Genome Characteristics Reveal the Biocontrol Potential of Actinobacteria Isolated From Sugarcane Rhizosphere

To understand the beneficial interaction of sugarcane rhizosphere actinobacteria in promoting plant growth and managing plant diseases, this study investigated the potential role of sugarcane rhizospheric actinobacteria in promoting plant growth and antagonizing plant pathogens. We isolated 58 actinobacteria from the sugarcane rhizosphere, conducted plant growth-promoting (PGP) characteristics research, and tested the pathogenic fungi in vitro. Results showed that BTU6 (Streptomyces griseorubiginosus), the most representative strain, regulates plant defense enzyme activity and significantly enhances sugarcane smut resistance by regulating stress resistance-related enzyme (substances (POD, PAL, PPO, TP) in sugarcane) activity in sugarcane. The genomic evaluation indicated that BTU6 has the ability to biosynthesize chitinase, b-1,3-glucanase, and various secondary metabolites and plays an essential role in the growth of sugarcane plants under biotic stress. Potential mechanisms of the strain in improving the disease resistance of sugarcane plants and its potential in biodegrading exogenous chemicals were also revealed. This study showed the importance of sugarcane rhizosphere actinobacteria in microbial ecology and plant growth promotion

Growth disturbance of extracts from several crops straw (residue) on Ageratina adenophora and biological-control implications in hazardous weed invasion for eco-restoration

Laboratory biological simulation experiment was conducted to investigate growth disturbance of high, moderate, low concentration of aqueous extracts (i.e. the original extracts with a solid liquid ratio of 1:40 g mL-1 and its 5 times diluents and 25 times diluents) from several crops straw (residue) on Ageratina adenophora, a worldwide notorious invasive weed. The results showed: (a) aqueous extracts from several crops straw (residue) brought about different impacts on the single index for germination and growth of A. adenophora, e.g., high concentration of aqueous extracts from Brassica oleracea waste leaves showed a strong inhibition against the germination rate (GR) and germination index (GI) of A. adenophora, while high concentration of aqueous extracts from Vicia cracca straw showed a strong inhibition against radicle length (RL) and hypocotyl length (HL) of A. adenophora; (b) high concentration of aqueous extracts from B. oleracea waste leaves and high, moderate and low concentration of aqueous extracts from Oryza sativa straw and Triticum aestivum straw showed rather strong synthetic effects (inhibition) on GR and GI of A. adenophora, which could be chosen for the control over the seeds germination of A. adenophora; (c) high and moderate concentrations of aqueous extracts from V. cracca straw, high concentration of aqueous extracts from B. campestris waste leaves, and moderate and low concentrations of aqueous extracts from O. sativa straw and T. aestivum straw showed rather strong synthetic effects (inhibition) on RL and HL of A. adenophora, which could be selected as ideal materials for the control over the seedlings growth of A. adenophora; and (d) high concentrations of aqueous extracts from V. cracca straw, B. oleracea waste leaves and B. campestris waste leaves, and high, moderate and low concentrations of aqueous extracts from O. sativa straw and T. aestivum straw showed rather strong synthetic effects (inhibition) on GR, GI, RL and HL of A. adenophora, which could be selected as ideal materials for the control over the seeds germination and seedlings growth of A. adenophora. Thus, this study would provide a theoretic guidance and technical support for the resources utilization of crops straw (residue) and the prevention and control over invasive weeds as well. (C) 2013 Elsevier B.V. All rights reserved.Laboratory biological simulation experiment was conducted to investigate growth disturbance of high, moderate, low concentration of aqueous extracts (i.e. the original extracts with a solid liquid ratio of 1:40 g mL-1 and its 5 times diluents and 25 times diluents) from several crops straw (residue) on Ageratina adenophora, a worldwide notorious invasive weed. The results showed: (a) aqueous extracts from several crops straw (residue) brought about different impacts on the single index for germination and growth of A. adenophora, e.g., high concentration of aqueous extracts from Brassica oleracea waste leaves showed a strong inhibition against the germination rate (GR) and germination index (GI) of A. adenophora, while high concentration of aqueous extracts from Vicia cracca straw showed a strong inhibition against radicle length (RL) and hypocotyl length (HL) of A. adenophora; (b) high concentration of aqueous extracts from B. oleracea waste leaves and high, moderate and low concentration of aqueous extracts from Oryza sativa straw and Triticum aestivum straw showed rather strong synthetic effects (inhibition) on GR and GI of A. adenophora, which could be chosen for the control over the seeds germination of A. adenophora; (c) high and moderate concentrations of aqueous extracts from V. cracca straw, high concentration of aqueous extracts from B. campestris waste leaves, and moderate and low concentrations of aqueous extracts from O. sativa straw and T. aestivum straw showed rather strong synthetic effects (inhibition) on RL and HL of A. adenophora, which could be selected as ideal materials for the control over the seedlings growth of A. adenophora; and (d) high concentrations of aqueous extracts from V. cracca straw, B. oleracea waste leaves and B. campestris waste leaves, and high, moderate and low concentrations of aqueous extracts from O. sativa straw and T. aestivum straw showed rather strong synthetic effects (inhibition) on GR, GI, RL and HL of A. adenophora, which could be selected as ideal materials for the control over the seeds germination and seedlings growth of A. adenophora. Thus, this study would provide a theoretic guidance and technical support for the resources utilization of crops straw (residue) and the prevention and control over invasive weeds as well. (C) 2013 Elsevier B.V. All rights reserved

Downregulation of Fat Mass and Obesity Associated (FTO) Promotes the Progression of Intrahepatic Cholangiocarcinoma

Intrahepatic cholangiocarcinoma (ICC) ranks as the second most malignant type of primary liver cancer with a high degree of incidence and a very poor prognosis. Fat mass and obesity-associated protein (FTO) functions as an eraser of the RNA m6A modification, but its roles in ICC tumorigenesis and development remain unknown. We showed here that the protein level of FTO was downregulated in clinical ICC samples and cell lines and that FTO expression was inversely correlated with the expression of CA19-9 and micro-vessel density (MVD). A Kaplan-Meier survival analysis showed that a low expression of FTO predicted poor prognosis in ICC. in vitro, decreased endogenous expression of FTO obviously reduced apoptosis of ICC cells. Moreover, FTO suppressed the anchorage-independent growth and mobility of ICC cells. Through mining the database, FTO was found to regulate the integrin signaling pathway, inflammation signaling pathway, epidermal growth factor receptor (EGFR) signaling pathway, angiogenesis, and the pyrimidine metabolism pathway. RNA decay assay showed that oncogene TEAD2 mRNA stability was impaired by FTO. In addition, the overexpression of FTO suppressed tumor growth in vivo. In conclusion, our study demonstrated the critical roles of FTO in ICC

Identification of microRNA-181 by genome-wide screening as a critical player in EpCAM-positive hepatic cancer stem cells

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that regulate gene expression with functional links to tumorigenesis. Hepatocellular carcinoma (HCC) is the most common type of liver cancer and it is heterogeneous in clinical outcomes and biological activities. Recently, we have identified a subset of highly invasive EpCAM+ HCC cells from AFP+ tumors with cancer stem/progenitor cell features, i.e., the abilities to self-renew, differentiate and initiate aggressive tumors in vivo. Here, using a global microarray-based microRNA profiling approach followed by validation with quantitative reverse transcription polymerase chain reaction, we have demonstrated that conserved miR-181 family members were upregulated in EpCAM+AFP+ HCCs and in EpCAM+ HCC cells isolated from AFP+ tumors. Moreover, miR-181 family members were highly expressed in embryonic livers and in isolated hepatic stem cells. Importantly, inhibition of miR-181 led to a reduction in EpCAM+ HCC cell quantity and tumor initiating ability, while exogenous miR-181 expression in HCC cells resulted in an enrichment of EpCAM+ HCC cells. We have found that miR-181 could directly target hepatic transcriptional regulators of differentiation (i.e., CDX2 and GATA6) and an inhibitor of wnt/β-catenin signaling (i.e., NLK). Taken together, our results define a novel regulatory link between miR-181s and human EpCAM+ liver cancer stem/progenitor cells and imply that molecular targeting of miR-181 may eradicate HCC

Mechanism and intervention of murine transfusion-related acute lung injury caused by anti-CD36 antibodies

Anti-CD36 Abs have been suggested to induce transfusion-related acute lung injury (TRALI) upon blood transfusion, particularly in Asian populations. However, little is known about the pathological mechanism of anti-CD36 Ab–mediated TRALI, and potential therapies have not yet been identified. Here, we developed a murine model of anti-CD36 Ab–mediated TRALI to address these questions. Administration of mouse mAb against CD36 (mAb GZ1) or human anti-CD36 IgG, but not GZ1 F(ab′)2 fragments, induced severe TRALI in Cd36+/+ male mice. Predepletion of recipient monocytes or complement, but not neutrophils or platelets, prevented the development of murine TRALI. Moreover, plasma C5a levels after TRALI induction by anti-CD36 Abs increased more than 3-fold, implying a critical role of complement C5 activation in the mechanism of Fc-dependent anti-CD36–mediated TRALI. Administration of GZ1 F(ab′)2, antioxidant (N-acetyl cysteine, NAC), or C5 blocker (mAb BB5.1) before TRALI induction completely protected mice from anti-CD36–mediated TRALI. Although no significant amelioration in TRALI was observed when mice were injected with GZ1 F(ab′)2 after TRALI induction, significant improvement was achieved when mice were treated postinduction with NAC or anti-C5. Importantly, anti-C5 treatment completely rescued mice from TRALI, suggesting the potential role of existing anti-C5 drugs in the treatment of patients with TRALI caused by anti-CD36

Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wild-type [Poncirus trifoliata (L.) Raf.] by massively parallel signature sequencing

<p>Abstract</p> <p>Background</p> <p>After several years in the juvenile phase, trees undergo flowering transition to become mature (florally competent) trees. This transition depends on the balanced expression of a complex network of genes that is regulated by both endogenous and environmental factors. However, relatively little is known about the molecular processes regulating flowering transition in woody plants compared with herbaceous plants.</p> <p>Results</p> <p>Comparative transcript profiling of spring shoots after self-pruning was performed on a spontaneously early flowering trifoliate orange mutant (precocious trifoliate orange, <it>Poncirus trifoliata</it>) with a short juvenile phase and the wild-type (WT) tree by using massively parallel signature sequencing (MPSS). A total of 16,564,500 and 16,235,952 high quality reads were obtained for the WT and the mutant (MT), respectively. Interpretation of the MPSS signatures revealed that the total number of transcribed genes in the MT (31,468) was larger than in the WT (29,864), suggesting that newly initiated transcription occurs in the MT. Further comparison of the transcripts revealed that 2735 genes had more than twofold expression difference in the MT compared with the WT. In addition, we identified 110 citrus flowering-time genes homologous with known elements of flowering-time pathways through sequencing and bioinformatics analysis. These genes are highly conserved in citrus and other species, suggesting that the functions of the related proteins in controlling reproductive development may be conserved as well.</p> <p>Conclusion</p> <p>Our results provide a foundation for comparative gene expression studies between WT and precocious trifoliate orange. Additionally, a number of candidate genes required for the early flowering process of precocious trifoliate orange were identified. These results provide new insight into the molecular processes regulating flowering time in citrus.</p

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Rapid Communication - cpSSR: a New Tool to Analyze Chloroplast Genome of Citrus Somatic Hybrids

Chloroplast simple sequence repeat (cpSSR) markers in Citrus were developed and success-fully used to analyze chloroplast genome inheritance of Citrus somatic hybrids. Twenty-two previously reported cpSSR primer pairs from pine (Pinus thunbergii Parl.), rice (Oryza sativa L.) and tobacco (Nicotiana tabacum L.) were tested in Citrus, nine of which could amplify intensive PCR products by agarose gel electrophoresis. Chloroplast genome inheritance of Citrus somatic hybrids from nine fusions was then analyzed, and five of the nine pre-screened primer pairs showed polymorphisms by polyacrylamide gel electrophoresis. The results revealed the random inheritance nature of chloroplast genome in all analyzed Citrus somatic hybrids, which was in agreement with previous reports based on RFLP or CAPS analyses. It was also shown that cpSSR is a more efficient tool in chloroplast genome analyses of somatic hybrids in higher plants, compared with the conventional RFLP or CAPS analyses