,N,N-trimethyl­propan-1-aminium bromide

In the title compound, C14H32NO2 +·Br−, organic cationsstacked parallel to the a axis andbromide anions placed between the head groups of the cations form ionic pairs via weak inter­molecular O—H⋯Br hydrogen bonds. The octyl chain in the cation adopts an all-trans conformation. The O—CH2—CH(—OH)—CH2 portion of the molecule is disordered over two sets of sites with occupancy factors of 0.57 (3) and 0.47 (3)

Rare decays B\to M\nu\bar{\nu} in the TC2 model and the LHT model

In the framework of the topcolor-assisted technicolor ($TC2$) model and the littlest Higgs model with $T$-parity ($LHT$ model), we consider the rare B decays $B\to M\nu\bar{\nu}$ with $M=\pi,K,\rho,$ or $K^{\ast}$. We find that the contributions of the $TC2$ model to the branching ratios of these decay processes are larger than those for the $LHT$ model. The experimental upper limits for some branching ratios can give severe constraints on the free parameters of the $TC2$ model.Comment: 25 pages, 7 figure

Monolithically integrated InAs/InGaAs quantum dot photodetectors on silicon substrates

We report InAs/InGaAs quantum dot (QD) waveguide photodetectors (PD) monolithically grown on silicon substrates. A high-crystalline quality GaAs-on-Si template was achieved by aspect ratio trapping together with the combined effects of cyclic thermal annealing and strain-balancing layer stacks. An ultra-low dark current of 0.8 nA and an internal responsivity of 0.9 A/W were measured in the O band. We also report, to the best of our knowledge, the first characterization of high-speed performance and the first demonstration of the on-chip photodetection for this QD-on-silicon system. The monolithically integrated waveguide PD shares the same platform as the previously demonstrated micro-ring lasers and can thus be integrated with laser sources for power monitors or amplifiers for pre-amplified receivers. (C) 2017 Optical Society of Americ