The RNA expression signature of the HepG2 cell line as determined by the integrated analysis of miRNA and mRNA expression profiles

Understanding miRNAs' regulatory networks and target genes could facilitate the development of therapies for human diseases such as cancer. Although much useful gene expression profiling data for tumor cell lines is available, microarray data for miRNAs and mRNAs in the human HepG2 cell line have only been compared with that of other cell lines separately. The relationship between miRNAs and mRNAs in integrated expression profiles for HepG2 cells is still unknown. To explore the miRNA–mRNA correlations in hepatocellular carcinoma (HCC) cells, we performed miRNA and mRNA expression profiling in HepG2 cells and normal liver HL-7702 cells at the genome scale using next-generation sequencing technology. We identified 193 miRNAs that are differentially expressed in these two cell lines. Of these, 89 miRNAs were down-regulated in HepG2 cells compared with HL-7702 cells, while 104 miRNAs were up-regulated. We also observed 3035 mRNAs that are significantly dys-regulated in HepG2 cells. We then performed an integrated analysis of the expression data for differentially expressed miRNAs and mRNAs and found several miRNA–mRNA pairs that are significantly correlated in HepG2 cells. Further analysis suggested that these differentially expressed genes were enriched in four tumorigenesis-related signaling pathways, namely, ErbB, JAK–STAT, mTOR, and WNT, which until now had not been fully reported. Our results could be helpful in understanding the mechanisms of HCC occurrence and development.     

黑曲霉催化雄甾-4-烯-3,17-二酮16β-羟基化

为进一步确定黑曲霉菌株TCCC41650的生物转化能力,以雄甾-4-烯-3,17-二酮(Androstenedione)为底物,利用黑曲霉菌株TCCC41650进行催化,产物经纯化、重结晶后,通过单晶衍射鉴定为16β-羟基雄甾-4-烯-3,17-二酮。转化条件为:培养液pH 6.0,乙醇添加量为2%,投料浓度为1‰时,72 h转化率为85.8%。目前甾体研究领域对于C16β-羟基化的微生物转化未见报道,研究结果为C16β-羟基甾体药物的研发奠定了基础。     

Identification of a novel MTOR activator and discovery of a competing endogenous RNA regulating autophagy in vascular endothelial cells

MTOR, a central regulator of autophagy, is involved in cancer and cardiovascular and neurological diseases. Modulating the MTOR signaling balance could be of great significance for numerous diseases. No chemical activators of MTOR have been found, and the urgent challenge is to find novel MTOR downstream components. In previous studies, we found a chemical small molecule, 3-benzyl-5-((2-nitrophenoxy) methyl)–dihydrofuran-2(3H)-one (3BDO), that inhibited autophagy in human umbilical vein endothelial cells (HUVECs) and neuronal cells. Here, we found that 3BDO activated MTOR by targeting FKBP1A (FK506-binding protein 1A, 12 kDa). We next used 3BDO to detect novel factors downstream of the MTOR signaling pathway. Activation of MTOR by 3BDO increased the phosphorylation of TIA1 (TIA1 cytotoxic granule-associated RNA binding protein/T-cell-restricted intracellular antigen-1). Finally, we used gene microarray, RNA interference, RNA-ChIP assay, bioinformatics, luciferase reporter assay, and other assays and found that 3BDO greatly decreased the level of a long noncoding RNA (lncRNA) derived from the 3′ untranslated region (3′UTR) of TGFB2, known as FLJ11812. TIA1 was responsible for processing FLJ11812. Further experiments results showed that FLJ11812 could bind with MIR4459 targeting ATG13 (autophagy-related 13), and ATG13 protein level was decreased along with 3BDO-decreased FLJ11812 level. Here, we provide a new activator of MTOR, and our findings highlight the role of the lncRNA in autophagy.     

Scanning electron microscope evidence of telocytes in vasculature

Here, we here present scanning electron microscope data for the existent telocytes (TCs) on the endothelial surface of the wall of pig coronary arteries, internal thoracic arteries and carotid arteries. These cells have a small (8.39 ± 1.97 μm/4.95 ± 0.91 μm) cell body of different shapes (from round to triangular, depending on the number of cellular prolongations) with very long (of about 30 μm) and thin cellular processes called telopodes (Tps), which have uneven calibre. The number of Tps ranges between 2 and 6. Tps typically present the alternation of podoms and podomers, and also have a dichotomic branching pattern. These data could influence the current attempts for elucidating the role(s) of TCs.     

Simulation of wastewater treatment by aerobic granules in a sequencing batch reactor based on cellular automata

In the present paper, aerobic granules were developed in a sequencing batch reactor (SBR) using synthetic wastewater, and 81 % of granular rate was obtained after 15-day cultivation. Aerobic granules have a 96 % BOD removal to the wastewater, and the reactor harbors a mount of biomass including bacteria, fungi and protozoa. In view of the complexity of kinetic behaviors of sludge and biological mechanisms of the granular SBR, a cellular automata model was established to simulate the process of wastewater treatment. The results indicate that the model not only visualized the complex adsorption and degradation process of aerobic granules, but also well described the BOD removal of wastewater and microbial growth in the reactor. Thus, CA model is suitable for simulation of synthetic wastewater treatment. This is the first report about dynamical and visual simulation of treatment process of synthetic wastewater in a granular SBR.     

Pressure-induced metallization of condensed phase β-HMX under shock loadings via molecular dynamics simulations in conjunction with multi-scale shock technique

Thanks to the advances in grid technologies, we are able to propose here an evolution of our molecular simulator that, when moving to larger systems, instead of reducing the granularity of the dynamical treatment (as is often done in molecular dynamics studies of such systems) exploits the extra power of the grid approach to the end of preserving the detailed nature of theatomistic formulation of the interaction. Key steps of such evolution are: (1) the assemblage of the interaction based on a composition of the ab initio intramolecular data and a portable parameterization of the intermolecular potential linking ab initio evaluation of intramolecular potentials and the partitioning of molecular polarizability; (2) the exploitation of an efficient coordinated porting and running of molecular dynamics codes on the European grid distributed computing infrastructure. As a prototype case study, the N-methylacetamide dimer in vacuo has been considered and the formation of possible conformers is analyzed.     

Assessing the cost of living with elephants (Loxodonta africana) in areas adjacent to Meru National Park,Kenya

Crop raiding by the elephants is a serious and recurring management problem around protected areas in Kenya such as Meru National Park. Crop-raiding menace is one of the most significant of human–elephant conflicts in Meru National Park. The distribution, impact, and conservation implications of the increased elephant crop raiding in areas adjacent to Meru National Park is attributed to the changes in land use systems within these areas. Crop raiding by African elephants (Loxodonta africana) was monitored in the area adjacent to Meru National Park between August 2010 and July 2011. From the study, 144 farms were raided and farmers lost crops amounting to USD 120,308.60. Crop raiding was higher during the month of August 2010 (KES 2,714,295 or USD 33,928). The study suggests capacity building for communities in order to safeguard their crops against elephant raiding. Other probable measures put forward to mitigate this include the development of alternative water sources and the need to implement electric fence around the remaining section of the Park boundary which is affected by elephant.