Genome-Wide Identification, Evolutionary Expansion, and Expression Profile of Homeodomain-Leucine Zipper Gene Family in Poplar (Populus trichocarpa)

BACKGROUND: Homeodomain-leucine zipper (HD-ZIP) proteins are plant-specific transcriptional factors known to play crucial roles in plant development. Although sequence phylogeny analysis of Populus HD-ZIPs was carried out in a previous study, no systematic analysis incorporating genome organization, gene structure, and expression compendium has been conducted in model tree species Populus thus far. PRINCIPAL FINDINGS: In this study, a comprehensive analysis of Populus HD-ZIP gene family was performed. Sixty-three full-length HD-ZIP genes were found in Populus genome. These Populus HD-ZIP genes were phylogenetically clustered into four distinct subfamilies (HD-ZIP I-IV) and predominately distributed across 17 linkage groups (LG). Fifty genes from 25 Populus paralogous pairs were located in the duplicated blocks of Populus genome and then preferentially retained during the sequential evolutionary courses. Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus HD-ZIP gene family. Microarray analysis has shown that 21 Populus paralogous pairs have been differentially expressed across different tissues and under various stresses, with five paralogous pairs showing nearly identical expression patterns, 13 paralogous pairs being partially redundant and three paralogous pairs diversifying significantly. Quantitative real-time RT-PCR (qRT-PCR) analysis performed on 16 selected Populus HD-ZIP genes in different tissues and under both drought and salinity stresses confirms their tissue-specific and stress-inducible expression patterns. CONCLUSIONS: Genomic organizations indicated that segmental duplications contributed significantly to the expansion of Populus HD-ZIP gene family. Exon/intron organization and conserved motif composition of Populus HD-ZIPs are highly conservative in the same subfamily, suggesting the members in the same subfamilies may also have conservative functionalities. Microarray and qRT-PCR analyses showed that 89% (56 out of 63) of Populus HD-ZIPs were duplicate genes that might have been retained by substantial subfunctionalization. Taken together, these observations may lay the foundation for future functional analysis of Populus HD-ZIP genes to unravel their biological roles

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Mesoporous Carbon Structure-Based Glass Nanopipettes as Micro pH Probes

Nanopore-based nanomaterials have been widely used to prepare the biosensor due to the unique structure, and the high sensitivity to the external stimuli under different environmental conditions. In this report, we ingeniously designed and prepared mesoporous carbon structure-based quartz nanopipettes. The mesoporous carbon was in situ grown in the tip working area of a single quartz nanopipette through the method of evaporation induced self-assembly (EISA). The mesoporous carbon could reduce the effective aperture of the nanopipette, while the surface area of nanopipette tip could be increased by the mesoporous carbon structure as well. The negative charges on the inner surface of the nanopipette increased significantly, which made the ionic current rectification of the nanopore more remarkable, with the ionic current rectification ratio increasing from 2.3 to 34.8. The mesoporous carbon-based glass nanopipette with good response to pH has been used for the probe of pH value of micro-volume solution. The test results were consistent with those obtained by using a commercial pH meter.</p

Blockage of TGF-β1-induced epithelial-tomesenchymal transition by oxymatrine prevents renal interstitial fibrosis

Most chronic kidney disease inevitably progress to renal fibrosis. Tubular epithelial- to-mesenchymal transition (EMT) is recognized to play major roles in renal fibrosis. Oxymatrine (OM) is a major alkaloid component found in a Chinese herb Sophora roots and has many effects. The aim is to investigate the effect of OM on renal tubular EMT and elucidate its mechanism. Mice underwent unilateral ureteral obstruction (UUO) followed by intraperitoneal injection of OM (120 mg/kg) or control vehicle. Human kidney proximal tubular cell line (HK-2) was used and EMT was induced with 5 ng/mL of transforming growth factor-β1 (TGF-β1).&nbsp;In vivo, renal tubulointerstitial fibrosis was induced and E-cadherin was down-regulated, while the expressions of fibronectin (FN), α-smooth muscle actin (α-SMA), TGF-β1 and its type I receptor (TGF-βRI) were up-regulated in UUO mice. In contrast, OM significantly ameliorated renal fibrotic lesions and attenuated the expressions of FN, α-SMA, TGF-β1 and TGF-βRI, but increased E-cadherin in the obstructed kidneys.&nbsp;In vitro, OM abolished TGF-β1-mediated E-cadherin suppression and FN, α-SMA and TGF-βRI induction in HK-2 cells in a dose-dependent manner. These observations strongly suggest that the renal protective effects of OM could be mediated by prevention of EMT and manifested as suppression of TGF-β1 and TGF-βRI expressions

Practical implementation of multichannel filtered-x least mean square algorithm based on the multiple-parallel-branch with folding architecture for large-scale active noise control

Multichannel active noise control (MCANC) is widely recognized as an effective and efficient solution for acoustic noise and vibration cancellation, such as in high-dimensional ventilation ducts, open windows, and mechanical structures. The feedforward multichannel filtered-x least mean square (FFMCFxLMS) algorithm is commonly used to dynamically adjust the transfer function of the multichannel controllers for different noise environments. The computational load incurred by the FFMCFxLMS algorithm, however, increases exponentially with increasing channel count, thus requiring high-end field-programmable gate array (FPGA) processors. Nevertheless, such processors still need specific configurations to cope with soaring computing loads as the channel count increases. To achieve a high-efficiency implementation of the FFMCFxLMS algorithm with floating-point arithmetic, a novel architecture based on multiple-parallel-branch with folding (MPBF) technique is proposed. This architecture parallelizes the branches and reuses the multiplier and adder in each folded branch so that the tradeoff between throughput and the usage of the hardware resources is balanced. The proposed architecture is validated in an experimental setup that implements the FFMCFxLMS algorithm for the MCANC system with 24 reference sensors, 24 secondary sources, and 24 error sensors, at a sampling and throughput rates of 25 kHz and 260 Mb/s, respectively.NRF (Natl Research Foundation, S’pore)Accepted versio

Exploiting the Underdetermined System in Multichannel Active Noise Control for Open Windows

Active noise control (ANC) is a re-emerging technique to mitigate noise pollution. To reduce the noise power in large spaces, multiple channels are usually required, which complicates the implementation of ANC systems. In this paper, we separate the multichannel ANC problem into two subproblems, where the subproblem of computing the control filter is usually an underdetermined problem. Therefore, we could leverage the underdetermined system to simplify the ANC system without degrading the noise reduction performance. For a single incidence, we compare the conventional fully-coupled (pseudoinverse) multichannel control with the colocated (diagonal) control method and find that they can achieve equivalent performance, but the colocated control method is less computationally intensive. Furthermore, the underdetermined system presents an opportunity to control noise from multiple incidences with one common fixed filter. Both the full-rank and the overdetermined optimal control filters are realized. The performance of these control methods was analyzed numerically with the Finite Element Method (FEM) and the results validate the feasibility of the full-rank and overdetermined optimal control methods, where the latter could even offer more robust performance in more complex noise scenarios

Application of Symbiotic Organisms Search Algorithm for Parameter Extraction of Solar Cell Models

Extracting accurate values for relevant unknown parameters of solar cell models is vital and necessary for performance analysis of a photovoltaic (PV) system. This paper presents an effective application of a young, yet efficient metaheuristic, named the symbiotic organisms search (SOS) algorithm, for the parameter extraction of solar cell models. SOS, inspired by the symbiotic interaction ways employed by organisms to improve their overall competitiveness in the ecosystem, possesses some noticeable merits such as being free from tuning algorithm-specific parameters, good equilibrium between exploration and exploitation, and being easy to implement. Three test cases including the single diode model, double diode model, and PV module model are served to validate the effectiveness of SOS. On one hand, the performance of SOS is evaluated by five state-of-the-art algorithms. On the other hand, it is also compared with some well-designed parameter extraction methods. Experimental results in terms of the final solution quality, convergence rate, robustness, and statistics fully indicate that SOS is very effective and competitive

Effect of highly branched hyphal morphology on the enhanced production of cellulase in Trichoderma reesei DES-15

The morphology of Trichoderma reesei is a vitally important factor for cellulase productivity. This study investigated the effect of hyphal morphology on cellulase production in the hyper-cellulolytic mutant, T. reesei DES-15. With a distinct morphology, T. reesei DES-15 was obtained through Diethyl sulfite (DES) mutagenesis. The hyphal morphology of DES-15 batch-cultured in a 5-L fermentor was significantly shorter and more branched than the parental strain RUT C30. The cellulase production of DES-15 during batch fermentation was 66 % greater than that of RUT C30 when cultured the same conditions. DES-15 secreted nearly 50 % more protein than RUT C30. The gene expression level of a set of genes (cla4, spa2, ras2, ras1, rhoA, cdc42, and racA) known to be involved in hyphae growth and hyphal branching was measured by quantitative real-time PCR. The transcriptional analysis of these genes demonstrated that a decrease in gene expressions might contribute to the increased hyphal branching seen in DES-15. These results indicated that the highly branching hyphae in DES-15 resulted in increased cellulase production, suggesting that DES-15 may be a good candidate for use in the large-scale production of cellulase

VELDA: Relating an Image Tweet’s Text and Images

Image tweets are becoming a prevalent form of socialmedia, but little is known about their content — textualand visual — and the relationship between the two mediums.Our analysis of image tweets shows that while visualelements certainly play a large role in image-text relationships, other factors such as emotional elements, also factor into the relationship. We develop Visual-Emotional LDA (VELDA), a novel topic model to capturethe image-text correlation from multiple perspectives (namely, visual and emotional). Experiments on real-world image tweets in both Englishand Chinese and other user generated content, show that VELDA significantly outperforms existingmethods on cross-modality image retrieval. Even in other domains where emotion does not factor in imagechoice directly, our VELDA model demonstrates good generalization ability, achieving higher fidelity modeling of such multimedia documents