Screening of significant biomarkers related with prognosis of liver cancer by lncRNA-associated ceRNAs analysis

This study aimed to identify significant biomarkers related to the prognosis of liver cancer using long noncoding RNA (lncRNA)-associated competing endogenous RNAs (ceRNAs) analysis. Differentially expressed mRNA and lncRNAs between liver cancer and paracancerous tissues were screened, and the functions of these mRNAs were predicted by gene ontology and pathway enrichment analyses. A ceRNA network consisting of differentially expressed mRNAs and lncRNAs was constructed. LncRNA FENDRR and lncRNA HAND2-AS1 were hub nodes in the ceRNA network. A risk score assessment model consisting of eight genes (PDE2A, ESR1, FBLN5, ALDH8A1, AKR1D1, EHHADH, ADRA1A, and GNE) associated with prognosis were developed. Multivariate Cox regression suggested that both pathologic_T and risk group could be regarded as independent prognostic factors. Furthermore, a nomogram model consisting of pathologic_T and risk group showed a good prediction ability for predicting the survival rate of liver cancer patients. The nomogram model consisting of pathologic_T and a risk score assessment model could be regarded as an independent factor for predicting prognosis of liver cancer.     

Identification of the quantitative trait loci (QTL) underlying water soluble protein content in soybean

Water soluble protein content (SPC) plays an important role in the functional efficacy of protein in food products. Therefore, for the identification of quantitative trait loci (QTL) associated with SPC, 212 F_2:9 lines of the recombinant inbred line (RIL) population derived from the cross of ZDD09454 × Yudou12 were grown along with the parents, in six different environments (location × year) to determine inheritance and map solubility-related genes. A linkage map comprising of 301 SSR markers covering 3,576.81 cM was constructed in the RIL population. Seed SPC was quantified with a macro-Kjeldahl procedure in samples collected over multiple years from three locations (Nantong in 2007 and 2008, Zhengzhou in 2007 and 2008, and Xinxiang in 2008 and 2009). SPC demonstrated transgressive segregation, indicating a complementary genetic structure between the parents. Eleven putative QTL were associated with SPC explaining 4.5–18.2 % of the observed phenotypic variation across the 6 year/location environments. Among these, two QTL (qsp8-4, qsp8-5) near GMENOD2B and Sat_215 showed an association with SPC in multiple environments, suggesting that they were key QTL related to protein solubility. The QTL × environment interaction demonstrated the complex genetic mechanism of SPC. These SPC-associated QTL and linked markers in soybean will provide important information that can be utilized by breeders to improve the functional quality of soybean varieties.     

Drought-induced H2O2 accumulation in subsidiary cells is involved in regulatory signaling of stomatal closure in maize leaves

Increasing H₂O₂ levels in guard cells in response to environmental stimuli are recently considered a general messenger involved in the signaling cascade for the induction of stomatal closure. But little is known as to whether subsidiary cells participate in the H₂O₂-mediated stomatal closure of grass plants. In the present study, 2-week-old seedlings of maize (Zea mays) were exposed to different degrees of soil water deficit for 3 weeks. The effects of soil water contents on leaf ABA and H₂O₂ levels and stomatal aperture were investigated using physiological, biochemical, and histochemical approaches. The results showed that even under well-watered conditions, significant amounts of H₂O₂ were observed in guard cells, whereas H₂O₂ concentrations in the subsidiary cells were negligible. Decreasing soil water contents led to a significant increase in leaf ABA levels associated with significantly enhanced O₂ ^? and H₂O₂ contents, consistent with reduced degrees of stomatal conductance and aperture. The significant increase in H₂O₂ appeared in both guard cells and subsidiary cells of the stomatal complex, and H₂O₂ levels increased with decreasing soil water contents. Drought-induced increase in the activity of antioxidative enzymes could not counteract the significant increase in H₂O₂ levels in guard cells and subsidiary cells. These results indicate that subsidiary cells participate in H₂O₂-mediated stomatal closure, and drought-induced H₂O₂ accumulation in subsidiary cells is involved in the signaling cascade regulating stomatal aperture of grass plants such as maize.     

Carbenoxolone Blocks Endotoxin-Induced Protein Kinase R (PKR) Activation and High Mobility Group Box 1 (HMGB1) Release

The pathogen- and damage-associated molecular patterns (for example, bacterial endotoxin and adenosine 5′-triphosphate [ATP]) activate the double-stranded RNA-activated protein kinase R (PKR) to trigger the inflammasome-dependent high mobility group box 1 (HMGB1) release. Extracellular ATP contributes to the inflammasome activation through binding to the plasma membrane purinergic P2X₇ receptor (P2X₇R), triggering the opening of P2X₇R channels and the pannexin-1 (panx-1) hemichannels permeable for larger molecules up to 900 daltons. It was previously unknown whether panx-1 channel blockers can abrogate lipopolysaccharide (LPS)-induced PKR activation and HMGB1 release in innate immune cells. Here we demonstrated that a major gancao (licorice) component (glycyrrhizin, or glycyrrhizic acid) derivative, carbenoxolone (CBX), dose dependently abrogated LPS-induced HMGB1 release in macrophage cultures with an estimated IC₅₀ ≈ 5 μmol/L. In an animal model of polymicrobial sepsis (induced by cecal ligation and puncture [CLP]), repetitive CBX administration beginning 24 h after CLP led to a significant reduction of circulating and peritoneal HMGB1 levels, and promoted a significant increase in animal survival rates. As did P2X₇R antagonists (for example, oxidized ATP, oATP), CBX also effectively attenuated LPS-induced P2X₇R/panx-1 channel activation (as judged by Lucifer Yellow dye uptake) and PKR phosphorylation in primary peritoneal macrophages. Collectively, these results suggested that CBX blocks LPS-induced HMGB1 release possibly through impairing PKR activation, supporting the involvement of PKR in the regulation of HMGB1 release.     

Medium chain carboxylic acids production from waste biomass: Current advances and perspectives

Alternative chemicals to diverse fossil-fuel-based products is urgently needed to mitigate the adverse impacts of fossil fuel depletion on human development. To this end, researchers have focused on the production of biochemical from readily available and affordable waste biomass. This is consistent with current guidelines for sustainable development and provides great advantages related to economy and environment. The search for suitable biochemical products is in progress worldwide. Therefore, this review recommends a biochemical (i.e., medium chain carboxylic acids (MCCAs)) utilizing an emerging biotechnological production platform called the chain elongation (CE) process. This work covers comprehensive introduction of the CE mechanism, functional microbes, available feedstock types and corresponding utilization strategies, major methods to enhance the performance of MCCAs production, and the challenges that need to be addressed for practical application. This work is expected to provide a thorough understanding of the CE technology, to guide and inspire researchers to solve existing problems in depth, and motivate large-scale MCCAs production.     

纳他霉素对芒果采后胶孢炭疽菌的抑菌效果及机理

以纳他霉素为抑菌剂, 实验测定了离体条件下不同浓度纳他霉素对胶孢炭疽菌(Colletotrichum gloeosporioides)的孢子萌发及菌丝生长的抑制效果, 以及活体损伤接种炭疽病菌后, 纳他霉素对芒果(Mangifera indica)果实炭疽病的防治效果。通过测定纳他霉素处理后胶孢炭疽菌的细胞膜相对渗透率、可溶性蛋白含量、细胞膜完整性、孢子内活性氧水平和线粒体分布情况, 初步探明其抑菌机理。结果表明, 3 mg∙L ^-1纳他霉素可显著抑制胶孢炭疽菌孢子萌发、芽管伸长和菌落生长, 80 mg∙L ^-1纳他霉素可有效抑制芒果贮存过程中果实炭疽病斑的扩展。纳他霉素处理后胶孢炭疽菌细胞膜相对渗透率和可溶性蛋白含量增加; 2 mg∙L ^-1纳他霉素处理8小时, 处理组胶孢炭疽菌孢子细胞膜损伤染色率为33.6%, 对照组染色率为13.9%; 处理组胞内活性氧产生染色率达46.9%, 比对照组高39.7%; 同时观察到纳他霉素使胞内线粒体分布不均且荧光信号微弱。以上结果表明, 纳他霉素可以破坏胶孢炭疽病菌细胞膜, 诱导活性氧大量积累, 并降低线粒体活性, 从而干扰菌体正常生理活性, 使其代谢活动受影响, 从而达到抑菌目的。     

Chromosome‐level reference genome of X12, a highly virulent race of the soybean cyst nematode Heterodera glycines

Soybean cyst nematode (SCN, Heterodera glycines) is a major pest of soybean that is spreading across major soybean production regions worldwide. Increased SCN virulence has recently been observed in both the United States and China. However, no study has reported a genome assembly for H. glycines at the chromosome scale. Herein, the first chromosome‐level reference genome of X12, an unusual SCN race with high infection ability, is presented. Using whole‐genome shotgun (WGS) sequencing, Pacific Biosciences (PacBio) sequencing, Illumina paired‐end sequencing, 10X Genomics linked reads and high‐throughput chromatin conformation capture (Hi‐C) genome scaffolding techniques, a 141.01‐megabase (Mb) assembled genome was obtained with scaffold and contig N50 sizes of 16.27 Mb and 330.54 kilobases (kb), respectively. The assembly showed high integrity and quality, with over 90% of Illumina reads mapped to the genome. The assembly quality was evaluated using Core Eukaryotic Genes Mapping Approach and Benchmarking Universal Single‐Copy Orthologs. A total of 11,882 genes were predicted using de novo, homolog and RNAseq data generated from eggs, second‐stage juveniles (J2), third‐stage juveniles (J3) and fourth‐stage juveniles (J4) of X12, and 79.0% of homologous sequences were annotated in the genome. These high‐quality X12 genome data will provide valuable resources for research in a broad range of areas, including fundamental nematode biology, SCN–plant interactions and co‐evolution, and also contribute to the development of technology for overall SCN management.     

How climate and soil properties affect the abundances of nitrogen-cycling genes in nitrogen-treated ecosystems: a meta-analysis

Plant and Soil - The abundance of nitrogen (N)-cycling genes is frequently used to indicate N cycling and predict N2O emissions. However, it remains difficult to clearly define how soil N-cycling...     

尿苷二磷酸糖固定化酶合成法研究

利用生物酶进行体外催化反应合成不同种类的尿苷二磷酸糖（uridine diphosphate sugar,UDP-糖）,生物酶的重复利用率较低。为提高尿苷二磷酸糖的合成效率及增加产物种类,以镍螯合聚丙烯酸酯树脂为载体,对带有HIS标签的N-乙酰己糖胺激酶（N-acetylhexosamine kinase,NahK）和尿苷转移酶（uridine transferase,GlmU）进行固定化。以固定化NahK和固定化GlmU为催化酶,不同单糖作为底物,研究尿苷二磷酸糖的一锅法合成情况。利用Q柱对产物进行纯化,通过高效液相色谱法、质谱法、核磁共振氢谱法对反应产物进行检测。确定了镍螯合聚丙烯酸酯树脂对游离NahK和GlmU的实际载量分别为10和20 mg·g^-1。固定化酶量的最优配比为5.5 g固定化NahK和2.5 g固定化GlmU。固定化酶的最适pH和温度分别为8.0和35℃,且能在重复反应中稳定反应5个批次。葡萄糖、N-乙酰氨基葡萄糖和甘露糖可以参与一锅法反应,生成UDP-糖的相对分子质量分别为566、607、566,而葡萄糖醛酸、半乳糖和果糖在该体系下不能合成相应的UDP-糖。基于固定化酶技术,一锅法可合成UDP-葡萄糖、UDP-N-乙酰氨基葡萄糖、UDP-甘露糖。