Comparative transcriptome analysis of the different tissues between the cultivated and wild tomato.

Although domesticated tomato is cultivated by wild tomato, there are a lot of differences between cultivated tomato and wild tomato, such as shape, physiological function and life history. Many studies show that wild tomato has better salt resistance and drought resistance. In addition to, domesticated tomato's fruit is bigger and has more nutritious than wild tomato. The different features are closely related to differentially expressed genes. We identified 126 up-regulated differentially expressed genes and 87 down-regulated differentially expressed genes in cultivated tomato and wild tomato by RNA-Seq. These differentially expressed genes may be associated with salt resistance, drought resistance and fruit nutrition. These differentially expressed genes also further highlight the large-scale reconstruction between wild and cultivated species. In this paper, we mainly study GO enrichment analysis and pathway analysis of the differentially expressed genes. After GO and pathway enrichment analysis, a set of significantly enriched GO annotations and pathways were identified for the differentially expressed genes. What's more, we also identified long non-coding RNAs and mRNAs in the two species and analyzed its essential features. In addition to, we construct a co-expression network of long non-coding RNAs and mRNAs, and annotate mRNAs associated with long non-coding RNAs as target genes, and speculate the regulation function of long non-coding RNAs. In total, our results reveal the effects of artificial and natural selection on tomato's transcript, providing scientific basis for tomato's research in the future

Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation

Sequence comparison is one of the foundations in bioinformatics, which can be used to study evolutionary relations among the sequences. In this study, a 2D spectrum-like graphical representation of protein sequences is presented based on the hydrophobicity scale of amino acids. The frequencies of amplitudes of 4-subsequences are adopted to characterize a spectrum-like graph, and a 17D vector is used as the descriptor of protein sequence. The Ç 2 value of compatibility test is performed. New similarity analysis approach is illustrated on the all protein sequences, which are encoded by the mitochondrion genome of 20 different species. Finally, comparison with the ClustalW method shows the utility of our method

Up-regulation of MIC19 promotes growth and metastasis of hepatocellular carcinoma by activating ROS/NF-κB signaling

Background: Mitochondrial malfunction has been well-recognized as a critical step in the pathogenesis of many types of diseases, including cancer. MIC19 is a core a subunit of the MICOS complex that plays a critical role in maintaining the normal function of mitochondria. However, the biological functions of MIC19 in human hepatocellular carcinoma (HCC) remain unclear. Methods: The expression level of MIC19 in HCC was evaluated by bioinformatics analysis, quantitative real-time PCR and immunohistochemistry staining assays. Cell growth and metastasis experiments were used to assess the biological functions of MIC19 in HCC cells. Findings: MIC19 expression was frequently upregulated in both human HCC specimens and cell lines, and its upregulation is closely associated with patients’ survival. Results from loss-of-function and gain-of-function experiments demonstrated that knockdown of MIC19 significantly attenuated, while overexpression of MIC19 enhanced, the proliferation, colony formation, migration and invasion abilities of HCC cells. Mechanistically, we found that MIC19 has no effect on mitochondrial energy production, while activated ROS/NF-κB signaling, which was required for MIC19-promoted HCC growth and metastasis. Interpretation: Our findings suggest that MIC19 play a critical oncogenic role in HCC, implying that MIC19 may serve as a potential therapeutic target in the treatment of HCC

The sequence number of the research data.

<p>The sequence number of the research data.</p

GO analysis of differentially expressed genes in each tissue.

<p>BP, MF and CC ontologies of DEGs shared by cultivated tomato and wild tomato.</p

KEGG analysis of differentially expressed genes.

<p>Pathway prediction of DEGs shared by cultivated tomato and wild tomato. In each category, the first 23 enriched terms were listed.</p

The volcano map of gene expression.

<p>The volcano map of gene expression.</p

Functional annotation of lncRNA target gene.

<p>Functional annotation of lncRNA target gene.</p

Co-expression network of between lncRNAs and mRNAs.

<p>Co-expression network of between lncRNAs and mRNAs.</p

Length distribution of lncRNA and mRNA.

<p>Length distribution of lncRNA and mRNA.</p