Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis. Here, we introduce agriGO, an integrated web-based GO analysis toolkit for the agricultural community, using the advantages of our previous GO enrichment tool (EasyGO), to meet analysis demands from new technologies and research objectives. EasyGO is valuable for its proficiency, and has proved useful in uncovering biological knowledge in massive data sets from high-throughput experiments. For agriGO, the system architecture and website interface were redesigned to improve performance and accessibility. The supported organisms and gene identifiers were substantially expanded (including 38 agricultural species composed of 274 data types). The requirement on user input is more flexible, in that user-defined reference and annotation are accepted. Moreover, a new analysis approach using Gene Set Enrichment Analysis strategy and customizable features is provided. Four tools, SEA (Singular enrichment analysis), PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA), are integrated as a toolkit to meet different demands. We also provide a cross-comparison service so that different data sets can be compared and explored in a visualized way. Lastly, agriGO functions as a GO data repository with search and download functions; agriGO is publicly accessible at http://bioinfo.cau.edu.cn/agriGO/.

In several approaches to the quantum-gravity problem evidence has emerged of the validity of a "GUP" (a Generalized position-momentum Uncertainty Principle) and/or a "MDR" (a modification of the energy-momentum dispersion relation), but very little is known about the implications of GUPs and MDRs for black-hole thermodynamics, another key topic for quantum-gravity research. We investigate an apparent link, already suggested in an earlier exploratory study involving two of us, between the possibility of a GUP and/or a MDR and the possibility of a log term in the area-entropy black-hole formula. We then obtain, from that same perspective, a modified relation between the mass of a black hole and its temperature, and we examine the validity of the "Generalized Second Law of black-hole thermodynamics" in theories with a GUP and/or a MDR. After an analysis of GUP-and MDR-modifications of the black-body radiation spectrum, we conclude the study with a description of the black-hole evaporation process.

MicroRNAs (miRNA) are ∼21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Glycine max, etc., it is desirable to develop a plant miRNA database through the integration of large amounts of information about publicly deposited miRNA data. The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, we included the possible target genes for each miRNA with a predicted interaction site in the database. Furthermore, we provided miRNA expression profiles in the PMRD, including our local rice oxidative stress related microarray data (LC Sciences miRPlants_10.1) and the recently published microarray data for poplar, Arabidopsis, tomato, maize and rice. The PMRD database was constructed by open source technology utilizing a user-friendly web interface, and multiple search tools. The PMRD is freely available at http://bioinformatics.cau.edu.cn/PMRD. We expect PMRD to be a useful tool for scientists in the miRNA field in order to study the function of miRNAs and their target genes, especially in model plants and major crops.

The formalism of rainbow gravity is studied in a cosmological setting. We consider the very early universe which is radiation dominated. A novel treatment in our paper is to look for an "averaged" cosmological metric probed by radiation particles themselves. Taking their cosmological evolution into account, we derive the modified Friedmann-Robertson-Walker(FRW) equations which is a generalization of the solution presented by Magueijo and Smolin. Based on this phenomenological cosmological model we argue that the spacetime curvature has an upper bound such that the cosmological singularity is absent. These modified F RW equations can be treated as effective equations in the semi-classical framework of quantum gravity and its analogy with the one recently proposed in loop quantum cosmology is also discussed.

We study the thermodynamics of modified black holes proposed in the context of gravity's rainbow. A notion of intrinsic temperature and entropy for these black holes is introduced. In particular for a specific class of modified Schwarzschild solutions, their temperature and entropy are obtained and compared with those previously obtained from modified dispersion relations in deformed special relativity. It turns out that the results of these two different strategies coincide, and this may be viewed as a support for the proposal of deformed equivalence principle.

We construct an ionic lattice background in the framework of Einstein-Maxwell-dilaton theory in four dimensional space time. The optical conductivity of the dual field theory on the boundary is investigated. Due to the lattice effects, we find the imaginary part of the conductivity is manifestly suppressed in the zero frequency limit, while the DC conductivity approaches a finite value such that the previous delta function reflecting the translation symmetry is absent. Such a behavior can be exactly fit by the Drude law at low frequency. Moreover, we find that the modulus of the optical conductivity exhibits a power-law behavior at intermediate frequency regime. Our results provides further support for the universality of such power-law behavior recently disclosed in Einstein-Maxwell theory

The first ncRNA found was an alanine tRNA in baker's yeast, and the first detected microRNAs (miRNAs) promoted ncRNA research to a whole new level. Research on ncRNAs in animals has focused on the medical field, while in plant scientists are more concerned with improving agronomic traits. In 2010, we constructed a plant miRNA database named PMRD to meet the demand for miRNA research in plants. To provide a way to do fundamental research on plant ncRNAs and take full advantage of tremendous public resources, we designed an updated platform called plant ncRNA database (PNRD) based on its predecessor PMRD, which is accessible at http://structuralbiology.cau.edu.cn/PNRD. We collected a total of 25739 entries of 11 different types of ncRNAs from 150 plant species. Targets of miRNAs were extended to 178138 pairs in 46 species, while the number of miRNA expression profiles reached 35. Improvements in PNRD are not only the larger amounts of data, but also better service, such as a more user-friendly interface, more multifunctional and browsing options and more background data for users to download. We also integrated currently prevalent technologies and toolkits to strengthen the capability of the database and provide a one-stop service for scientific users.

Loop quantum cosmology provides a nice solution of avoiding the big bang singularity through a big bounce mechanism in the high energy region. In loop quantum cosmology an inflationary universe is emergent after the big bounce, no matter what matter component is filled in the universe. A super-inflation phase without phantom matter will appear in a certain way in the initial stage after the bounce; then the universe will undergo a normal inflation stage. We discuss the condition of inflation in detail in this framework. Also, for slow-roll inflation, we expect the imprint from the effects of the loop quantum cosmology should be left in the primordial perturbation power spectrum. However, we show that this imprint is too weak to be observed.