Reconsideration of the QCD corrections to the ηc\eta_c decays into light hadrons using the principle of maximum conformality

In the paper, we analyze the $\eta_c$ decays into light hadrons at the next-to-leading order QCD corrections by applying the principle of maximum conformality (PMC). The relativistic correction at the ${\cal{O}}(\alpha_s v^2)$-order level has been included in the discussion, which gives about $10\%$ contribution to the ratio $R$. The PMC, which satisfies the renormalization group invariance, is designed to obtain a scale-fixed and scheme-independent prediction at any fixed order. To avoid the confusion of treating $n_f$-terms, we transform the usual $\overline{\rm MS}$ pQCD series into the one under the minimal momentum space subtraction scheme. To compare with the prediction under conventional scale setting, $R_{\rm{Conv,mMOM}-r}= \left(4.12^{+0.30}_{-0.28}\right)\times10^3$, after applying the PMC, we obtain $R_{\rm PMC,mMOM-r}=\left(6.09^{+0.62}_{-0.55}\right) \times10^3$, where the errors are squared averages of the ones caused by $m_c$ and $\Lambda_{\rm mMOM}$. The PMC prediction agrees with the recent PDG value within errors, i.e. $R^{\rm exp}=\left(6.3\pm0.5\right)\times10^3$. Thus we think the mismatching of the prediction under conventional scale-setting with the data is due to improper choice of scale, which however can be solved by using the PMC.Comment: 5 pages, 2 figure

Bis(4-acetyl-3-methyl-1-phenyl-1H-pyrazol-5-olato-κ2 O,O′)bis­(N,N-dimethyl­formamide-κO)nickel(II)

The title complex, [Ni(C12H11N2O2)2(C3H7NO)2], lies on on an inversion center. The NiII ion is coordinated in a slightly distorted octa­hedral coordination enviroment by four O atoms from two bis-chelating 4-acety-3-methyl-1-phenyl-1H-pyrazol-5-olate ligands in the equatorial plane and two O atoms from two N,N-dimethyl­formamide ligands in the axial sites. In the crystal structure, weak inter­molecular π–π stacking inter­actions with centroid–centroid distances of 3.7467 (13) Å link mol­ecules into chains extending alongthe b axis

N′-[(5-Methyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)(thio­phen-2-yl)methyl­idene]benzohydrazide

In the title compound, C22H18N4O2S, the seven-membered ring generated by an intra­molecular N—H⋯O hydrogen bond adopts an envelope conformation in both of the two independent mol­ecules in the asymmetric unit. In the crystal, mol­ecules are linked into C(9) chains along [100] by N—H⋯O hydrogen bonds. The mol­ecules are also weakly linked by C—H⋯O and C—H⋯N inter­actions, forming dimers with edge-connected R 2 2(9) rings. The dimers are inter­linked by further weak C—H⋯N hydrogen bonds into chains along [010]

A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs

Transcription factors (TFs), microRNAs (miRNAs), small interfering RNAs (siRNAs) and other functional non-coding small RNAs (sRNAs) are important gene regulators. Comparison of sRNA expression profiles between transgenic barley overexpressing a drought tolerant TF (TaDREB3) and non-transgenic control barley revealed many group-specific sRNAs. In addition, 42% of the shared sRNAs were differentially expressed between the two groups (|log2|>1). Furthermore, TaDREB3- derived sRNAs were only detected in transgenic barley despite the existence of homologous genes in non-transgenic barley. These results demonstrate that the TF strongly affects the expression of sRNAs and siRNAs could in turn affect the TF stability. The TF also affects size distribution and abundance of sRNAs including miRNAs. About half of the sRNAs in each group were derived from chloroplast. A sRNA derived from tRNA-His(GUG) encoded by the chloroplast genome is the most abundant sRNA, accounting for 42.2% of the total sRNAs in transgenic barley and 28.9% in non-transgenic barley. This sRNA, which targets a gene (TC245676) involved in biological processes, was only present in barley leaves but not roots. 124 and 136 miRNAs were detected in transgenic and non-transgenic barley, respectively. miR156 was the most abundant miRNA and up-regulated in transgenic barley, while miR168 was the most abundant miRNA and up-regulated in non-transgenic barley. Eight out of 20 predicted novel miRNAs were differentially expressed between the two groups. All the predicted novel miRNA targets were validated using a degradome library. Our data provide an insight into the effect of TF on the expression of sRNAs in barley.Michael Hackenberg, Bu-Jun Shi, Perry Gustafson and Peter Langridg

The cucumovirus 2b gene drives selection of inter-viral recombinants affecting the crossover site, the acceptor RNA and the rate of selection

RNA–RNA recombination is an important pathway in virus evolution and has been described for many viruses. However, the factors driving recombination or promoting the selection of recombinants are still unclear. Here, we show that the small movement protein (2b) was able to promote selection of RNA 1/2–RNA 3 recombinants within a chimeric virus having RNAs 1 and 2 from cucumber mosaic virus, and RNA 3 from the related tomato aspermy virus, along with heterologous 2b genes. The source of the 2b also determined the selection of the acceptor RNA and the crossover site, as well as affecting the rate of selection of the recombinant RNAs. The nature of the RNA 3 also influenced the selection of the recombinant RNAs. A 163-nt tandem repeat in RNA 3 significantly affected the rate of selection of the recombinant RNA, while a single nucleotide within the repeat affected the crossover site. The recombination occurred in a non-random manner, involved no intermediates and probably was generated via a copy-choice mechanism during (+) strand RNA synthesis

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing

Extent: 15p.BACKGROUND: Lupinus angustifolius L, also known as narrow-leafed lupin (NLL), is becoming an important grain legume crop that is valuable for sustainable farming and is becoming recognised as a potential human health food. Recent interest is being directed at NLL to improve grain production, disease and pest management and health benefits of the grain. However, studies have been hindered by a lack of extensive genomic resources for the species. RESULTS: A NLL BAC library was constructed consisting of 111,360 clones with an average insert size of 99.7 Kbp from cv Tanjil. The library has approximately 12 × genome coverage. Both ends of 9600 randomly selected BAC clones were sequenced to generate 13985 BAC end-sequences (BESs), covering approximately 1% of the NLL genome. These BESs permitted a preliminary characterisation of the NLL genome such as organisation and composition, with the BESs having approximately 39% G:C content, 16.6% repetitive DNA and 5.4% putative gene-encoding regions. From the BESs 9966 simple sequence repeat (SSR) motifs were identified and some of these are shown to be potential markers. CONCLUSIONS: The NLL BAC library and BAC-end sequences are powerful resources for genetic and genomic research on lupin. These resources will provide a robust platform for future high-resolution mapping, map-based cloning, comparative genomics and assembly of whole-genome sequencing data for the species.Ling-Ling Gao, James K. Hane, Lars G. Kamphuis, Rhonda Foley, Bu-Jun Shi, Craig A. Atkins and Karam B. Sing