Metabolic Pathways Enhancement Confers Poor Prognosis in p53 Exon Mutant Hepatocellular Carcinoma.

RNA-Sequencing (RNA-Seq), the most commonly used sequencing application tool, is not only a method for measuring gene expression but also an excellent media to detect important structural variants such as single nucleotide variants (SNVs), insertion/deletion (Indels), or fusion transcripts. The Cancer Genome Atlas (TCGA) contains genomic data from a variety of cancer types and also provides the raw data generated by TCGA consortium. p53 is among the top 10 somatic mutations associated with hepatocellular carcinoma (HCC). The aim of the present study was to analyze concordant different gene profiles and the priori defined set of genes based on p53 mutation status in HCC using RNA-Seq data. In the study, expression profile of 11 799 genes on 42 paired tumor and adjacent normal tissues was collected, processed, and further stratified by the mutated versus normal p53 expression. Furthermore, we used a knowledge-based approach Gene Set Enrichment Analysis (GSEA) to compare between normal and p53 mutation gene expression profiles. The statistical significance (nominal P value) of the enrichment score (ES) genes was calculated. The ranked gene list that reflects differential expression between p53 wild-type and mutant genotypes was then mapped to metabolic process by KEGG, an encyclopedia of genes and genomes to assign functional meanings. These approaches enable us to identify pathways and potential target gene/pathways that are highly expressed in p53 mutated HCC. Our analysis revealed 2 genes, the hexokinase 2 (HK2) and Enolase 1 (ENO1), were conspicuous of red pixel in the heatmap. To further explore the role of these genes in HCC, the overall survival plots by Kaplan-Meier method were performed for HK2 and ENO1 that revealed high HK2 and ENO1 expression in patients with HCC have poor prognosis. These results suggested that these glycolysis genes are associated with mutated-p53 in HCC that may contribute to poor prognosis. In this proof-of-concept study, we proposed an approach for identifying novel potential therapeutic targets in human HCC with mutated p53. These approaches can take advantage of the massive next-generation sequencing (NGS) data generated worldwide and make more out of it by exploring new potential therapeutic targets

An \textit{ab initio} study of magnetic structure transitions of FePS3_3 under high pressure

Recent experimental work shows that FePS$_3$ undergoes phase transitions from $C2/m$ ($\beta\sim107^{\circ}$) to $C2/m$ ($\beta\sim90^{\circ}$) at $6$ GPa and then to metallic $P\bar{3}1m$ at $14$ GPa, with the magnetic ordering wave vector turning from $k=(01\frac{1}{2})$ to $k=(010)$ at $2$ GPa and to short-range magnetic order accompanying the insulator-metal transition. By preserving the magnetic point groups in $ab \ initio$ calculations we report the following: (1) We successfully reproduce the first magnetic structure transition at $1.2$ GPa and briefly discuss the influence of the Hubbard U parameter on this transition. This isostructural transition causes a change of the Brillouin zone from base-centered monoclinic to primitive monoclinic, and an indrect band gap to direct band gap transition. (2) There is a rotation of the Fe-S octahedron about $0.5^\circ$ through the $[001]$ axis before the neighboring layers shift. (3) The shift between neighboring layers is predicted to occur at $10.0$ GPa and reverses the energy order between $d_{x^2-y^2}$ and $d_{xy}$. (4) A sudden decrease of Fe-S bond length to $2.20$ \AA \ accompanies the vanishing of magnetic moment in the insulator-metal transition. Our work shows the importance of symmetries of magnetic structures in pressure-induced phase transition of magnetic systems

From kinetic-structure analysis to engineering crystalline fiber networks in soft materials

10.1039/c2cp43747cPhysical Chemistry Chemical Physics1593313-3319PPCP

Planar carbon nanotube-graphene hybrid films for high-performance broadband photodetectors

Graphene has emerged as a promising material for photonic applications fuelled by its superior electronic and optical properties. However, the photoresponsivity is limited by the low absorption cross section and ultrafast recombination rates of photoexcited carriers. Here we demonstrate a photoconductive gain of $\sim$ 10$^5$ electrons per photon in a carbon nanotube-graphene one dimensional-two dimensional hybrid due to efficient photocarriers generation and transport within the nanostructure. A broadband photodetector (covering 400 nm to 1550 nm) based on such hybrid films is fabricated with a high photoresponsivity of more than 100 AW$^{-1}$ and a fast response time of approximately 100 {\mu}s. The combination of ultra-broad bandwidth, high responsivities and fast operating speeds affords new opportunities for facile and scalable fabrication of all-carbon optoelectronic devices.Comment: 21 pages, 3 figure