AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>Construction of transcriptional regulatory networks (TRNs) is of priority concern in systems biology. Numerous high-throughput approaches, including microarray and next-generation sequencing, are extensively adopted to examine transcriptional expression patterns on the whole-genome scale; those data are helpful in reconstructing TRNs. Identifying transcription factor binding sites (TFBSs) in a gene promoter is the initial step in elucidating the transcriptional regulation mechanism. Since transcription factors usually co-regulate a common group of genes by forming regulatory modules with similar TFBSs. Therefore, the combinatorial interactions of transcription factors must be modeled to reconstruct the gene regulatory networks.</p> <p>Description For systems biology applications, this work develops a novel database called <it>Arabidopsis thaliana </it>Promoter Analysis Net (AtPAN), capable of detecting TFBSs and their corresponding transcription factors (TFs) in a promoter or a set of promoters in <it>Arabidopsis</it>. For further analysis, according to the microarray expression data and literature, the co-expressed TFs and their target genes can be retrieved from AtPAN. Additionally, proteins interacting with the co-expressed TFs are also incorporated to reconstruct co-expressed TRNs. Moreover, combinatorial TFs can be detected by the frequency of TFBSs co-occurrence in a group of gene promoters. In addition, TFBSs in the conserved regions between the two input sequences or homologous genes in <it>Arabidopsis </it>and rice are also provided in AtPAN. The output results also suggest conducting wet experiments in the future.</p> <p>Conclusions</p> <p>The AtPAN, which has a user-friendly input/output interface and provide graphical view of the TRNs. This novel and creative resource is freely available online at <url>http://AtPAN.itps.ncku.edu.tw/</url>.</p

Modeling the JWST high-redshift galaxies with a general formation scenario and the consistency with the Λ\LambdaCDM model

Early results from the James Webb Space Telescope (JWST) observations have hinted at two traces beyond the standard cosmological framework. One is the extraordinarily high stellar masses and their density at $z=7.5\sim9.1$, another is the unexpected abundance of ultra-violet (UV) bright galaxies at $z\ge10$. Nevertheless, both pieces of evidence are not statistically robust, yet. In this work, we construct rest-frame UV luminosity functions (LFs) based on a general formation model for these high-redshift galaxy candidates, since UV LFs always carry the information of stellar formation efficiency (SFE), initial mass function (IMF), dust attenuation, and other crucial elements for galaxy evolution. By updating the massive galaxies candidates with spectroscopic observations and exploring the parameter space of SFE, we are able to reasonably explain the cumulative stellar mass density within the redshift range of $7.5\sim9.1$, with only one galaxy exhibiting unusual characteristics. We also reveal a potential non-monotonic trend of SFE with the increasing redshift. At higher redshift ($z\sim13$), bright UV LFs can be well fitted with non-dust attenuation or Top-heavy IMF for Population III stars. The Population III star scenario can also naturally account for the possible dip of SFE at $z\sim9$.Comment: 9 pages, 4 figures, and 1 tabl

How the Design Leadership and Strategic Design Drive New Value in Enterprises and Organizations

Today's design has shifted from the original primary pursuit of appearance and function to processes and systems, creating new meanings for corporate strategies, products and services. Nowadays, enterprises are increasingly paying attention to the power of design, and regard design as the main innovation method and incorporate it into the organizations. Design began to be considered a key role at the top of large organizations. Although people recognize that design can bring good effects to enterprises and organizations, and there is growing interest in cultivating design thinking, what are the leaders who can lead enterprises, organizations and have design thinking? Their characteristics and how to formulate and plan strategic design still not fully elucidated. Therefore, this research uses related theories to understand the way of thinking and characteristics of design leaders, only in this way we formulate good strategic design for enterprises and organizations, and become an indispensable and important help in today rapidly changing world