The Genome of Ganderma lucidum Provide Insights into Triterpense Biosynthesis and Wood Degradation

BACKGROUND: Ganoderma lucidum (Reishi or Ling Zhi) is one of the most famous Traditional Chinese Medicines and has been widely used in the treatment of various human diseases in Asia countries. It is also a fungus with strong wood degradation ability with potential in bioenergy production. However, genes, pathways and mechanisms of these functions are still unknown. METHODOLOGY/PRINCIPAL FINDINGS: The genome of G. lucidum was sequenced and assembled into a 39.9 megabases (Mb) draft genome, which encoded 12,080 protein-coding genes and ∼83% of them were similar to public sequences. We performed comprehensive annotation for G. lucidum genes and made comparisons with genes in other fungi genomes. Genes in the biosynthesis of the main G. lucidum active ingredients, ganoderic acids (GAs), were characterized. Among the GAs synthases, we identified a fusion gene, the N and C terminal of which are homologous to two different enzymes. Moreover, the fusion gene was only found in basidiomycetes. As a white rot fungus with wood degradation ability, abundant carbohydrate-active enzymes and ligninolytic enzymes were identified in the G. lucidum genome and were compared with other fungi. CONCLUSIONS/SIGNIFICANCE: The genome sequence and well annotation of G. lucidum will provide new insights in function analyses including its medicinal mechanism. The characterization of genes in the triterpene biosynthesis and wood degradation will facilitate bio-engineering research in the production of its active ingredients and bioenergy

A Policy-Driven Large Scale Ecological Restoration: Quantifying Ecosystem Services Changes in the Loess Plateau of China

As one of the key tools for regulating human-ecosystem relations, environmental conservation policies can promote ecological rehabilitation across a variety of spatiotemporal scales. However, quantifying the ecological effects of such policies at the regional level is difficult. A case study was conducted at the regional level in the ecologically vulnerable region of the Loess Plateau, China, through the use of several methods including the Universal Soil Loss Equation (USLE), hydrological modeling and multivariate analysis. An assessment of the changes over the period of 2000–2008 in four key ecosystem services was undertaken to determine the effects of the Chinese government's ecological rehabilitation initiatives implemented in 1999. These ecosystem services included water regulation, soil conservation, carbon sequestration and grain production. Significant conversions of farmland to woodland and grassland were found to have resulted in enhanced soil conservation and carbon sequestration, but decreased regional water yield under a warming and drying climate trend. The total grain production increased in spite of a significant decline in farmland acreage. These trends have been attributed to the strong socioeconomic incentives embedded in the ecological rehabilitation policy. Although some positive policy results have been achieved over the last decade, large uncertainty remains regarding long-term policy effects on the sustainability of ecological rehabilitation performance and ecosystem service enhancement. To reduce such uncertainty, this study calls for an adaptive management approach to regional ecological rehabilitation policy to be adopted, with a focus on the dynamic interactions between people and their environments in a changing world

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Reactive oxygen species and male reproductive hormones

Reports of the increasing incidence of male infertility paired with decreasing semen quality have triggered studies on the effects of lifestyle and environmental factors on the male reproductive potential. There are numerous exogenous and endogenous factors that are able to induce excessive production of reactive oxygen species (ROS) beyond that of cellular antioxidant capacity, thus causing oxidative stress. In turn, oxidative stress negatively affects male reproductive functions and may induce infertility either directly or indirectly by affecting the hypothalamus-pituitary-gonadal (HPG) axis and/or disrupting its crosstalk with other hormonal axes. This review discusses the important exogenous and endogenous factors leading to the generation of ROS in different parts of the male reproductive tract. It also highlights the negative impact of oxidative stress on the regulation and cross-talk between the reproductive hormones. It further describes the mechanism of ROS-induced derangement of male reproductive hormonal profiles that could ultimately lead to male infertility. An understanding of the disruptive effects of ROS on male reproductive hormones would encourage further investigations directed towards the prevention of ROS-mediated hormonal imbalances, which in turn could help in the management of male infertility

Submicron aerosols at thirteen diversified sites in China: size distribution, new particle formation and corresponding contribution to cloud condensation nuclei production

Understanding the particle number size distributions in diversified atmospheric environments is important in order to design mitigation strategies related to submicron particles and their effects on regional air quality, haze and human health. In this study, we conducted 15 different field measurement campaigns between 2007 and 2011 at 13 individual sites in China, including five urban sites, four regional sites, three coastal/background sites and one ship cruise measurement along eastern coastline of China. Size resolved particles were measured in the 15–600 nm size range. The median particle number concentrations (PNCs) were found to vary in the range of 1.1−2.2 × 104 cm−3 at urban sites, 0.8−1.5 × 104 cm−3 at regional sites, 0.4−0.6 × 104 cm−3 at coastal/background sites, and 0.5 × 104 cm−3 during cruise measurement. Peak diameters at each of these sites varied greatly from 24 to 115 nm. Particles in the 15–25 nm (nucleation mode), 25–100 nm (Aitken mode) and 100–600 nm (accumulation mode) range showed different characteristics at each sites, indicating the features of primary emissions and secondary formation in these diversified atmospheric environments. Diurnal variations show a build-up of accumulation mode particles belt at regional sites, suggesting the contribution of regional secondary aerosol pollution. Frequencies of new particle formation (NPF) events were much higher at urban and regional sites than at coastal sites and during cruise measurement. The average growth rates (GRs) of nucleation mode particles were 8.0–10.9 nm h−1 at urban sites, 7.4–13.6 nm h−1 at regional sites and 2.8–7.5 nm h−1 at coastal sites and during cruise measurement. The high gaseous precursors and strong oxidation at urban and regional sites not only favored the formation of particles, but also accelerated the growth rate of the nucleation mode particles. No significant difference in condensation sink (CS) during NPF days were observed among different site types, suggesting that the NPF events in background areas were more influenced by the pollutant transport. In addition, average contributions of NPF events to potential cloud condensation nuclei (CCN) at 0.2% super-saturation in the afternoon of all sampling days were calculated as 11% and 6% at urban sites and regional sites, respectively. On the other hand, NPF events at coastal sites and during cruise measurement had little impact on potential production of CCN. This study provides a large data set of particle size distribution in diversified atmosphere of China, improving our general understanding of emission, secondary formation, new particle formation and corresponding CCN activity of submicron aerosols in Chinese environments