m6Aexpress-enet: Predicting the regulatory expression m6A sites by an enet-regularization negative binomial regression model.

As the most abundant mRNA modification, m6A controls and influences many aspects of mRNA metabolism including the mRNA stability and degradation. However, the role of specific m6A sites in regulating gene expression still remains unclear. In additional, the multicollinearity problem caused by the correlation of methylation level of multiple m6A sites in each gene could influence the prediction performance. To address the above challenges, we propose an elastic-net regularized negative binomial regression model (called m6Aexpress-enet) to predict which m6A site could potentially regulate its gene expression. Comprehensive evaluations on simulated datasets demonstrate that m6Aexpress-enet could achieve the top prediction performance. Applying m6Aexpress-enet on real MeRIP-seq data from human lymphoblastoid cell lines, we have uncovered the complex regulatory pattern of predicted m6A sites and their unique enrichment pathway of the constructed co-methylation modules. m6Aexpress-enet proves itself as a powerful tool to enable biologists to discover the mechanism of m6A regulatory gene expression. Furthermore, the source code and the step-by-step implementation of m6Aexpress-enet is freely accessed at https://github.com/tengzhangs/m6Aexpress-enet.

Protective effects of the active fraction from the tuber of Scirpus yagara in mouse endotoxin shock model.

ETHNOPHARMACOLOGICAL RELEVANCE: Scirpus yagara Ohwi is a perennial, aquatic plant, whose dry tubers have long been used as Traditional Chinese Medicine (TCM) "Sanleng" for the treatment of postpartum abdominal pain, hyperemesis gravidarum, amenorrhea, dyspepsia and several inflammatory related diseases. Although it is known to have anti-inflammatory activities, its mechanism of action on lipopolysaccharide (LPS)-induced inflammation has not yet been identified in detail.This study was designed to investigate the anti-inflammatory activity of the active fraction (AF) from the tuber of Scirpusyagara both in vitro and in vivo. MATERIALS AND METHODS: RAW264.7 macrophage was incubated for 16h with 1µg/ml of LPS in absence or presence of AF (0, 10, 50 and 100µg/ml) and the secretions of tumor necrosis-alpha (TNF-α) and interleukin-6 (IL-6) in the medium were determined by using an enzyme-linked immunosorbent assay (ELISA). In the in vivo study, mice were orally administrated with AF (50 and 300mg/kg) for three days consecutively. 1h after the last AF administration, the mice were intraperitoneally injected with LPS (15mg/kg), and the life span of LPS-challenged mice were determined. Furthermore, the levels of pro-inflammatory cytokines TNF-α and IL-6 in the serum, lung and liver were measured using ELISA kit, and histological change in lungs was examined by light microscopy. Additionally, the components of AF were analyzed by high performance liquid chromatography (HPLC) using a C18 column. RESULTS: AF significantly decreased TNF-α and IL-6 production induced by LPS in RAW264.7 macrophage. In LPS-induced mouse endotoxin shock model, AF pre-treatment significantly improved the survival rate of mice. And LPS-induced increases of pro-inflammatory cytokines TNF-α and IL-6 in the serum, lung and liver were markedly suppressed by AF. Moreover, the histopathological examination indicated that AF could significantly attenuate lung tissues injury in endotoxemic mice. In addition, eight compounds (protocatechuic acid, vanillic acid, p-coumaric acid, ferulic acid, methyl-3,6-dihydroxy-2-[2-(2-hydroxyphenyl)-ethynyl] benzoate, sciryagarol I, sparstolonin B, SanLeng diphenyllactone) of AF were quantified by HPLC analysis. CONCLUSIONS: These results suggested that AF protected mice against LPS-induced lethality by inhibiting the production of multiple cytokines and organ dysfunction. Thus AF may prove beneficial in the prevention and treatment of endotoxin shock.

[Effects of extracellular matrix on biological characteristics of late endothelial progenitor cells].

The present study was designed to investigate the effects of various extracellular matrix (ECM) proteins on the biological characteristics of late endothelial progenitor cells (EPCs). Density gradient centrifugation-isolated rat bone marrow mononuclear cells were cultured in complete M199 medium, which contained 15% fetal calf serum, 10 µg/L vascular endothelial growth factor (VEGF) and 5 µg/L basic fibroblast growth factor (bFGF). EPCs were plated on substrates containing fibronectin (Fn), laminin (Ln) or rat tail tendon collagen (Col), and the corresponding cells were defined as Fn, Ln and Col groups. The 3rd generation EPCs, namely late EPCs, were harvested. The proliferation, adhesion, migration and the ability of forming tubes were assayed using CCK-8, adhesion test, wound healing assay and Matrigel, respectively. The mRNA expressions of endothelial cell differentiation markers, vWF and CD31, were analyzed by real time RT-PCR. The apoptosis was assayed by flow cytometry (FCM). The results showed that cell proliferation ability of Fn and Col groups were higher than that of Ln group; Fn group showed increased adhesion compared to Col and Ln groups (P < 0.01); The migration ability of Fn and Col groups were higher than that of Ln group. Moreover, Fn group showed increased tube formation abilities compared to Col and Ln groups (P < 0.05). Although 24-hour free-serum-induced apoptosis in Ln group was the highest, there was no difference of auto-apoptosis among the three groups. Furthermore, the mRNA expressions of vWF and CD31 exhibited no difference among the three groups. These results suggest the ECM affects the biological functions of late EPCs, which would have a high probability of providing new directions that lead to the development of artificial heart and blood vessels.

[Anticancer activity of Crocodylus siamensis blood in vitro and in vivo].

OBJECTIVE: To study the anticancer effects of the blood of Crocodylus siamensis in vitro and in vivo. METHODS: The inhibitory effects of serum and plasma of Crocodylus siamensis on proliferation of HepG2, BGC823, HeLa and SKOV3 cell were measured by MTT assay. The mouse S180 tumor model was used to evaluate the anti-tumor effect in vivo. RESULTS: High dosage serum and plasma of Crocodylus siamensis could inhibit the proliferation of HepG2, BGC823, HeLa and SKOV3 cell. The tumor inhibitory rate of high dosage blood of Crocodylus siamensis on S180 tumor was up to 57.55%. CONCLUSION: The blood of breeding Crocodylus siamensis has anticancer activity.

[Preparation and identification of the rat antibody against recombinant buckwheat trypsin inhibitor].

AIM: To prepare the rat antibody against the recombinant buckwheat trypsin inhibitor. METHODS: The recombinant buckwheat trypsin inhibitor was expressed in E.coli. BL21 (DE3) and used as an immunogen to immunize the rat. The titer and specificity of the anti-BTI antibody from the rat were analyzed by ELISA, Western blot and immunohistochemistry, respectively. RESULTS: ELISA detection indicated the titer of the antiserum was about 1:128 000. Western blot analysis showed the antibody reacted specifically with rBTI. The immunohistochemistry analysis proved that rBTI was expressed in the cytoplast and nucleus of EC9706 cells. CONCLUSION: The rat antibody against rBTI has high titer and specificity, which is beneficial to further study on the molecular mechanisms in rBTI-induced apoptosis of tumor cells and also provide an important theory basis for further exploring the relationship between the structure and function of BTI.