Cross-cell DNA methylation annotation and analysis for pan-cancer study

Pan-cancer study can uncover cell- and tissue-specific genomic loci and regions with underlying biological functions, as one of fundamental procedures toward precision medicine. We utilized the online curated resource of DNA methylation annotation knowledgebase, to implement the cross-cell interrogation of pan-cancer study of breast cancer. The study revealed genome-wide differentially-methylated loci and regions by the reduced representation bisulfite sequencing profiling. The knowledgebase contains three level of curated information across multiple cancer and normal cells from the ENCODE Consortium. The reference base covers all identified differentially-methylation CpG sites and regions of interest, further annotated gene information, together with tumor suppressor gene and methylation level. Lastly, it includes the inferred functional association network and related Gene Ontology analysis results based on all the tumor suppressor genes identified from the differentially-methylated regions of interest. Our knowledgebase and analysis results provide a thorough reference source for biomedical researchers and clinicians. The cross-cell analysis results are deposited at: http://github.com/gladex/DMAK.

Protocol for preparation of highly durable superhydrophobic bulks with hierarchical porous structures

Superhydrophobic surfaces face challenges in comprehensive durability when used in extreme outdoor environments. Here, we present a protocol for preparing nanocomposite bulks with hierarchical structures using the template technique. We describe steps for using hybrid nanoparticles of polytetrafluoroethylene and multi-walled carbon nanotube to fill inside and dip on the polyurethane (PU) foam. We then detail procedures for its removal by sintering treatment. The extra accretion layer on the PU foam surface was highlighted to construct hierarchical porous structures. For complete details on the use and execution of this protocol, please refer to Wu et al.

Expression of apolipoprotein M in human hepatocellular carcinoma tissues

The present study examined mRNA levels and protein mass of apolipoprotein M (apoM) in human hepatocellular carcinoma (HCC) tissues and in the adjacent tissues. Plasma apoM levels in these HCC patients were also determined and compared to the normal subjects. The mean level of plasma apoM in the HCC patients was 0.61 +/- 0.30 OD mm(-2), which was significantly higher than that in the normal subjects 0.37 +/- 0.07 OD mm(-2) (P < 0.01). However, both apoM mRNA levels and apoM protein mass in the HCC tissues were significantly lower than in the adjacent tissues (P < 0.05). It is concluded that human hepatocellular carcinoma tissues had a reduced capacity to produce apoM than the adjacent non-tumor tissues. However, the plasma apoM levels were higher in the HCC patients than in normal subjects, which suggested that tissues adjacent to the tumors or extra-hepatic apoM production in the HCC patients may contribute to the higher plasma apoM levels in these patients. The clinical significance of apoM in relation to HCC still needs further investigation. (C) 2009 Published by Elsevier GmbH

Porous bulk superhydrophobic nanocomposites for extreme environments

Robust superhydrophobic materials providing protections from harsh weather events such as hurricanes, high temperatures, and humid/frigid conditions have proven challenging to achieve. Here, we report a porous bulk nanocomposite comprising carbon nanotube (CNT)-reinforced polytetrafluoroethylene (PTFE). The nanocomposites are prepared using a templated approach by infusing a CNT/PTFE dispersion into a sponge followed by thermal annealing and decomposition of the sponge template. Importantly, an excess accretion of CNT/PFFE particle mixture on the sponge resulted in nanocomposites with unique and hierarchical porous microstructure, featuring nanochannels near the surface connected to microscale pores inside. The superhydrophobic nanocomposite could resist liquid jets impacting at a velocity of �85.4 m s1 (Weber number of �202,588) and exhibits excellent high-temperature resistance as well as mechanochemical robustness. The porous nanocomposites display excellent icephobicity both with and without infusion with polydimethylsiloxane/silicone oil. These properties should facilitate exploitation as stiff/strong structural polymeric foams used in a variety of fields

A self-induced mechanism of large-scale helical structures in compressible turbulent flows

A novel self-sustaining mechanism is proposed for large-scale helical structures in compressible turbulent flows. The existence of two channels of subgrid-scale and viscosity terms for large-scale helicity evolution is confirmed for the first time, through selecting a physical definition of the large-scale helicity in compressible turbulence. Under the influence of the fluid element expansion, it is found that the helicity is generated at small scales via the second-channel viscosity, and the inverse cross-scale helicity transfers at inertial scales through the second-channel helicity flux. Together, they form a self-induced mechanism, which provides a physical insight into the long-period characteristic of large-scale helical structures in the evolution of compressible flow systems

Increased plasma apoM levels in the patients suffered from hepatocellular carcinoma and other chronic liver diseases

<p>Abstract</p> <p>Objective</p> <p>To determine plasma apolipoprotein M (apoM) levels and other lipid profiles in hepatocellular carcinoma (HCC) patients compared to other chronic liver diseases and normal subjects.</p> <p>Materials and methods</p> <p>36 HCC, 68 chronic hepatitis, 29 liver cirrhosis patients and 64 normal controls were subjected in the present study. Serum lipids, lipoproteins, apolipoprotein AI (apoAI) and apoB were determined by the conventional methods. Plasma apoM levels were semi-quantitatively determined by both dot-blotting and western blotting analysis.</p> <p>Results</p> <p>Serum levels of triglycerides (TG), HDL-cholesterol, apoAI and lipoprotein (a) (Lp(a)) were significantly lower in the HCC patients than in the normal subjects, whereas there were no obvious differences on serum total cholesterol, LDL-cholesterol and apoB between HCC patients and normal subjects. However, plasma apoM levels in HCC patients were significantly increased than those in the normal subjects, but lower than those in the chronic hepatitis and cirrhosis patients.</p> <p>Conclusion</p> <p>It is concluded that serum TG, apoAI, HDL-C and Lp(a) were significantly decreased in HCC patients than in controls, whereas plasma apoM levels were significantly increased in the HCC patients. Decreased serum TG, apoAI, HDL-C and Lp(a) may reflect the liver damage in HCC patients, whereas the clinical significance of increased plasma apoM levels in relation to HCC is not clear.</p

Polyploidy events shaped the expansion of transcription factors in Cucurbitaceae and exploitation of genes for tendril development

Cucurbitaceae is one of the most important plant families distributed worldwide. Transcription factors (TFs) regulate plant growth at the transcription level. Here, we performed a systematic analysis of 42 641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species. Whole-genome duplication (WGD) was the dominant event type in almost all Cucurbitaceae plants. The TF families were divided into 1 210 orthogroups (OGs), of which, 112 were unique to Cucurbitaceae. Although the loss of several gene families was detected in Cucurbitaceae, the gene families expanded in five species that experienced a WGD event comparing with grape. Our findings revealed that the recent WGD events that had occurred in Cucurbitaceae played important roles in the expansion of most TF families. The functional enrichment analysis of the genes that significantly expanded or contracted uncovered five gene families, AUX/IAA, NAC, NBS, HB, and NF-YB. Finally, we conducted a comprehensive analysis of the TCP gene family and identified 16 tendril-related (TEN) genes in 11 Cucurbitaceae species. Interestingly, the characteristic sequence changed from CNNFYFP to CNNFYLP in the TEN gene (Bhi06M000087) of Benincasa hispida. Furthermore, we identified a new characteristic sequence, YNN, which could be used for TEN gene exploitation in Cucurbitaceae. In conclusion, this study will serve as a reference for studying the relationship between gene family evolution and genome duplication. Moreover, it will provide rich genetic resources for functional Cucurbitaceae studies in the future

IL-1β-Mediated Up-Regulation of WT1D via miR-144-3p and Their Synergistic Effect with NF-κB/COX-2/HIF-1α Pathway on Cell Proliferation in LUAD

Background/Aims: IL-1β is an important mediator of “inflammation-cancer" transformation through IL-1β/NF-κB/COX-2/HIF-1α signaling pathway, whereas certain portion of patients with lung adenocarcinoma (LUAD) still suffer from rapid tumor progression in clinical practice, indicating the occurrence of potential bypass. Methods: Real-time polymerase chain reaction was applied to examine the expressions of mir-144-3p, WT1, NF-κB, COX2 and HIF-1α at the mRNA level in 127 LUAD samples and corresponding adjacent tissues. miR-144-3p mimic and antagormiR were used to trigger activation and suppression of miR-144-3p in A549 cells, respectively. MTT assay and Western blotting analysis were carried out to evaluate the cell proliferation. Stable clones with over-expression or knockdown of WT1 were generated with plasmid or shRNA by lentiviral vector technology in H1568 and H1650 NSCLC cell lines, respectively. Dual luciferase reporter assay was performed to validate the effect of miR-144-3p on WT1D. Xenograft model was established for in vivo experiment, and TCGA data were extracted for validation. Results: miR-144-3p could suppress the WT1D expression at the post-transcriptional level, hence regulating cell proliferation in LUAD. WT1 and COX-2 were independent prognostic factors of LUAD patients. In addition, inhibition of IL-1β/miR-144-3p/WT1D and IL-1β/NF-κB/COX-2/HIF-1α pathways using miR-144-3p mimic and Celecoxib, respectively, displayed synergistic suppressive effect on cell proliferation in LUAD. Conclusion: A de novo IL-1β/miR-144-3p/WT1D axis was involved in proliferative regulation of LUAD. Moreover, simultaneous blockade of both IL-1β/miR-144-3p/WT1D and IL-1β/NF-κB/COX-2/ HIF-1α pathways might have synergistic suppressive effect on cell proliferation in LUAD

Mesenchymal stem cells alleviate bacteria‐induced liver injury in mice by inducing regulatory dendritic cells

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102718/1/hep26670.pd