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BackgroundSeveral de novo transcriptome assemblers have been developed recently to assemble the short reads generated from the next-generation sequencing platforms and different strategies were employed for assembling transcriptomes of various eukaryotes without genome sequences. Though there are some comparisons among these de novo assembly tools for assembling transcriptomes of different eukaryotic organisms, there is no report about the relationship between assembly strategies and ploidies of the organisms.ResultsWhen we de novo assembled transcriptomes of sweet potato (hexaploid), Trametes gallica (a diploid fungus), Oryza meyeriana (a diploid wild rice), five assemblers, including Edena, Oases, Soaptrans, IDBA-tran and Trinity, were used in different strategies (Single-Assembler Single-Parameter, SASP; Single-Assembler Multiple-Parameters, SAMP; Combined De novo Transcriptome Assembly, CDTA, that is multiple assembler multiple parameter). It was found that CDTA strategy has the best performance compared with other two strategies for assembling transcriptome of the hexaploid sweet potato, whereas SAMP strategy with assembler Oases is better than other strategies for assembling transcriptomes of diploid fungus and the wild rice transcriptomes.ConclusionBased on the results from ours and others, it is suggested that CDTA strategy is better used for transcriptome assembly of polyploidy organisms and SAMP strategy of Oases is outperformed for those diploid organisms without genome sequences.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-014-1192-7) contains supplementary material, which is available to authorized users.

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The ethanologenic bacterium Zymomonas mobilis is usually tolerant to high concentrations of glucose. The addition of sorbitol decreases the lag phase and increases ethanol yield and productivity of the bacteria in high glucose concentrations. The molecular mechanisms of adaptation to high glucose concentrations and the effect of sorbitol are still unclear. In this study, microarray analysis was used to study the global transcriptional adaptation responses of Z. mobilis to high glucose concentrations. A total of 235 genes were differentially expressed when 220 g/L glucose was added with or without 10 mM sorbitol. These genes are involved in diverse aspects of cell metabolism and regulation, including membrane transporters, nitrogen metabolism, and plasmid-encoded genes. However, most differentially expressed genes were downregulated when sorbitol was added. Notably, the transcription of almost all genes involved in the Entner-Doudoroff and ethanol production pathways was not significantly affected. In addition, a prophage and a nitrogen-fixation cluster were significantly induced. These results revealed that Z. mobilis cells responded to high glucose concentrations by regulating the transcriptional levels of genes related to membrane channels and transporters, stress response mechanisms, and metabolic pathways. These data provide insight into the intracellular adaptation responses to high glucose concentrations and reveal strategies to engineer efficient ethanol fermentation in Z. mobilis.

Receptor-interacting protein kinase-3 (RIPK3) is a multifunctional regulator of cell death and inflammation. RIPK3 controls cellular signalling through the formation of the domain-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome, which is recognised to mediate renal fibrogenesis. The role of RIPK3 in diabetic kidney disease (DKD) induced renal fibrosis has not been previously determined. To define the action of RIPK3 in the development of diabetic kidney disease, wild-type (WT), RIPK3 -/- and endothelium-derived nitric oxide synthase (eNOS)-/- mice were induced to develop diabetes mellitus using multiple low doses of streptozotocin and maintained for 24 weeks. RIPK3 activity and NLRP3 expression were upregulated and fibrotic responses were increased in the kidney cortex of WT mice with established diabetic nephropathy compared to control mice. Consistently, mRNA expression of inflammasome components, as well as transforming growth factor beta 1 (TGFβ1), α smooth muscle actin (α-SMA) and collagen deposition were increased in diabetic kidneys of WT mice compared to control mice. However, these markers were normalised or significantly reversed in kidneys of diabetic RIPK3 -/- mice. Renoprotection was also observed using the RIPK3 inhibitor dabrafenib in eNOS-/- diabetic mice as demonstrated by reduced collagen deposition and myofibroblast activation. These results suggest that RIPK3 is associated with the development of renal fibrosis in DKD due to the activation of the NLRP3 inflammasome. Inhibition of RIPK3 results in renoprotection. Thus, RIPK3 may be a potential target for therapeutic intervention in patients with diabetic kidney disease.

It is well-known that all progressive chronic kidney disease (CKD) is pathologically characterized by tubulointerstitial fibrosis process. Multiple studies have shown the critical role of inflammation and fibrosis in the development of CKD. Hence strategies that target inflammatory and fibrotic signaling pathways may provide promising opportunities to protect against renal fibrosis. Metformin has been used as the first-line glucose-lowering agent to treat patients with type 2 diabetes mellitus (T2DM) for over 50 years. Accumulating evidence suggests the potential for additional therapeutic applications of metformin, including mitigation of renal fibrosis. In this study, the anti-fibrotic effects of metformin independent of its glucose-lowering mechanism were examined in an adenine -induced mouse model of CKD. Expressions of inflammatory markers MCP-1, F4/80 and ICAM, fibrotic markers type IV collagen and fibronectin, and the cytokine TGF-β1 were increased in adenine-induced CKD when compared to control groups and significantly attenuated by metformin treatment. Moreover, treatment with metformin inhibited the phosphorylation of Smad3, ERK1/2, and P38 and was associated with activation of the AMP-activated protein kinase (AMPK) in the kidneys of adenine-treated mice. These results indicate that metformin attenuates adenine-induced renal fibrosis through inhibition of TGF-β1 signaling pathways and activation of AMPK, independent of its glucose-lowering action.

Chronic kidney disease (CKD) is a worldwide public health issue, accounting for 82% of premature mortality. 1 Regardless of the cause of initial renal injury, CKD leads to renal fibrosis, characterized by renal dysfunction, extracellular matrix (ECM) accumulation, myofibroblast activation, and inflammatory responses. 2,3 To date, the most widely used strategy to limit the progression of CKD is the blockade of the renin-angiotensin system, an approach that was