Exploring Splicing Variants and Novel Genes in Sacred Lotus Based on RNA-seq Data

Sacred lotus (Nelumbo nucifera) is a typical aquatic plant, belonging to basal eudicot plant, which is ideal for genome and genetic evolutionary study. Understanding lotus gene diversity is important for the study of molecular genetics and breeding. In this research, public RNA-seq data and the annotated reference genome were used to identify the genes in lotus. A total of 26,819 consensus and 1,081 novel genes were identified. Meanwhile, a comprehensive analysis of gene alternative splicing events was conducted, and a total of 19,983 “internal” alternative splicing (AS) events and 14,070 “complete” AS events were detected in 5,878 and 5,881 multi-exon expression genes, respectively. Observations made from the AS events show the predominance of intron retention (IR) subtype of AS events representing 33%. IR is followed by alternative acceptor (AltA), alternative donor (AltD) and exon skipping (ES), highlighting the universality of the intron definition model in plants. In addition, functional annotations of the gene with AS indicated its relationship to a number of biological processes such as cellular process and metabolic process, showing the key role for alternative splicing in influencing the growth and development of lotus. The results contribute to a better understanding of the current gene diversity in lotus, and provide an abundant resource for future functional genome analysis in lotus.     

一株兼具秸秆腐解能力玉米促生菌的筛选、鉴定及发酵优化

【背景】砂姜黑土地区存在秸秆腐解缓慢、秸秆还田后作物幼苗生长不良等问题。【目的】从砂姜黑土区农田筛选一株兼具秸秆腐解能力的玉米促生菌MC29,以促进秸秆腐解和玉米作物生长。【方法】通过16S rRNA基因序列分析对该菌株进行鉴定;采用液态摇瓶及盆栽试验验证菌株实际促腐、促生能力及土壤养分的提升效果,并且探究菌株的最佳生长及产吲哚乙酸(indole-3-acetic acid, IAA)条件;采用电击转化法将绿色荧光蛋白(green fluorescent protein, GFP)基因导入菌株细胞,并通过PCR琼脂糖凝胶电泳进行验证。【结果】分离筛选的玉米促生菌鉴定为纤维化纤维微细菌(Cellulosimicrobium cellulans)。该菌株MC29羧甲基纤维素(carboxymethyl cellulose, CMC)酶活可达13.32 U/mL,产IAA量为8.63 mg/L。与对照相比,施用菌株MC29后秸秆腐解率显著提高24.8%;玉米soil and plant analyzer development (SPAD)值、植株总重、根表面积和根长分别提高7.6%、21.3%、30.9%和18.3%;土壤碱解氮含量显著提高68.1%,土壤速效磷及土壤速效钾含量分别提高5.8%及6.0%。菌株MC29最佳生长条件为pH 7.0、装液量为25/250 mL、碳源为麦芽糖、氮源为酵母粉;最佳产IAA条件为pH 7.0、装液量为50/250 mL、碳源为果糖、氮源为硝酸钾;成功构建荧光标记菌株MC29-GFP,并据此追踪到其接入砂姜黑土15 d后定殖量为2.8×10⁵-9.5×10⁵ copies/g。【结论】所筛选的纤维化纤维微细菌MC29对于指导砂姜黑土区多功能秸秆促腐菌剂、微生物菌肥的研制及提升作物产量有一定的积极意义,并为探究其在砂姜黑土中的实际应用奠定基础。     

球孢白僵菌的侵染特性及应用研究进展

球孢白僵菌是一种重要的虫生真菌,具有致病力强、侵染范围广、安全无污染等优点,其制剂可作为一种真菌类杀虫剂应用于农林业害虫的防治,也可用于人工生产中药材僵蚕。本文综述了球孢白僵菌的培养性状、侵染特性、应用生产和存在的问题,并提出了发展对策,为球孢白僵菌的进一步开发应用提供参考。     

Retro-Inverso Carbohydrate Mimetic Peptides with Annexin1-Binding Selectivity,Are Stable In Vivo,and Target Tumor Vasculature

Previous research suggests that carbohydrate mimetic peptide IF7 (IFLLWQR) has an excellent targeting property to annexin1 (Anxa1), a specific marker on the tumor endothelium. However, IF7 is susceptible to proteolysis and has a poor stability in vivo. We prepared a D-amino acid, reverse sequence peptide of IF7, designated RIF7, to confer protease resistance while retaining bioactivity. Experimental results indicate that RIF7 had significantly increased stability and an increased receptor binding affinity than IF7, and this new moiety may represent a clinically relevant vehicle for anticancer drugs.     

miR-627/HMGB1/NF-κB regulatory loop modulates TGF-β1-induced pulmonary fibrosis

Pulmonary fibrosis (PF) is a fibroproliferative disease that can eventually lead to fatal lung failure. It is characterized by abnormal proliferation of fibroblasts, dysregulated fibroblast differentiation to myofibroblast, and disorganized collagen and extracellular matrix production, deposition and degradation. There is still a lack of effective treatment strategies for PF. Extracellular high-mobility group box protein 1 (HMGB1) induces PF through NF-κB-mediated TGF-β1 release. Herein, we first validate the suppressive effect of HMGB1 knockdown on TGF-β1-induced α-smooth muscle actin (α-SMA) and collagen I protein expression. In PF, miRNAs exert different effects through targeting various downstream target messenger RNAs. We searched an online database for dysregulated miRNAs in PF tissues; among them, miR-627 was predicted by online tools to target HMGB1 to inhibit its expression. miR-627 overexpression could partially reverse TGF-β1-induced normal human lung fibroblast proliferation, as well as α-SMA and collagen I protein expression. miR-627 inhibition could partially reverse the suppressive effect of HMGB1 knockdown on TGF-β1-induced α-SMA and collagen I protein expression through direct binding to the 3′-untranslated region of HMGB1. Moreover, miR-627/HMGB1 affected TGF-β1 release through RAGE/NF-κB signaling; miR-627/HMGB1 and RAGE/NF-κB signaling formed a regulatory loop to modulate TGF-β1-induced PF in vitro. In conclusion, miR-627 may be a potential agent that targets HMGB1 to inhibit its expression, thereby improving TGF-β1-induced PF in vitro.     

面向可持续城市生态系统管理的国土空间开发适宜性评价——以烟台市为例

国土空间开发适宜性评价是国土空间规划编制的基础和前提。面向可持续城市生态系统管理目标,基于生态保护红线和永久基本农田的"底线"思维,以资源环境禀赋为基础,构建了本底约束—综合限制—承载力评价-多空间适宜评价的资源环境承载力和国土空间开发适宜性评价的逻辑框架和指标体系,并以烟台为例,设置城市生态系统保护的不同情景,综合运用特尔斐法及多要素空间叠置等方法,开展了城市资源环境承载力与国土空间开发适宜性评价的实践应用。研究结果表明:①资源环境对烟台经济社会发展的阻碍与限制总体较小,高限制区面积仅占烟台国土面积的6.09%。②烟台市不同区县之间的资源环境承载力差异较大。从西北部向东南,烟台市资源环境承载力呈现出逐渐提高的变化趋势。③面向可持续城市生态系统管理情景,烟台市各县市国土空间开发建设适宜性差异显著,适宜建设区范围为2380 km~2。面向城市生态系统一般保护情景,烟台市适宜建设区面积达2610 km~2,不适宜建设开发区与适宜建设开发区数量结构为1.12∶1,未来国土空间开发利用潜力较大。两种情景下烟台市国土空间开发适宜性适宜建设区面积均大于现状建设用地面积,为城市未来发展提供了用地保障,同时确保了烟台市水资源安全和生态安全。研究结果可为烟台市国土空间优化以及相关地区政府部门重大决策、战略部署等提供决策信息支持和技术服务。     

Clopidogrel and Aspirin versus Aspirin Alone for Stroke Prevention: A Meta-Analysis

Background and Purpose

Antiplatelet therapy is widely used for the primary or secondary prevention of stroke. Drugs like clopidogrel have emerged as alternatives for traditional antiplatelet therapy, and dual therapy with clopidogrel and aspirin is of particular interest. We conducted this meta-analysis to systematically review studies about dual therapy comparing monotherapy with aspirin alone.

Methods

Randomized controlled trials were searched in PubMed (1966-May, 2015), EMBASE (1947-May, 2015), the Cochrane Central Register of Controlled Trials (CENTRAL) (1948-May, 2015), WHO International Clinical Trial (ICTRP) (2004-May, 2015), China Biology Medicine disc (CBM disc) (1978-May, 2015) and were included into the final analysis according to the definite inclusion criteria mentioned in the study selection section. Risk ratio (RR) was pooled with 95% confidence interval (CI) for dichotomous data. The heterogeneity was considered significant if the χ² test was significant (P value < 0.10) or the I² > 50.00%. Subgroup analyses were carried out on the long and short time periods, the race and region.

Results

We included 5 studies involving 24,084 patients. A pooled analysis showed that dual therapy with clopidogrel and aspirin had a lower stroke incidence than monotherapy in both the short term and long term (RR = 0.69, 95% CI: 0.59–0.82, P <0.05; RR = 0.84, 95% CI: 0.72–0.98, P = 0.03, respectively). With regard to safety, dual therapy had a higher risk of bleeding than monotherapy for both periods (RR = 1.51, 95% CI: 1.03–2.23, P = 0.04; RR = 1.54, 95% CI: 1.32–1.79, P<0.05, respectively).

Conclusions

Dual therapy with clopidogrel and aspirin could be a preferable choice to prevent stroke in patients who have had a previous stroke or transient ischemic attack, as well as those who are at high risk for stroke. And the effect of dual therapy seems to be more obvious for short-term. However, it is associated with a higher risk of bleeding.     

The Identification of Novel Protein-Protein Interactions in Liver that Affect Glucagon Receptor Activity

Glucagon regulates glucose homeostasis by controlling glycogenolysis and gluconeogenesis in the liver. Exaggerated and dysregulated glucagon secretion can exacerbate hyperglycemia contributing to type 2 diabetes (T2D). Thus, it is important to understand how glucagon receptor (GCGR) activity and signaling is controlled in hepatocytes. To better understand this, we sought to identify proteins that interact with the GCGR to affect ligand-dependent receptor activation. A Flag-tagged human GCGR was recombinantly expressed in Chinese hamster ovary (CHO) cells, and GCGR complexes were isolated by affinity purification (AP). Complexes were then analyzed by mass spectrometry (MS), and protein-GCGR interactions were validated by co-immunoprecipitation (Co-IP) and Western blot. This was followed by studies in primary hepatocytes to assess the effects of each interactor on glucagon-dependent glucose production and intracellular cAMP accumulation, and then in immortalized CHO and liver cell lines to further examine cell signaling. Thirty-three unique interactors were identified from the AP-MS screening of GCGR expressing CHO cells in both glucagon liganded and unliganded states. These studies revealed a particularly robust interaction between GCGR and 5 proteins, further validated by Co-IP, Western blot and qPCR. Overexpression of selected interactors in mouse hepatocytes indicated that two interactors, LDLR and TMED2, significantly enhanced glucagon-stimulated glucose production, while YWHAB inhibited glucose production. This was mirrored with glucagon-stimulated cAMP production, with LDLR and TMED2 enhancing and YWHAB inhibiting cAMP accumulation. To further link these interactors to glucose production, key gluconeogenic genes were assessed. Both LDLR and TMED2 stimulated while YWHAB inhibited PEPCK and G6Pase gene expression. In the present study, we have probed the GCGR interactome and found three novel GCGR interactors that control glucagon-stimulated glucose production by modulating cAMP accumulation and genes that control gluconeogenesis. These interactors may be useful targets to control glucose homeostasis in T2D.     

Effect of the combination of bio-organic fertiliser with Bacillus amyloliquefaciens NJN-6 on the control of banana Fusarium wilt disease,crop production and banana rhizosphere culturable microflora

Soil amended with organic amendments has been suggested to be a strategy for managing the Fusarium wilt disease which severely hindered the banana production. The effects of four fertilisation regimes, including chemical fertiliser, manure composts and bio-organic fertiliser (BIO) containing Bacillus amyloliquefaciens NJN-6 for 2-year continuous application on the banana Fusarium wilt disease incidence, crop yield and rhizosphere culturable microbial community were investigated. To explore the soil microflora, plate counting method, in vitro screening method for antagonism, eco-physiological index and culture-dependent denaturing gradient gel electrophoresis method (CD DGGE) were used. The highest banana yield, culturable bacteria, actinobacteria and Bacillus populations, culturable bacteria to fungi (B/F) value, antagonistic Bacillus ratio and lowest Fusarium wilt disease incidence were observed in the BIO treatment. Based on CD DGGE results, the BIO application significantly altered the soil bacteria structure and showed highest richness and diversity. The phylogenetic analysis of the selected bands showed that the most abundant phyla were Proteobacteria and Bacteroidetes and BIO application enriched the genera Comamonas, Chitinophaga, the species Bacillus flexus and uncultured Bacillus. All the results showed that 2-year continuous application of BIO containing B. amyloliquefaciens NJN-6 more effectively controlled Fusarium wilt disease and improved fruit yields under field conditions and modulated banana rhizosphere microflora.