The genome of Populus alba x Populus tremula var. glandulosa clone 84K

Poplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Originated in South Korea, this hybrid has been extensively cultivated in northern China. Due to the economic and ecological importance of this hybrid and high transformability, we now report the de novo sequencing and assembly of a male individual of poplar 84K using PacBio and Hi-C technologies. The final reference nuclear genome (747.5 Mb) has a contig N50 size of 1.99 Mb and a scaffold N50 size of 19.6 Mb. Complete chloroplast and mitochondrial genomes were also assembled from the sequencing data. Based on similarities to the genomes of P. alba var. pyramidalis and P. tremula, we were able to identify two subgenomes, representing 356 Mb from P. alba (subgenome A) and 354 Mb from P. tremula var. glandulosa (subgenome G). The phased assembly allowed us to detect the transcriptional bias between the two subgenomes, and we found that the subgenome from P. tremula displayed dominant expression in both 84K and another widely used hybrid, P. tremula x P. alba. This high-quality poplar 84K genome will be a valuable resource for poplar breeding and for molecular biology studies.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

He-Jie-Shen-Shi Decoction as an Adjuvant Therapy on Severe Coronavirus Disease 2019: A Retrospective Cohort and Potential Mechanistic Study

Combination therapy using Western and traditional Chinese medicines has shown notable effects on coronavirus disease 2019 (COVID-19). The He-Jie-Shen-Shi decoction (HJSS), composed of Bupleurum chinense DC., Scutellaria baicalensis Georgi, Pinellia ternata (Thunb.) Makino, Glycyrrhiza uralensis Fisch. ex DC., and nine other herbs, has been used to treat severe COVID-19 in clinical practice. The aim of this study was to compare the clinical efficacies of HJSS combination therapy and Western monotherapy against severe COVID-19 and to study the potential action mechanism of HJSS. From February 2020 to March 2020, 81 patients with severe COVID-19 in Wuhan Tongji Hospital were selected for retrospective cohort study. Network pharmacology was conducted to predict the possible mechanism of HJSS on COVID-19-related acute respiratory distress syndrome (ARDS). Targets of active components in HJSS were screened using the Traditional Chinese Medicine Systems Pharmacology (TCMSP) and PharmMapper databases. The targets of COVID-19 and ARDS were obtained from GeneCards and Online Mendelian Inheritance in Man databases. The key targets of HJSS in COVID-19 and ARDS were obtained based on the protein–protein interaction network (PPI). Kyoto Encyclopedia of Genes and Genomes analysis (KEGG) was conducted to predict the pathways related to the targets of HJSS in COVID-19 and ARDS. A “herb-ingredient-target-pathway” network was established using Cytoscape 3.2.7. Results showed that the duration of the negative conversion time of nucleic acid was shorter in patients who received HJSS combination therapy. HJSS combination therapy also relieved fever in patients with severe COVID-19. Network pharmacology analysis identified interleukin (IL) 6, tumor necrosis factor (TNF), vascular endothelial growth factor A (VEGFA), catalase (CAT), mitogen-activated protein kinase (MAPK) 1, tumor protein p53 (TP53), CC-chemokine ligand (CCL2), MAPK3, prostaglandin-endoperoxide synthase 2 (PTGS2), and IL1B as the key targets of HJSS in COVID-19-related ARDS. KEGG analysis suggested that HJSS improved COVID-19-related ARDS by regulating hypoxia-inducible factor (HIF)-1, NOD-like receptor, TNF, T cell receptor, sphingolipid, PI3K-Akt, toll-like receptor, VEGF, FoxO, and MAPK signaling pathways. In conclusion, HJSS can be used as an adjuvant therapy on severe COVID-19. The therapeutic mechanisms may be involved in inhibiting viral replication, inflammatory response, and oxidative stress and alleviating lung injury. Further studies are required to confirm its clinical efficacies and action mechanisms

Toxicological effects of cadmium on deep-sea mussel Gigantidas platifrons revealed by a combined proteomic and metabolomic approach

IntroductionMarine metal contamination caused by deep-sea mining activities has elicited great concern from both social and scientific communities. Among the various metals deep-sea organisms might encounter, cadmium (Cd) is a widely detected metal that in very small amounts is nonetheless capable of severe toxicity. Yet due to both remoteness and technical challenges, insights into the effects of metal exposure resulting from mining activities upon deep-sea organisms are limited.MethodsHere, we investigated Cd’s toxicological effects on deep-sea mussels of Gigantidas platifrons exposed to 100 or 1000 g/L of Cd for 7 days; an integrated approach was used that incorporated proteomics and metabolomics along with traditional approaches (metal concentrations, metal subcellular distribution, and anti-oxidative and immune-related biochemical indexes).Results and DiscussionResults showed that Cd exposure caused significant Cd’s accumulation in mussel gills and redistribution of Cd among subcellular compartments, with cellular debris being the primary binding site. Although anti-oxidative enzymes activities (superoxide dismutase and catalase) were not significantly altered in mussel gills of both exposed groups, the markedly increased level of glutathione S-transferase detected via proteomic technique clearly evinced that deep-sea mussels suffered from oxidative stress under Cd exposure. Besides, altered activities of acid phosphatase and alkaline phosphatase assayed by traditional methods along with the predominant presence of largely altered immune-related proteins detected by proteomic data strongly revealed an immune response of deep-sea mussels elicited by Cd. In addition, results of proteomics combined with those of non-targeted metabolomics demonstrated that Cd could exert toxicity by disrupting cytoskeleton structure, ion homeostasis, and primary metabolisms of energy, lipid, and nucleotide in deep-sea mussels. As demonstrated in this study, proteomics and metabolomics can be used in tandem to provide valuable insights into the molecular mechanisms of deep-sea organisms’ response to Cd exposure and for helping to discover potential biomarkers for application during deep-sea mining assessments

Regional metallogeny of Mo-bearing deposits in northeastern China, with new Re-Os Dates of porphyry Mo deposits in the northern Xilamulun district

With many new discoveries of giant Mo deposits in the past decade, northeastern China has become the largest molybdenum mineralization region in China. The Xilamulun district is in the southern part of northeastern China and contains 25 Mo deposits and prospects, dominantly of porphyry type. These deposits are mostly along the E-striking Xilamulun fault. Re-Os dating of hydrothermal molybdenite from four deposits in the northern Xilamulun district revealed mineralization ages of 137 to 129 Ma (129.4 ± 3.4 Ma for Aolunhua, 135.3± 2.6 Ma for Shabutai, 136.4 ± 0.8 Ma for Haisugou, and 136.1 ± 6.6 Ma for Banlashan), in general agreement with the crystallization ages of their host granitoids.\ud \ud The compilation of existing data on Mo-bearing deposits in northeastern China, including the new data of this study, shows that Mesozoic Mo deposits in this region have a wide range of ages, from ~250 to 90 Ma. We propose that they are linked to three tectonic-magmatic events: (1) Triassic Mo deposits (250–220 Ma) are mainly distributed along the E-trending Xilamulun fault and are related to postcollisional crustal extension following the final closure of the Paleo-Asian ocean; (2) Jurassic Mo mineralization (200–140 Ma) displays a clear younging trend from southeast to northwest, coincides with the regional magmatism trend, and is interpreted to be related to the northwestward flat-slab subduction of the Paleo-Pacific plate beneath the Eurasian continent that started in the Early Jurassic (ca. 200 Ma); (3) Cretaceous Mo mineralization (140–90 Ma) shows a reversed migration trend from northwest to southeast, and can be explained by the coastward migration of slab rollback related to lower crust delamination, asthenospheric upwelling, and lithospheric thinning in eastern China. The spatial-temporal distribution of Mesozoic Mo mineralization is important for regional metallogeny and exploration. Recently numerous epithermal Au (Cu, Mo) deposits have been recognized in the southeast margin of northeastern China. According to this study, we predict that hidden porphyry/skarn systems could be located beneath these epithermal deposits

The geological and geochemical characteristics of the Nihe iron deposit, Anhui Province, China

The Nihe iron deposit is a newly discovered large scale iron deposit in the central part of the Middle and Lower Yangtze River region in eastern China. This study presents the latest discoveries from field and laboratory works about the iron deposit. The hydrothermal alteration and mineralization are newly subdivided into six stages and each stage is described in detail. Moreover, petrological, geochemical, geochronological (U-Pb dating and Ar-Ar dating) study results are also reported. Our results show the age of the magmatic and mineralization is corresponding to the Early Cretaceous. Mineral chemistry (EPMA and LAICPMS) show fluids get more oxide towards to the late hydrothermal stage, and the trace elements in the magnetite are similar with the selected skarn and IOCG deposits

New advances in detecting the distal geochemical footprints of porphyry systems – epidote mineral chemistry as a tool for\ud vectoring and fertility assessments

Propylitic alteration halos to porphyry deposits are characterized by low- to moderate intensity replacements of primary feldspars and mafic minerals by epidote, chlorite, calcite ± actinolite, pyrite, prehnite and zeolites. The pyrite halo that surrounds porphyry deposits typically extends part way through the propylitic halo, and provides strong responses to conventional geochemical and geophysical exploration techniques. When exploring outside\ud of the pyrite halo, porphyry deposits have proven to be difficult to detect based simply on the presence of weak epidote-chlorite alteration.\ud \ud Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analyses of epidote from propylitic alteration zones around porphyry and skarn deposits in the central Baguio district, Philippines, have shown that low-level hypogene geochemical dispersion halos can be detected at considerably greater distances than can be achieved by conventional rock chip sampling of altered rocks. Epidote chemistry can provide vectoring information to the deposit center and potentially provides insights into the potential metal endowment of the porphyry system, providing explorers with both vectoring and fertility assessment tools.\ud \ud Epidote chemistry varies with respect to distance from porphyry deposit centers, with the highest concentrations of proximal pathfinder elements (e.g., Cu, Mo, Au, Sn) detected in epidote from close to the potassic alteration zone. Distal pathfinder elements (e.g., As, Sb, Pb, Zn, Mn) are most enriched in epidote more than 1.5 km from the deposit center. Rare earth elements and Zr are most enriched in epidote from the edge of the pyrite halo. The lateral zonation in epidote chemistry implies that at Baguio the geochemical dispersion patterns were produced by lateral outflow of spent fluids from the porphyry center, rather than from ingress of peripheral, non-magmatic waters