Phylogenetic relationships of Cyrtandromoea and Wightia revisited: A new tribe in Phrymaceae and a new family in Lamiales

The familial placements of Cyrtandromoea Zoll. and Wightia Wall., two small and enigmatic South‐East Asian genera, have long been controversial in Lamiales. Here we adopt a two‐step approach to resolve their phylogenetic relationships. We initially reconstructed a large‐scale phylogeny of Lamiales using six chloroplast markers (atpB, matK, ndhF, psbBTNH, rbcL, and rps4). The results showed that both Cyrtandromoea and Wightia emerged in the LMPO clade, including Lamiaceae, Mazaceae, Phrymaceae, Paulowniaceae, and Orobanchaceae. Based on the second set of six chloroplast markers (atpB, matK, ndhF, rbcL, rps16, and trnL‐F) and two nuclear ribosomal regions (external transcribed spacer and internal transcribed spacer) for the analyses focusing on the LMPO clade, our results revealed that Cyrtandromoea was consistently nested within Phrymaceae, whereas Wightia was supported as sister to Phrymaceae by the chloroplast DNA dataset or sister to Paulowniaceae by the nuclear ribosomal DNA dataset. Morphological and anatomical evidence fully supports the inclusion of Cyrtandromoea in Phrymaceae, and an updated tribal classification is done for Phrymaceae with five tribes, that is, Cyrtandromoeeae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Diplaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Leucocarpeae, Mimuleae, and Phrymeae. The conflicting phylogenetic position of Wightia indicated by different genome markers results in difficulty placing the genus in either Phrymaceae or Paulowniaceae. Considering the distinct morphological differences between Wightia and other families in the LMPO clade, we here propose a new family, Wightiaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, fam. nov., to accommodate it, which is the 26th family recognized in Lamiales.     

Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen‐based phylogenomic approach in resolving species boundaries

Species concept and delimitation are fundamental to taxonomic and evolutionary studies. Both inadequate informative sites in the molecular data and limited taxon sampling have often led to poor phylogenetic resolution and incorrect species delineation. Recently, the whole chloroplast genome sequences from extensive herbarium specimen samples have been shown to be effective to amend the problem. Stachyuraceae are a small family consisting of only one genus Stachyurus of six to 16 species. However, species delimitation in Stachyurus has been highly controversial because of few and generally unstable morphological characters used for classification. In this study, we sampled 69 individuals of seven species (each with at least three individuals) covering the entire taxonomic diversity, geographic range, and morphological variation of Stachyurus from herbarium specimens for genome‐wide plastid gene sequencing to address species delineation in the genus. We obtained high‐quality DNAs from specimens using a recently developed DNA reconstruction technique. We first assembled four whole chloroplast genome sequences. Based on the chloroplast genome and one nuclear ribosomal DNA sequence of Stachyurus, we designed primers for multiplex polymerase chain reaction and high throughput sequencing of 44 plastid loci for species of Stachyurus. Data of these chloroplast DNA and nuclear ribosomal DNA internal transcribed spacer sequences were used for phylogenetic analyses. The phylogenetic results showed that the Japanese species Stachyurus praecox Siebold & Zucc. was sister to the rest in mainland China, which indicated a typical Sino‐Japanese distribution pattern. Based on diagnostic morphological characters, distinct distributional range, and monophyly of each clade, we redefined seven species for Stachyurus following an integrative species concept, and revised the taxonomy of the family based on previous reports and specimens, in particular the type specimens. Furthermore, our divergence time estimation results suggested that Stachyuraceae split from its sister group Crossosomataceae from the New World at ca. 54.29 Mya, but extant species of Stachyuraceae started their diversification only recently at ca. 6.85 Mya. Diversification time of Stachyurus in mainland China was estimated to be ca. 4.45 Mya. This research has provided an example of using the herbarium specimen‐based phylogenomic approach in resolving species boundaries in a taxonomically difficult genus.     

不同病理分期肺腺癌患者血清代谢组学研究

肺癌是当今世界最常见的恶性肿瘤之一,其新发率和死亡率多年来都居于各类癌症之首,其中85%的肺癌都是非小细胞癌,而腺癌又是最常见的非小细胞癌。肺癌的高隐匿性是造成其高死亡率的最主要原因,因此为肺癌的早期诊断和病理分期寻求高效可靠的方法是十分必要的。代谢组学揭示了小分子代谢物的一系列变化,反映了生命活动的最终状态,因此也能直接反映疾病不同发展阶段的病理生理变化。本研究利用核磁共振氢谱(1H-NMR),对在我院就诊的27例不同病理分期的肺腺癌患者和13例健康志愿者进行了血清代谢物分析,运用正交偏最小二乘判别分析(OPLS-DA)对1H-NMR数据进行建模,单变量统计分析对模型进行评价。结果表明肺腺癌患者组的血清中有14种代谢物出现明显差异,其中丙酮酸、丙氨酸、NAC1、乳酸、GPC和甘氨酸比起对照组来有显著上升,而葡萄糖、谷氨酰胺、亮氨酸、异亮氨酸、缬氨酸、丙酮、乙酰乙酸和苏氨酸则显著下降。而在不同分期肺腺癌患者间进行比较后发现,异亮氨酸、乙酰乙酸、NAC1和乳酸的变化与肺腺癌的发展有相关性,可能是肺腺癌早期诊断和分期的潜在生物标志物。     

Allotransplantation of adult spinal cord tissues after complete transected spinal cord injury: Long-term survival and functional recovery in canines

Science China Life Sciences - Spinal cord injury (SCI), especially complete transected SCI, leads to loss of cells and extracellular matrix and functional impairments. In a previous study, we...     

The fungal community and its interaction with the concentration of short-chain fatty acids in the faeces of Chenghua,Yorkshire and Tibetan pigs

Despite their important roles in host nutrition and metabolism, and potential to cause disease, our knowledge of the fungal community in the mammalian gut is quite limited. To date, diversity and composition of fungi in swine gut still remains unknown. Therefore, the first internal transcribed spacer of fungi in faecal samples from three breeds of pigs (10 pigs for each breed) was sequenced based on an Illumina HiSeq 2500 platform, and the relationship between the fungal community and the concentrations of main short-chain fatty acids (SCFAs) was also analysed. Results indicated that Chenghua (local, higher body fat rate), Yorkshire (foreign, higher lean meat and growth rate) and Tibetan (plateau, stronger disease resistance) pigs harboured distinct fungal community. The Basidiomycota and Ascomycota presented as the two predominant phyla, with Loreleia, Russula and Candida as the top three genera in all samples. Network analysis revealed a total of 35 correlations among different fungal genera, with 27 (77.14%) positive and 8 (22.86%) negative pairwise interactions. Canonical correspondence analysis suggested that fungi in the faeces of pigs were more correlated to the concentration of acetate and butyrate rather than propionate. Spearman’s correlation further showed that Tomentella was positively correlated to both acetate and butyrate, and Loreleia was positively correlated to propionate (P < 0.05), while Nephroma and Taiwanofungus were negatively correlated to acetate and propionate (P < 0.05). These findings expanded our knowledge on the intestinal fungi in pigs with different genotypes and phenotypes, indicating that fungi may play an indispensable role during the metabolism of host and the maintenance of intestinal health. The cross-feeding between fungi and other microorganisms may be crucial during the digestion of dietary carbohydrates and the associated physiological processes, which is worthy to be further studied.     

Depth‐dependent soil organic carbon dynamics of croplands across the Chengdu Plain of China from the 1980s to the 2010s

Agricultural soils have tremendous potential to sequester soil organic carbon (SOC) and mitigate global climate change. However, agricultural land use has a profound impact on SOC dynamics, and few studies have explored how agricultural land use combined with soil conditions affect SOC changes throughout the soil profile. Based on a paired soil resampling campaign in the 1980s and 2010s, this study investigated the SOC changes of the soil profile caused by agricultural land use and the correlations with parent material and topography across the Chengdu Plain of China. The results showed that the SOC content increased by 3.78 g C/kg in the topsoil (0–20 cm), but decreased in the 20–40 cm and 40–60 cm soil layers by 0.90 and 1.26 g C/kg respectively. SOC increases in topsoil were observed for all types of agricultural land. Afforestation on former agricultural land also caused SOC decreases in the 20–60 cm soil layers, while SOC decreases only occurred in the 40–60 cm soil layer for agricultural land using a traditional crop rotation (i.e. traditional rice–wheat/rapeseed rotation) and with rice–vegetable rotations converted from the traditional rotations. For each agricultural land use, SOC decreases in deep soils only occurred in high relief areas and in soils formed from Q4 (Quaternary Holocene) grey‐brown alluvium and Q4 grey alluvium that had a relatively low soil bulk density and clay content. The results indicated that SOC change caused by agricultural land use was depth dependent and that the effects of agricultural land use on soil profile SOC dynamics varied with soil characteristics and topography. Subsoil SOC decreases were more likely to occur in high relief areas and in soils with low soil bulk density and low clay content.     

Increased miR‐34c mediates synaptic deficits by targeting synaptotagmin 1 through ROS‐JNK‐p53 pathway in Alzheimer’s Disease

Alzheimer's disease (AD) and cancer have inverse relationship in many aspects. Some tumor suppressors, including miR‐34c, are decreased in cancer but increased in AD. The upstream regulatory pathways and the downstream mechanisms of miR‐34c in AD remain to be investigated. The expression of miR‐34c was detected by RT–qPCR in oxidative stressed neurons, hippocampus of SAMP8 mice, or serum of patients with amnestic mild cognitive impairment (aMCI). Dual luciferase assay was performed to confirm the binding sites of miR‐34c in its target mRNA. The Morris water maze (MWM) was used to evaluate learning and memory in SAMP8 mice administrated with miR‐34c antagomir (AM34c). Golgi staining was used to evaluate the synaptic function and structure. The dramatically increased miR‐34c was mediated by ROS‐JNK‐p53 pathway and negatively regulated synaptotagmin 1 (SYT1) expression by targeting the 3′‐untranslated region (3′‐UTR) of syt1 in AD. The expression of SYT1 protein was reduced by over expression of miR‐34c in the HT‐22 cells and vice versa. Administration of AM34c by the third ventricle injection or intranasal delivery markedly increased the brain levels of SYT1 and ameliorated the cognitive function in SAMP8 mice. The serum miR‐34c was significantly increased in patients with aMCI and might be a predictive biomarker for diagnosis of aMCI. These results indicated that increased miR‐34c mediated synaptic and memory deficits by targeting SYT1 through ROS‐JNK‐p53 pathway and the miR‐34c/SYT1 pathway could be considered as a promising novel therapeutic target for patients with AD.     

Molten salt synthesis and luminescence of Dy3+‐doped Y3Al5O12 phosphors

Dy³⁺‐doped Y₃Al₅O₁₂ phosphors were prepared at a relatively low temperature using molten salt synthesis. The phase of the prepared Dy³⁺‐doped Y₃Al₅O₁₂ phosphors was confirmed using X‐ray powder diffraction. Results indicated that Dy³⁺ doping did not change the Y₃Al₅O₁₂ phase. Following excitation at 352 nm, emission spectra of the Dy³⁺‐doped Y₃Al₅O₁₂ phosphors consisted of blue, yellow, and red emission bands. The influence of Dy³⁺ concentration and excitation wavelength on emission was investigated. The ratio of yellow light to blue light varied with change in Dy³⁺ doping concentration, due to changes in the structure around Dy³⁺. Emission intensities also changed when the excitation wavelength was changed. This variation is luminescence generated a system for tunable white light for Dy³⁺‐doped Y₃Al₅O₁₂ phosphors.     

MiR‐16, as a potential NF‐κB‐related miRNA,exerts anti‐inflammatory effects on LPS‐induced myocarditis via mediating CD40 expression: A preliminary study

The purpose of this study was to investigate the biological effect of miR‐16 on myocarditis and the underlying molecular mechanism. H9c2 cells were treated with 10 µg/mL lipopolysaccharide (LPS) for 12 hours to form a myocarditis injury model. We observed that LPS treatment distinctly decreased the level of miR‐16 in H9c2 cells. Upregulation of miR‐16 increased cell proliferation and reduced cell apoptosis. Then, CD40 was predicted and verified as a target gene of miR‐16 by TargetScan and luciferase reporter assay, respectively. Furthermore, the messenger RNA and protein expression of CD40 are negatively regulated by miR‐16. The relative expression of inflammatory factors was dramatically decreased by the miR‐16 mimic. Cells cotransfected with miR‐16 mimic and si‐CD40 could significantly abolish the injury of cardiomyocytes caused by myocarditis. Our study illustrated that the upregulation of miR‐16 has a protective effect on LPS‐damaged H9c2 cells, which may be achieved by regulating CD40 and the nuclear factor kappa B pathway.