Identification of key genes and novel immune infiltration-associated biomarkers of sepsis

Sepsis is the major cause of mortality in the intensive care unit. The aim of this study was to identify the key prognostic biomarkers of abnormal expression and immune infiltration in sepsis. In this study, a total of 36 differentially expressed genes were identified to be mainly involved in a number of immune-related Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. The hub genes (MMP9 and C3AR1) were significantly related to the prognosis of sepsis patients. The immune infiltration analysis indicated a significant difference in the relative cell content of naive B cells, follicular Th cells, activated NK cells, eosinophils, neutrophils and monocytes between sepsis and normal controls. Weighted gene co-expression network analysis and a de-convolution algorithm that quantifies the cellular composition of immune cells were used to analyse the sepsis expression data from the Gene Expression Omnibus database and to identify modules related to differential immune cells. CEBPB is the key immune-related gene that may be involved in sepsis. Gene set enrichment analysis revealed that CEBPB is involved in the processes of T cell selection, B cell–mediated immunity, NK cell activation and pathways of T cells, B cells and NK cells. Therefore, CEBPB may play a key role in the biological and immunological processes of sepsis.     

Analysis of microRNA expression profiles in porcine PBMCs after LPS stimulation

In the present study, we used microRNA (miRNA) sequencing to discover and explore the expression profiles of known and novel miRNAs in 1000 ng/ml LPS stimulated for 8 h vis-à-vis non-stimulated (i.e. control) PBMCs isolated from the blood of healthy pigs. A total of 291 known miRNAs were bio-computationally identified in porcine PBMCs, and 228 novel miRNAs (not enlisted in the swine mirBase) were identified. Among these miRNAs, ssc-miR-148a-3p, ssc-let-7g, ssc-let-7f, 3_8760, ssc-miR-26a, ssc-miR-451, ssc-miR-21, ssc-miR-30d, ssc-miR-99a and ssc-miR-103 were the top 10 most abundant miRNAs in porcine PBMCs. Through miRNA differential analysis combined with quantitative PCR, we found the expressions of ssc-miR-122, ssc-miR-129b, ssc-miR-17-5p and ssc-miR-152 were significantly changed in porcine PBMCs after LPS stimulation. Furthermore, targets prediction and function analysis indicated a significant enrichment in gene ontology functional categories related to diseases, immunity and inflammation. In conclusion, this study on profiling of miRNAs expressed in LPS-stimulated PBMCs provides an important reference point for future studies on regulatory roles of miRNAs in porcine immune system.     

The impacts of warming and nitrogen addition on competitive ability of native and invasive populations of Plantago virginica

全球变化因子(如增温和氮沉降)可能会影响生物入侵,但是这些因子如何影响入侵物种的表现并进一步调节入侵物种与本地竞争者之间的相互作用仍不清楚。本文通过为期五个月的温室实验,研究了增温(开顶式增温箱,+0.62°C)和氮添加(4.2 g N m⁻²)对入侵物种北美 车前(Plantago virginica)原产地和入侵地种群与本地车前草(Plantago asiatica)竞争的影响。实验结果表明,在增温及其与氮添加处理(W × N) 的相互作用下,P. virginica的入侵种群(PV-In)和原产地种群(PV-Na)在与本地竞争者P. asiatica竞争时具有不同的生物量分配策略。其中,PV-Na在与P. asiatica竞争时增加了地下生物量,而PV-In增加了地上生物量。我们还发现,P. virginica对增温和氮添加比P. asiatica的反应更强 烈。增温显著降低了P. virginica的竞争能力,这表明P. virginica比P. asiatica对增温的响应更为敏感。同样,在竞争条件下,氮添加及 其和增温交互作用减少了PV-In地下生物量,但增加了PV-Na地上和总生物量。这些发现表明,P. virginica在入侵过程中改变了生物量分配 策略,PV-In展示出更具弹性的竞争能力以适应环境变化(特别是增温)。这些发现可能有助于我们预测气候变化下的植物入侵并制定相应的 管理策略。     

Fluorescence characterization and microbial degradation of dissolved organic matter leached from salt marsh plants in the Yellow River Delta

盐沼植被是沿海水体中溶解有机物(Dissolved Organic Matter, DOM)的重要贡献者。然而,不同盐沼植物释放DOM的动力学特征尚缺乏系统研究和比较。黄河三角洲湿地是中国东海岸面积最大,保护最完善的沿海生态系统之一。本论文研究了2016年10月从黄河三角洲(Yellow River Delta, YRD)盐沼中采集的三种常见沼泽植物(芦苇(Phragmites australis),碱蓬(Suaeda salsa)和獐茅(Aeluropus littoralis)的DOM释放过程。通过测定溶解有机碳(Dissolved Organic Carbon, DOC)和溶解氮(Dissolved Nitrogen, DN)发现,植物叶片释放的DOM浓度远高于其根和茎。在27天的培养期内,平均有15%的生物碳和30%的生物氮以DOC和DN的形式通过植物叶片释放。从植物中释放的DOM非常不稳定,在27天的培养期内,细菌共消耗了92.4%–98.1%的DOC和88.0%–94.6%的DN。植物释放DOM的荧光特性表明,发色溶解的有机物(Chromophoric Dissolved Organic Matter, CDOM)是DOM的主要组分,而类蛋白组分是植物释放CDOM的主要组分。细菌的降解作用改变了DOM的荧光性质和化学组成。上述的室内研究结果得到了实地调查的充分支撑,表明在深秋时期黄河口湿地有大量DOM溢出。本研究结果表明,盐沼植物释放的DOM是沼泽和沿海水域DOC和DN的重要来源,而且易降解DOC和DN为黄河口湿地和邻近沿海水域中的微生物群落提供了重要的食物来源。     

A chromosome‐level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest,Chilo suppressalis

The rice stem borer, Chilo suppressalis, is one of the most damaging insect pests to rice production worldwide. Although C. suppressalis has been the focus of numerous studies examining cold tolerance and diapause, plant–insect interactions, pesticide targets and resistance, and the development of RNAi‐mediated pest management, the absence of a high‐quality genome has limited deeper insights. To address this limitation, we generated a draft C. suppressalis genome constructed from both Illumina and PacBio sequences. The assembled genome size was 824.35 Mb with a contig N₅₀ of 307 kb and a scaffold N₅₀ of 1.75 Mb. Hi‐C scaffolding assigned 99.2% of the bases to one of 29 chromosomes. Based on universal single‐copy orthologues (BUSCO), the draft genome assembly was estimated to be 97% complete and is predicted to encompass 15,653 protein‐coding genes. Cold tolerance is an extreme survival strategy found in animals. However, little is known regarding the genetic basis of the winter ecology of C. suppressalis. Here, we focused our orthologous analysis on those gene families associated with animal cold tolerance. Our finding provided the first genomic evidence revealing specific cold‐tolerant strategies in C. suppressalis, including those involved in glucose‐originated glycerol biosynthesis, triacylglycerol‐originated glycerol biosynthesis, fatty acid synthesis and trehalose transport‐intermediate cold tolerance. The high‐quality C. suppressalis genome provides a valuable resource for research into a broad range of areas in molecular ecology, and subsequently benefits developing modern pest control strategies.     

A ROCK inhibitor promotes keratinocyte survival and paracrine secretion,enhancing establishment of primary human melanocytes and melanocyte–keratinocyte co‐cultures

Primary melanocytes isolated from skin and expanded in culture have been widely used for laboratory research and clinical applications. The conventional method to isolate primary melanocytes from skin usually requires about 3–4 weeks of culture for melanocytes to grow sufficiently to passage. Considering that melanocytes comprise only 3%–7% of epidermal cells in normal human skin, it would be extremely helpful to increase the isolation efficiency and shorten the initial culture time to quickly meet various application needs. Here, we report that adding Y‐27632, a Rho kinase inhibitor, into the initial culture medium for 2 days can dramatically increase the yield of melanocytes. We found that Y‐27632 can promote keratinocyte attachment and survival in the melanocyte culture system, resulting in not only better recovery, but also increased proliferation of melanocytes by a paracrine signaling pathway. More specifically, Y‐27632 significantly induced keratinocyte expression of stem cell factor, which played an important role in enhancing the growth of melanocytes. In summary, Y‐27632 could profoundly enhance the yield of primary melanocytes in the initial culture through paracrine effects on keratinocytes.     

Bacillus amyloliquefaciens Ameliorates H2O2-Induced Oxidative Damage by Regulating Transporters,Tight Junctions,and Apoptosis Gene Expression in Cell Line IPEC-1

Probiotics have always been considered as a supplementary therapy for many diseases especially gut disorders. The absorption and barrier function of the gut play a vital role in the maintenance of body homeostasis. This study was to investigate the protective effects of Bacillus amyloliquefaciens SC06 (Ba) on H₂O₂-induced oxidative stress on intestinal porcine epithelial cells (IPEC-1) based on the level of gene expression. We demonstrated that Ba was a safe probiotic strain in the first place. Results showed that treatment with H₂O₂ significantly increased the mRNA expression of absorptive transporters glucose transporter 2 (GLUT2), Ala/Ser/Cys/Thr transporter 1 (ASCT1), and ASCT2 compared with the control group. Meanwhile, oxidative stress induced a significant improvement in the mRNA expression of occludin (OCLN) and caspase-3, and remarkably inhibited the expression of L-type amino acid transporter 1 (LAT1) or B cell lymphoma-2 (Bcl-2), respectively. Pretreatment with Ba dramatically reversed the disturbance induced by oxidative stress on the mRNA expression of ASCT1, ASCT2, and OCLN, which also significantly prevented H₂O₂-inhibited LAT1 and Bcl-2 mRNA expression. However, Ba failed to exert any significant protective effect on GLUT2 and caspase-3 mRNA expression. We concluded that pretreatment with Ba could alleviate the damage caused by oxidative stress to a certain extent and conferred a protective effect to the intestine.