Showing papers by "Southwest University published in 2010"

The International Pulsar Timing Array project: using pulsars as a gravitational wave detector

Abstract: The International Pulsar Timing Array project combines observations of pulsars from both northern and southern hemisphere observatories with the main aim of detecting ultra-low frequency (similar to 10(-9)-10(-8) Hz) gravitational waves. Here we introduce the project, review the methods used to search for gravitational waves emitted from coalescing supermassive binary black-hole systems in the centres of merging galaxies and discuss the status of the project.

New parametrization for the nuclear covariant energy density functional with a point-coupling interaction

Abstract: A new parametrization PC-PK1 for the nuclear covariant energy density functional with nonlinear point-coupling interaction is proposed by fitting to observables of 60 selected spherical nuclei, including the binding energies, charge radii, and empirical pairing gaps. The success of PC-PK1 is illustrated in the description of infinite nuclear matter and finite nuclei including the ground-state and low-lying excited states. In particular, PC-PK1 provides a good description for the isospin dependence of binding energy along either the isotopic or the isotonic chain, which makes it reliable for application in exotic nuclei. The predictive power of PC-PK1 is also illustrated for the nuclear low-lying excitation states in a five-dimensional collective Hamiltonian in which the parameters are determined by constrained calculations for triaxial shapes.

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Abstract: Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis and human, demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

Stability Analysis for Continuous-Time Positive Systems With Time-Varying Delays

Abstract: This note addresses the stability problem of continuous-time positive systems with time-varying delays. It is shown that such a system is asymptotically stable for any continuous and bounded delay if and only if the sum of all the system matrices is a Hurwitz matrix. The result is a time-varying version of the widely-known asymptotic stability criterion for constant-delay positive systems. A numerical example illustrates the correctness of our result.

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology

Abstract: The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). Since the draft sequence was completed and the SilkDB was first released 5 years ago, we have collaborated with other groups to make much remarkable progress on silkworm genome research, such as the completion of a new high-quality assembly of the silkworm genome sequence as well as the construction of a genome-wide microarray to survey gene expression profiles. To accommodate these new genomic data and house more comprehensive genomic information, we have reconstructed SilkDB database with new web interfaces. In the new version (v2.0) of SilkDB, we updated the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently. SilkDB is publicly available at the new URL of http://www.silkdb.org.

Evaluation of endogenous references for gene expression profiling in different tissues of the oriental fruit fly Bactrocera dorsalis (Diptera: Tephritidae).

Abstract: Quantitative real-time reverse transcriptase PCR (RT-qPCR) has been widely used for quantification of mRNA as a way to determine key genes involved in different biological processes. For accurate gene quantification analysis, normalization of RT-qPCR data is absolutely essential. To date, normalization is most frequently achieved by the use of internal controls, often referred to as reference genes. However, several studies have shown that the reference genes used for the quantification of mRNA expression can be affected by the experimental set-up or cell type resulting in variation of the expression level of these key genes. Therefore, the evaluation of reference genes is critical for gene expression profiling, which is often neglected in gene expression studies of insects. For this purpose, ten candidate reference genes were investigated in three different tissues (midgut, Malpighian tubules, and fat body) of the oriental fruit fly, Bactrocera dorsalis (Hendel). Two different programs, geNorm and Normfinder, were used to analyze the data. According to geNorm, α-TUB + ACT5 are the most appropriate reference genes for gene expression profiling across the three different tissues in the female flies, while ACT3 + α-TUB are considered as the best for males. Furthermore, we evaluated the stability of the candidate reference genes to determine the sexual differences in the same tissue. In the midgut and Malpighian tubules, ACT2 + α-TUB are the best choice for both males and females. However, α-TUB + ACT1 are the best pair for fat body. Meanwhile, the results calculated by Normfinder are quite the same as the results with geNorm; α-TUB is always one of the most stable genes in each sample validated by the two programs. In this study, we validated the suitable reference genes for gene expression profiling in different tissues of B. dorsalis. Moreover, appropriate reference genes were selected out for gene expression profiling of the same tissues taking the sexual differences into consideration. This work not only formed a solid basis for future gene expression study in B. dorsalis, but also will serve as a resource to screen reference genes for gene expression studies in any other insects.

Doublesex- and Mab-3-Related Transcription Factor-1 Repression of Aromatase Transcription, a Possible Mechanism Favoring the Male Pathway in Tilapia

Abstract: Doublesex- and Mab-3-related transcription factor-1 (Dmrt1) is an important transcription factor implicated in early testicular differentiation in vertebrates, but its target genes are largely unknown. In the Nile tilapia, estrogen is the natural inducer of ovarian differentiation. Our recent studies have shown that Forkhead-l2 up-regulated transcription of the Cyp19a1a gene (aromatase) in the gonads in a female-specific manner. However, the upstream factor(s) down-regulating Cyp19a1a expression during testicular differentiation remains unclear. In the present study, we used in vitro (promoter analysis) and in vivo (transgenesis and in situ hybridization) approaches to examine whether Dmrt1 inhibits Cyp19a1a's transcriptional activity. The in vitro analysis using luciferase assays revealed that Dmrt1 repressed basal as well as Ad4BP/SF-1-activated Cyp19a1a transcription in HEK 293 cells. Luciferase assays with various deletions of Dmrt1 also showed that the Doublesex and Mab-3 domain is essential for the repression. In vitro-translated Dmrt1 and the nuclear extract from tilapia testis could directly bind to the palindrome sequence ACATATGT in the Cyp19a1a promoter, as determined by EMSAs. Transgenic overexpression of Dmrt1 in XX fish resulted in decreased aromatase gene expression, reduced serum estradiol-17beta levels, retardation of the ovarian cavity's development, varying degrees of follicular degeneration, and even a partial to complete sex reversal. Our results indicate that aromatase is one of the targets of Dmrt1. Dmrt1 suppresses the female pathway by repressing aromatase gene transcription and estrogen production in the gonads of tilapia and possibly other vertebrates.

Issues of cultural appropriateness and pedagogical efficacy: exploring peer review in a second language writing class

Abstract: This paper reports on a study designed to investigate (a) whether peer review is an effective pedagogical activity with adult Chinese students in the teaching of second language (L2) academic writing and (b) how factors such as perceptions of the influence of peer reviewers’ L2 proficiency, previous experience with peer review, feedback preferences, and culturally-based beliefs and practices relate to the effectiveness of the pedagogical activity. Participants were 20 English-as-an-L2 learners from China who were enrolled in an academic writing class for postgraduate students at a Singaporean university. Data included first drafts of an academic writing assignment, written peer comments, revised drafts of the assignment, responses to a questionnaire, and interviews. Quantitative analyses of the peer comments and revisions to the drafts show that significant improvement in the revised drafts was linked to peer feedback. Further statistical analyses indicate that the learner variables of interest did not affect the effectiveness of the peer review activity. In addition, qualitative analyses of the questionnaire data and the interviews reveal a general acceptance of peer review as a socioculturally appropriate pedagogical activity for Chinese students. The results of the study are interpreted with an understanding of its limitations, and directions for further research are also discussed.

Configuration mixing of angular-momentum-projected triaxial relativistic mean-field wave functions

Abstract: The framework of relativistic energy-density functionals is extended to include correlations related to the restoration of broken symmetries and to fluctuations of collective variables. The generator coordinate method is used to perform configuration mixing of angular-momentum-projected wave functions, generated by constrained self-consistent relativistic mean-field calculations for triaxial shapes. The effects of triaxial deformation and of K mixing is illustrated in a study of spectroscopic properties of low-spin states in {sup 24}Mg.

Polycentric urban development: the case of Hangzhou

Abstract: Despite the advantages of polycentric structure and its rich literature drawn from cities in industialized countries, little attention has been paid to the study of polycentric urban development in developing countries based on land-use information. With Hangzhou used as a case study, the authors investigate polycentric urban development through an analysis of directions of urban expan- sion, urban^rural gradients, and growth types. The multidisciplinary methodology employed, based on theories and methods in remote sensing, geographic information systems, and landscape ecology, has been proved to be useful in the morphological study of polycentric urban development. It was found that Hangzhou has expanded in different directions at various speeds, shifting to a polycentric urban pattern through radial expansion. Along the main transportation corridors, the values of the mean patch sizes of urban patches displayed multiple peaks, and the landscape-shape index main- tained a horizontal trend in urban fringes, reflecting the formation of polycentricity. Further, as edge growth and spontaneous growth accounted for 40%^50% and 30^40% of urban growth, respec- tively, and infill growth was responsible for only a small proportion of urban growth, it is suggested that dispersed urban patches have been increasingly agglomerated into big ones, especially along road corridors. Hangzhou's polycentric urban development was shaped both by the planning efforts of the government and by market forces. The municipal government guided the polycentric development through drafting and revising master plans, annexing nearby districts, and establishing development zones. Nevertheless, market forces played an increasingly important role in Hangzhou's polycentric development through the implementation of an urban land market, the inflow of migrant workers, and the relocation of industries.

Transgenic silkworms (Bombyx mori) produce recombinant spider dragline silk in cocoons

Abstract: Spider dragline silk is a unique fibrous protein with a combination of tensile strength and elasticity, but the isolation of large amounts of silk from spiders is not feasible. In this study, we generated germline-transgenic silkworms (Bombyx mori) that spun cocoons containing recombinant spider silk. A piggyBac-based transformation vector was constructed that carried spider dragline silk (MaSp1) cDNA driven by the sericin 1 promoter. Silkworm eggs were injected with the vector, producing transgenic silkworms displaying DsRed fluorescence in their eyes. Genotyping analysis confirmed the integration of the MaSp1 gene into the genome of the transgenic silkworms, and silk protein analysis revealed its expression and secretion in the cocoon. Compared with wild-type silk, the recombinant silk displayed a higher tensile strength and elasticity. The results indicate the potential for producing recombinant spider silk in transgenic B. mori.

Carbon nanotubes as a low background signal platform for a molecular aptamer beacon on the basis of long-range resonance energy transfer.

Abstract: Although holding the advantages of both an aptamer and a molecular beacon (MB), a molecular aptamer beacon (MAB) needs complicated and expensive modifications at both of its ends and usually has a high background signal because of the low energy transfer efficiency between the donor and the acceptor. To overcome these shortcomings, in this study, we develop a long-range resonance energy transfer (LrRET) system by separating the donor from the acceptor, wherein only one end of the MAB is fluorescently labeled and acts as the energy donor and multiwalled carbon nanotubes (MWCNTs) are introduced as the energy acceptor. To test the feasibility of the newly designed MAB system, adenosine triphosphate (ATP) has been employed as a proof-of-concept target. It is found that the fluorescence of the designed MAB is completely quenched by MWCNTs, supplying a very low background signal. Then the quenched fluorescence is recovered significantly with the addition of ATP, so that ATP can be detected in the range of 0.8−8...

MicroRNAs of Bombyx mori identified by Solexa sequencing.

Abstract: MicroRNA (miRNA) and other small regulatory RNAs contribute to the modulation of a large number of cellular processes. We sequenced three small RNA libraries prepared from the whole body, and the anterior-middle and posterior silk glands of Bombyx mori, with a view to expanding the repertoire of silkworm miRNAs and exploring transcriptional differences in miRNAs between segments of the silk gland. With the aid of large-scale Solexa sequencing technology, we validated 257 unique miRNA genes, including 202 novel and 55 previously reported genes, corresponding to 324 loci in the silkworm genome. Over 30 known silkworm miRNAs were further corrected in their sequence constitutes and length. A number of reads originated from the loop regions of the precursors of two previously reported miRNAs (bmo-miR-1920 and miR-1921). Interestingly, the majority of the newly identified miRNAs were silkworm-specific, 23 unique miRNAs were widely conserved from invertebrates to vertebrates, 13 unique miRNAs were limited to invertebrates, and 32 were confined to insects. We identified 24 closely positioned clusters and 45 paralogs of miRNAs in the silkworm genome. However, sequence tags showed that paralogs or clusters were not prerequisites for coordinated transcription and accumulation. The majority of silkworm-specific miRNAs were located in transposable elements, and displayed significant differences in abundance between the anterior-middle and posterior silk gland. Conservative analysis revealed that miRNAs can serve as phylogenetic markers and function in evolutionary signaling. The newly identified miRNAs greatly enrich the repertoire of insect miRNAs, and provide insights into miRNA evolution, biogenesis, and expression in insects. The differential expression of miRNAs in the anterior-middle and posterior silk glands supports their involvement as new levels in the regulation of the silkworm silk gland.