microRNAs (miRNAs) are a new class of non-protein-coding, endogenous, small RNAs. They are important regulatory molecules in animals and plants. miRNA regulates gene expression by translational repression, mRNA cleavage, and mRNA decay initiated by miRNA-guided rapid deadenylation. Recent studies show that some miRNAs regulate cell proliferation and apoptosis processes that are important in cancer formation. By using multiple molecular techniques, which include Northern blot analysis, real-time PCR, miRNA microarray, up- or down-expression of specific miRNAs, it was found that several miRNAs were directly involved in human cancers, including lung, breast, brain, liver, colon cancer, and leukemia. In addition, some miRNAs may function as oncogenes or tumor suppressors. More than 50% of miRNA genes are located in cancer-associated genomic regions or in fragile sites, suggesting that miRNAs may play a more important role in the pathogenesis of a limited range of human cancers than previously thought. Overexpressed miRNAs in cancers, such as mir-17-92, may function as oncogenes and promote cancer development by negatively regulating tumor suppressor genes and/or genes that control cell differentiation or apoptosis. Underexpressed miRNAs in cancers, such as let-7, function as tumor suppressor genes and may inhibit cancers by regulating oncogenes and/or genes that control cell differentiation or apoptosis. miRNA expression profiles may become useful biomarkers for cancer diagnostics. In addition, miRNA therapy could be a powerful tool for cancer prevention and therapeutics.

The production of clean and renewable hydrogen through water splitting using photocatalysts has received much attention due to the increasing global energy crises. In this study, a high efficiency of the photocatalytic H(2) production was achieved using graphene nanosheets decorated with CdS clusters as visible-light-driven photocatalysts. The materials were prepared by a solvothermal method in which graphene oxide (GO) served as the support and cadmium acetate (Cd(Ac)(2)) as the CdS precursor. These nanosized composites reach a high H(2)-production rate of 1.12 mmol h(-1) (about 4.87 times higher than that of pure CdS nanoparticles) at graphene content of 1.0 wt % and Pt 0.5 wt % under visible-light irradiation and an apparent quantum efficiency (QE) of 22.5% at wavelength of 420 nm. This high photocatalytic H(2)-production activity is attributed predominantly to the presence of graphene, which serves as an electron collector and transporter to efficiently lengthen the lifetime of the photogenerated charge carriers from CdS nanoparticles. This work highlights the potential application of graphene-based materials in the field of energy conversion.

miRDeepFinder is a software package developed to identify and functionally analyze plant microRNAs (miRNAs) and their targets from small RNA datasets obtained from deep sequencing. The functions available in miRDeepFinder include pre-processing of raw data, identifying conserved miRNAs, mining and classifying novel miRNAs, miRNA expression profiling, predicting miRNA targets, and gene pathway and gene network analysis involving miRNAs. The fundamental design of miRDeepFinder is based on miRNA biogenesis, miRNA-mediated gene regulation and target recognition, such as perfect or near perfect hairpin structures, different read abundances of miRNA and miRNA*, and targeting patterns of plant miRNAs. To test the accuracy and robustness of miRDeepFinder, we analyzed a small RNA deep sequencing dataset of Arabidopsis thaliana published in the GEO database of NCBI. Our test retrieved 128 of 131 (97.7%) known miRNAs that have a more than 3 read count in Arabidopsis. Because many known miRNAs are not associated with miRNA*s in small RNA datasets, miRDeepFinder was also designed to recover miRNA candidates without the presence of miRNA*. To mine as many miRNAs as possible, miRDeepFinder allows users to compare mature miRNAs and their miRNA*s with other small RNA datasets from the same species. Cleaveland software package was also incorporated into miRDeepFinder for miRNA target identification using degradome sequencing analysis. Using this new computational tool, we identified 13 novel miRNA candidates with miRNA*s from Arabidopsis and validated 12 of them experimentally. Interestingly, of the 12 verified novel miRNAs, a miRNA named AC1 spans the exons of two genes (UTG71C4 and UGT71C3). Both the mature AC1 miRNA and its miRNA* were also found in four other small RNA datasets. We also developed a tool, "miRNA primer designer" to design primers for any type of miRNAs. miRDeepFinder provides a powerful tool for analyzing small RNA datasets from all species, with or without the availability of genome information. miRDeepFinder and miRNA primer designer are freely available at http://www.leonxie.com/DeepFinder.php and at http://www.leonxie.com/miRNAprimerDesigner.php , respectively. A program (called RefFinder: http://www.leonxie.com/referencegene.php ) was also developed for assessing the reliable reference genes for gene expression analysis, including miRNAs.

Bright two-photon fluorescent probes are highly desirable to be able to optically probe biological activities deep inside living organisms with larger imaging depth, minor autofluorescence background, and less photodamage. In this study, we report the biocompatible nitrogen-doped graphene quantum dots (N-GQDs) as efficient two-photon fluorescent probes for cellular and deep-tissue imaging. The N-GQD was prepared by a facile solvothermal method using dimethylformamide as a solvent and nitrogen source. The two-photon absorption cross-section of N-GQD reaches 48,000 Göppert-Mayer units, which far surpasses that of the organic dyes and is comparable to that of the high performance semiconductor QDs, achieving the highest value ever reported for carbon-based nanomaterials. More importantly, a study of penetration depth in tissue phantom demonstrates that the N-GQD can achieve a large imaging depth of 1800 μm, significantly extending the fundamental two-photon imaging depth limit. In addition, the N-GQD is nontoxic to living cells and exhibits super photostability under repeated laser irradiation. The high two-photon absorption cross-section, large imaging depth, good biocompatibility, and extraordinary photostability render the N-GQD an attractive alternative probe for efficient two-photon imaging in biological and biomedical applications.

MicroRNA (miRNA) is one class of newly identified, small, non-coding RNAs that play versatile and important roles in post-transcriptional gene regulation. All miRNAs have similar secondary hairpin structures; many of these are evolutionarily conserved. This suggests a powerful approach to predict the existence of new miRNA orthologs or homologs in other species. We developed a comprehensive strategy to identify new miRNA homologs by mining the repository of available ESTs. A total of 481 miRNAs, belonging to 37 miRNA families in 71 different plant species, were identified from more than 6 million EST sequences in plants. The potential targets of the EST-predicted miRNAs were also elucidated from the EST and protein databases, providing additional evidence for the real existence of these miRNAs in the given plant species. Some plant miRNAs were physically clustered together, suggesting that these miRNAs have similar gene expression patterns and are transcribed together as a polycistron, as observed among animal miRNAs. The uracil nucleotide is dominant in the first position of 5' mature miRNAs. Our results indicate that many miRNA families are evolutionarily conserved across all major lineages of plants, including mosses, gymnosperms, monocots and eudicots. Additionally, the number of miRNAs discovered was directly related to the number of available ESTs and not to evolutionary relatedness to Arabidopsis thaliana, indicating that miRNAs are conserved and little phylogenetic signal exists in the presence or absence of these miRNAs. Regulation of gene expression by miRNAs appears to have existed at the earliest stages of plant evolution and has been tightly constrained (functionally) for more than 425 million years.