Arable acronyms analysed – a review of integrated arable farming systems research in Western Europe

Arable production has come under increasing economic and environmental pressures, especially in the last decade. These have derived from over-production, decreased farm incomes and a concern with the possible environmental effects of intensive pesticide use associated with such intensive cultivation. A number of long-term research programmes on integrated farming systems and their sustainability have recently been completed or are currently under way. In the UK, these include the ‘Boxworth’ project, ‘SCARAB’, TALISMAN’, RISC, ‘LINK Integrated Farming Systems’, ‘LIFE’ and the demonstration-only programme ‘LEAF’. These projects are reviewed in terms of their objectives, designs and results to date, and are compared with some parallel programmes in Germany, the Netherlands, Switzerland and France.     

Combined small RNA and degradome sequencing reveals microRNA regulation during immature maize embryo dedifferentiation

Genetic transformation of maize is highly dependent on the development of embryonic calli from the dedifferentiated immature embryo. To better understand the regulatory mechanism of immature embryo dedifferentiation, we generated four small RNA and degradome libraries from samples representing the major stages of dedifferentiation. More than 186 million raw reads of small RNA and degradome sequence data were generated. We detected 102 known miRNAs belonging to 23 miRNA families. In total, we identified 51, 70 and 63 differentially expressed miRNAs (DEMs) in the stage I, II, III samples, respectively, compared to the control. However, only 6 miRNAs were continually up-regulated by more than fivefold throughout the process of dedifferentiation. A total of 87 genes were identified as the targets of 21 DEM families. This group of targets was enriched in members of four significant pathways including plant hormone signal transduction, antigen processing and presentation, ECM-receptor interaction, and alpha-linolenic acid metabolism. The hormone signal transduction pathway appeared to be particularly significant, involving 21 of the targets. While the targets of the most significant DEMs have been proved to play essential roles in cell dedifferentiation. Our results provide important information regarding the regulatory networks that control immature embryo dedifferentiation in maize.     

Dicer1 敲除对肝脏胆酸代谢和转运功能的影响

目的:微小RNA(microRNAs,miRNAs)在胆固醇的合成,代谢和转运中起着重要作用,而mi RNAs在胆固醇代谢物胆酸的代谢和转运中的作用尚不清楚。Dicer基因是miRNAs生成过程的关键酶。本课题使用肝脏特异的Dicer1基因敲除小鼠,考察肝脏Dicer1基因敲除对C57BL/6小鼠肝脏胆酸代谢和转运的影响。方法:使用白蛋白启动子驱动的Cre重组酶和Loxp系统(Alb-Cre/Loxp)在小鼠肝脏中特异的敲除Dicer1基因;分别收集3~12周龄的小鼠血液和肝脏组织,使用Cobas生化仪检测小鼠血液和肝脏中总胆酸含量;利用实时定量PCR的方法分析肝脏中胆汁酸代谢转运相关基因的表达。结果:实验发现,肝脏Dicer基因敲除后,胆酸在血液和肝脏中明显蓄积,弥漫性肝细胞轻微空泡化,偶见单个肝细胞坏死。检测胆酸代谢和转运相关基因的表达发现,胆酸合成相关基因的表达有轻度升高,但缺乏统计学差异;在肝脏细胞血管侧的胆酸摄取转运体中,Oatp1a1在Dicer1敲除小鼠肝脏中明显下调,Ntcp和Oatp1b2则无明显改变;而肝细胞血管侧胆酸外排转运体的表达均有显著升高,胆管侧的外排转运体中Abcb11表达有明显增加。结论:Dicer基因敲除后,胆酸在血液和肝脏中明显蓄积,肝脏和血液中胆酸总量显著增加。血液中胆酸的蓄积可能与肝脏细胞血管侧摄取转运体的低表达和血管侧外排转运体的高表达有关;而肝脏中胆酸的蓄积可能部分来自于轻度升高的胆酸合成酶,胆酸在肝细胞内运输途径的紊乱可能与肝脏和血液中胆酸总量的显著增加相关。     

Evidence for targeting common siRNA hotspots and GC preference by plant Dicer-like proteins

Small interfering (si)RNAs isolated from Brassica juncea leaves infected by Turnip mosaic virus (TuMV) were characterized by cloning and sequencing. The TuMV siRNA population was dominated by 21 and 22-nt long species originated mainly from the same siRNA hotspots, indicating operational similarity between the plant Dicer-like (DCL) enzymes. Robust GC bias was observed for TuMV siRNAs versus the virus genome, indicating that DCL was more likely to target GC-rich regions. Furthermore, dicot micro-(mi)RNAs displayed higher GC% than their DCL1 substrate RNAs, implicating that the GC bias may be ancient, therefore may be important for the RNAi technology.     

Polyomavirus BK-encoded microRNA suppresses autoregulation of viral replication

Polyomavirus BK (BKV) infection is an important cause of renal allograft failure. Viral microRNAs are known to play a crucial role in viral replication. This study investigated the expression of BKV-encoded microRNAs (miR-B1) in patients with polyomavirus-associated nephropathy (PVAN) and their role in viral replication. Following BKV infection in renal proximal tubular cells, the 3p and 5p miR-B1 levels were significantly increased. Cells transfected with the vector containing the miR-B1 precursor (the miR-B1 vector) showed a significant increase in expression of 3p and 5p miR-B1 and decrease in luciferase activity of a reporter containing the 3p and 5p miR-B1 binding sites, compared to cells transfected with the miR-B1-mutated vector. Transfection of the miR-B1 expression vector or the 3p and 5p miR-B1 oligonucleotides inhibited expression of TAg. TAg-enhanced promoter activity and BKV replication were inhibited by miR-B1. In contrast, inhibition of miR-B1 expression by addition of miR-B1 antagomirs or silencing of Dicer upregulated the expression of TAg and VP1 proteins in BKV-infected cells. Importantly, patients with PVAN had significantly higher levels of 3p and 5p miR-B1 compared to renal transplant patients without PVAN. In conclusion, we demonstrated that (1) miR-B1 expression was upregulated during BKV infection and (2) miR-B1 suppressed TAg-mediated autoregulation of BKV replication. Use of miR-B1 can be evaluated as a potential treatment strategy against BKV infection.     

Polerovirus protein P0 prevents the assembly of small RNA‐containing RISC complexes and leads to degradation of ARGONAUTE1

RNA silencing plays an important role in plants in defence against viruses. To overcome this defence, plant viruses encode suppressors of RNA silencing. The most common mode of silencing suppression is sequestration of double‐stranded RNAs involved in the antiviral silencing pathways. Viral suppressors can also overcome silencing responses through protein–protein interaction. The poleroviral P0 silencing suppressor protein targets ARGONAUTE (AGO) proteins for degradation. AGO proteins are the core component of the RNA‐induced silencing complex (RISC). We found that P0 does not interfere with the slicer activity of pre‐programmed siRNA/miRNA containing AGO1, but prevents de novo formation of siRNA/miRNA containing AGO1. We show that the AGO1 protein is part of a high‐molecular‐weight complex, suggesting the existence of a multi‐protein RISC in plants. We propose that P0 prevents RISC assembly by interacting with one of its protein components, thus inhibiting formation of siRNA/miRNA–RISC, and ultimately leading to AGO1 degradation. Our findings also suggest that siRNAs enhance the stability of co‐expressed AGO1 in both the presence and absence of P0.