Estimation of divergence times for major lineages of galliform birds: Evidence from complete mitochondrial genome sequences

Determining an absolute timescale for avian evolutionary history has been recently challenged by the relaxed molecular clock methods, that rates of molecular evolution can vary significantly among organisms. In this study, we used relaxed molecular clocks to date the divergence of major lineages of Galliformes based on complete mitochondrial genomes. A nucleotide dataset of 13 concatenated protein-coding genes from 22 species of Galliformes was used to investigate the evolutionary divergences within the group. Using Gallus bravardi, Schaubortyx and Gallinuloides fossils ascalibration points, divergence times analyses were performed with four relaxed molecular clock methods as follows: (1) Bayesian method of Multidivtime; (2) Bayesian Markov chain Monte Carlo (MCMC) analysis of the Bayesian evolutionary analysis by sampling trees (BEAST); (3) local rate minimum deformation method (LRMD) of TREEFINDER; and (4) nonparametric rate smoothing (NPRS) of TREEFINDER. The various relaxed clock methods all indicated that (1) Megapodiidae originated in theLate Cretaceous; (2) Numididae, Phasianidae, Arborophilinae and Coturnicinae originated in the Eocene of Palaeogene; (3) Pavoninae and Gallininae originated at the Eocene-Oligocene boundary; (4) Phasianinae and Meleagridinae originated in the Oligocene; (5) divergence times estimation among most genera of Phasianidae were much older than those of the previous studies. Our results might provide a more likely time scale for evolutionary history of the galliform birds

The Evolving Beef Industry and Its Sustainability in Western China

The beef industry in China has started to develop since the 1980s. Since then, its production system has been evolving significantly from subsistence production towards business operation in farmer households. As demands continue to grow, China will become the largest beef consumption country in the world by the year of 2025. The beef production in China’s western agriculture regions is gaining significant role in the beef industry of China. Utilization of corn stover and other agriculture aftermath is seen as the competitive advantage of development of the beef industry. Over the last 30 years the beef production efficiency has been improved remarkably. But, the beef industry faces many challenges along with the evolving beef production system. As a result, both beef population and production are declining steadily in the last 5 years. In order to establish a sustained beef industry in western China, there is need to discuss and study the challenges and issues, as well as prepare the technologies and regulations for the evolving beef industry to ensure its sustainability. Efficiency of production system, technologies available for animal health, straw and agriculture aftermath utilization, are the key aspects for the sustained beef industry in western China. Establishment of the effective breeding program suited to production system in Western China is a cornerstone of a sustained beef industry. Effective animal health and vaccination programs need to be established and implemented to ensure the food safety and quality. Finally, optimizations of beef production systems need to ensure the competitiveness of the beef industry and its sustainability

Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents

OBJECTIVE: Patients with renal failure suffer from symptoms caused by uraemic toxins, possibly of gut microbial origin, as deduced from studies in animals. The aim of the study is to characterise relationships between the intestinal microbiome composition, uraemic toxins and renal failure symptoms in human end-stage renal disease (ESRD). DESIGN: Characterisation of gut microbiome, serum and faecal metabolome and human phenotypes in a cohort of 223 patients with ESRD and 69 healthy controls. Multidimensional data integration to reveal links between these datasets and the use of chronic kidney disease (CKD) rodent models to test the effects of intestinal microbiome on toxin accumulation and disease severity. RESULTS: A group of microbial species enriched in ESRD correlates tightly to patient clinical variables and encode functions involved in toxin and secondary bile acids synthesis; the relative abundance of the microbial functions correlates with the serum or faecal concentrations of these metabolites. Microbiota from patients transplanted to renal injured germ-free mice or antibiotic-treated rats induce higher production of serum uraemic toxins and aggravated renal fibrosis and oxidative stress more than microbiota from controls. Two of the species, Eggerthella lenta and Fusobacterium nucleatum, increase uraemic toxins production and promote renal disease development in a CKD rat model. A probiotic Bifidobacterium animalis decreases abundance of these species, reduces levels of toxins and the severity of the disease in rats. CONCLUSION: Aberrant gut microbiota in patients with ESRD sculpts a detrimental metabolome aggravating clinical outcomes, suggesting that the gut microbiota will be a promising target for diminishing uraemic toxicity in those patients. TRIAL REGISTRATION NUMBER: This study was registered at ClinicalTrials.gov (NCT03010696)

Integrative analyses of transcriptome sequencing identify novel functional lncRNAs in esophageal squamous cell carcinoma.

Long non-coding RNAs (lncRNAs) have a critical role in cancer initiation and progression, and thus may mediate oncogenic or tumor suppressing effects, as well as be a new class of cancer therapeutic targets. We performed high-throughput sequencing of RNA (RNA-seq) to investigate the expression level of lncRNAs and protein-coding genes in 30 esophageal samples, comprised of 15 esophageal squamous cell carcinoma (ESCC) samples and their 15 paired non-tumor tissues. We further developed an integrative bioinformatics method, denoted URW-LPE, to identify key functional lncRNAs that regulate expression of downstream protein-coding genes in ESCC. A number of known onco-lncRNA and many putative novel ones were effectively identified by URW-LPE. Importantly, we identified lncRNA625 as a novel regulator of ESCC cell proliferation, invasion and migration. ESCC patients with high lncRNA625 expression had significantly shorter survival time than those with low expression. LncRNA625 also showed specific prognostic value for patients with metastatic ESCC. Finally, we identified E1A-binding protein p300 (EP300) as a downstream executor of lncRNA625-induced transcriptional responses. These findings establish a catalog of novel cancer-associated functional lncRNAs, which will promote our understanding of lncRNA-mediated regulation in this malignancy

Observation of ηc→ωω\eta_c\to\omega\omega in J/ψ→γωωJ/\psi\to\gamma\omega\omega

Using a sample of $(1310.6\pm7.0)\times10^6$ $J/\psi$ events recorded with the BESIII detector at the symmetric electron positron collider BEPCII, we report the observation of the decay of the $(1^1 S_0)$ charmonium state $\eta_c$ into a pair of $\omega$ mesons in the process $J/\psi\to\gamma\omega\omega$. The branching fraction is measured for the first time to be $\mathcal{B}(\eta_c\to\omega\omega)= (2.88\pm0.10\pm0.46\pm0.68)\times10^{-3}$, where the first uncertainty is statistical, the second systematic and the third is from the uncertainty of $\mathcal{B}(J/\psi\to\gamma\eta_c)$. The mass and width of the $\eta_c$ are determined as $M=(2985.9\pm0.7\pm2.1)\,$MeV/$c^2$ and $\Gamma=(33.8\pm1.6\pm4.1)\,$MeV.Comment: 13 pages, 6 figure

Observation and study of the decay J/ψ→ϕηη′J/\psi\rightarrow\phi\eta\eta'

We report the observation and study of the decay $J/\psi\rightarrow\phi\eta\eta'$ using $1.3\times{10^9}$ $J/\psi$ events collected with the BESIII detector. Its branching fraction, including all possible intermediate states, is measured to be $(2.32\pm0.06\pm0.16)\times{10^{-4}}$. We also report evidence for a structure, denoted as $X$, in the $\phi\eta'$ mass spectrum in the $2.0-2.1$ GeV/$c^2$ region. Using two decay modes of the $\eta'$ meson ($\gamma\pi^+\pi^-$ and $\eta\pi^+\pi^-$), a simultaneous fit to the $\phi\eta'$ mass spectra is performed. Assuming the quantum numbers of the $X$ to be $J^P = 1^-$, its significance is found to be 4.4$\sigma$, with a mass and width of $(2002.1 \pm 27.5 \pm 21.4)$ MeV/$c^2$ and $(129 \pm 17 \pm 9)$ MeV, respectively, and a product branching fraction $\mathcal{B}(J/\psi\rightarrow\eta{}X)\times{}\mathcal{B}(X\rightarrow\phi\eta')=(9.8 \pm 1.2 \pm 1.7)\times10^{-5}$. Alternatively, assuming $J^P = 1^+$, the significance is 3.8$\sigma$, with a mass and width of $(2062.8 \pm 13.1 \pm 7.2)$ MeV/$c^2$ and $(177 \pm 36 \pm 35)$ MeV, respectively, and a product branching fraction $\mathcal{B}(J/\psi\rightarrow\eta{}X)\times{}\mathcal{B}(X\rightarrow\phi\eta')=(9.6 \pm 1.4 \pm 2.0)\times10^{-5}$. The angular distribution of $J/\psi\rightarrow\eta{}X$ is studied and the two $J^P$ assumptions of the $X$ cannot be clearly distinguished due to the limited statistics. In all measurements the first uncertainties are statistical and the second systematic.Comment: 10 pages, 6 figures and 4 table

The DArk Matter Particle Explorer mission

The DArk Matter Particle Explorer (DAMPE), one of the four scientific space science missions within the framework of the Strategic Pioneer Program on Space Science of the Chinese Academy of Sciences, is a general purpose high energy cosmic-ray and gamma-ray observatory, which was successfully launched on December 17th, 2015 from the Jiuquan Satellite Launch Center. The DAMPE scientific objectives include the study of galactic cosmic rays up to $\sim 10$ TeV and hundreds of TeV for electrons/gammas and nuclei respectively, and the search for dark matter signatures in their spectra. In this paper we illustrate the layout of the DAMPE instrument, and discuss the results of beam tests and calibrations performed on ground. Finally we present the expected performance in space and give an overview of the mission key scientific goals.Comment: 45 pages, including 29 figures and 6 tables. Published in Astropart. Phy