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The article focuses on a research conducted in order to identify basic helix-loop-helix (bHLH) transcription factor family in the pea aphid, Acyrthosiphon pisum (A. pisum). It discusses the role of bHLH in a wide range of developmental processes in higher organisms including fruit fly, zebrafish, and human. The study revealed the useful information for future studies on structure and function of bHLH proteins in the regulation of A. pisum development.

The material transformation of the Chinese economy is forcing a concomitant process of political adjustment-and not just in China. Other states are being forced to accommodate the 'rise of China'. In this context, this article first presents a comparative analysis of China's impact on two countries, Australia and South Africa, which have little in common other than a wealth of natural resources and a possible status as middle powers; this is a particularly useful exercise because these states are geographically distant and have very different political structures and general developmental histories. Second, the authors consider how China's bilateral ties look from a Chinese perspective in these two very different relationships. Such an analysis serves as a reminder that resource dependency is a two-way street. The article argues that underlying material realities are constraining and to some extent determining the domestic and foreign policies of three very different states that otherwise have little in common. [ABSTRACT FROM AUTHOR]

Cold-induced changes of gene expression and metabolism are critical for plants to survive freezing. Largely by changing gene expression, exposure to a period of non-freezing low temperatures increases plant tolerance to freezing—a phenomenon known as cold acclimation. Cold also induces rapid metabolic changes, which provide instant protection before temperature drops below freezing point. The molecular mechanisms for such rapid metabolic responses to cold remain largely unknown. Here, we use two-dimensional difference gel electrophoresis (2-D DIGE) analysis of sub-cellular fractions of Arabidopsis thaliana proteome coupled with spot identification by tandem mass spectrometry to identify early cold-responsive proteins in Arabidopsis. These proteins include four enzymes involved in starch degradation, three HSP100 proteins, several proteins in the tricarboxylic acid cycle, and sucrose metabolism. Upon cold treatment, the Disproportionating Enzyme 2 (DPE2), a cytosolic transglucosidase metabolizing maltose to glucose, increased rapidly in the centrifugation pellet fraction and decreased in the soluble fraction. Consistent with cold-induced inactivation of DPE2 enzymatic activity, the dpe2 mutant showed increased freezing tolerance without affecting the C-repeat binding transcription factor (CBF) transcriptional pathway. These results support a model that cold-induced inactivation of DPE2 leads to rapid accumulation of maltose, which is a cold-induced compatible solute that protects cells from freezing damage. This study provides evidence for a key role of rapid post-translational regulation of carbohydrate metabolic enzymes in plant protection against sudden temperature drop. [ABSTRACT FROM PUBLISHER]

In 2007, an outbreak of foodborne botulism occurred in Hebei province, China. An epidemiological investigation and laboratory detection studies showed that sausage contaminated by type A Clostridium botulinum caused this outbreak of food poisoning. Its clinical and epidemiological features were different from previous reports of food poisoning. [ABSTRACT FROM AUTHOR]

The article presents a study concerning the purification of a foreign protein. The study shows that the fusion of polyhedrin (Polh)-green fluorescene protein (GFP) will lead to the formation of granular structures. It shows that Polh fusion and enterokinase digestion can be used for easy and fast purification of other proteins.

Motivation: Protein–RNA interactions play a key role in a number of biological processes, such as protein synthesis, mRNA processing, mRNA assembly, ribosome function and eukaryotic spliceosomes. As a result, a reliable identification of RNA binding site of a protein is important for functional annotation and site-directed mutagenesis. Accumulated data of experimental protein–RNA interactions reveal that a RNA binding residue with different neighbor amino acids often exhibits different preferences for its RNA partners, which in turn can be assessed by the interacting interdependence of the amino acid fragment and RNA nucleotide. [ABSTRACT FROM PUBLISHER]

Most methods for studying divergence with gene flow rely upon data from many individuals at few loci. Such data can be useful for inferring recent population history but they are unlikely to contain sufficient information about older events. However, the growing availability of genome sequences suggests a different kind of sampling scheme, one that may be more suited to studying relatively ancient divergence. Data sets extracted from whole-genome alignments may represent very few individuals but contain a very large number of loci. To take advantage of such data we developed a new maximum-likelihood method for genomic data under the isolation-with-migration model. Unlike many coalescent-based likelihood methods, our method does not rely on Monte Carlo sampling of genealogies, but rather provides a precise calculation of the likelihood by numerical integration over all genealogies. We demonstrate that the method works well on simulated data sets. We also consider two models for accommodating mutation rate variation among loci and find that the model that treats mutation rates as random variables leads to better estimates. We applied the method to the divergence of Drosophila melanogaster and D. simulans and detected a low, but statistically significant, signal of gene flow from D. simulans to D. melanogaster. [ABSTRACT FROM AUTHOR]

The shallow seismic velocity structure of the Kunlun fault zone (KLFZ) was jointly deduced from seismic refraction profiling and the records of trapped waves that were excited by five explosions. The data were collected after the 2001 Kunlun Ms8.1 earthquake in the northern Tibetan Plateau. Seismic phases for the in-line record sections (26 records up to a distance of 15 km) along the fault zone were analysed, and 1-D P- and S-wave velocity models of shallow crust within the fault zone were determined by using the seismic refraction method. Sixteen seismic stations were deployed along the off-line profile perpendicular to the fault zone. Fault-zone trapped waves appear clearly on the record sections, which were simulated with a 3-D finite difference algorithm. Quantitative analysis of the correlation coefficients of the synthetic and observed trapped waveforms indicates that the Kunlun fault-zone width is 300 m, and S-wave quality factor Q within the fault zone is 15. Significantly, S-wave velocities within the fault zone are reduced by 30–45 per cent from surrounding rocks to a depth of at least 1–2 km, while P-wave velocities are reduced by 7–20 per cent. A fault-zone with such P- and S-low velocities is an indication of high fluid pressure because Vs is affected more than Vp. The low-velocity and low- Q zone in the KLFZ model is the effect of multiple ruptures along the fault trace of the 2001 Ms8.1 Kunlun earthquake. [ABSTRACT FROM AUTHOR]

Motivation: One goal of metabolomics is to define and monitor the entire metabolite complement of a cell, while it is still far from reach since systematic and rapid approaches for determining the biotransformations of newly discovered metabolites are lacking. For drug development, such metabolic biotransformation of a new chemical entity (NCE) is of more interest because it may profoundly affect its bioavailability, activity and toxicity profile. The use of in silico methods to predict the site of metabolism (SOM) in phase I cytochromes P450-mediated reactions is usually a starting point of metabolic pathway studies, which may also assist in the process of drug/lead optimization. Results: This article reports the Cytochromes P450 (CYP450)-mediated SOM prediction for the six most important metabolic reactions by incorporating the use of machine learning and semi-empirical quantum chemical calculations. Non-local models were developed on the basis of a large dataset comprising 1858 metabolic reactions extracted from 1034 heterogeneous chemicals. For validation, the overall accuracies of all six reaction types are higher than 0.81, four of which exceed 0.90. In further receiver operating characteristic (ROC) analyses, each of the SOM model gave a significant area under curve (AUC) value over 0.86, indicating a good predicting power. An external test was made on a previously published dataset, of which 80% of the experimentally observed SOMs can be correctly identified by applying the full set of our SOM models. Availability: The program package SOME_v1.0 (Site Of Metabolism Estimator) developed based on our models is available at http://www.dddc.ac.cn/adme/myzheng/SOME_1_0.tar.gz. Contact: xmluo@mail.shcnc.ac.cn; hljiang@mail.shcnc.ac.cn [ABSTRACT FROM AUTHOR]

The article reports on the study of nest-dismantling behavior of the hair-crested drongo in China in 2007. According to the study, 12 out of 13 nests that fledged young were dismantled by the adults. It indicates that some individuals started dismantling behavior on the time the young birds left the nest and completed dismantling within how many days, while others waited several days and took longer to finish. The author believes that Hair-crested Drongo's nest-dismantling is an adaptive behavior to increase fitness by reducing risk of future predation and competition for nest sites.

Zhao, X., Wang, Y., and Dai, F. 2008. Depth-dependent target strength of anchovy (Engraulis japonicus) measured in situ. – ICES Journal of Marine Science, 65: 882–888.Three sets of target strength (TS) data were collected in the southern part of the Yellow Sea using a calibrated, 38 kHz, Simrad EK500 split-beam echosounder. Midwater trawl sampling showed that >97% of the catch by number was anchovy (Engraulis japonicus), with total lengths ranging from 6 to 15 cm, and that the arithmetic-mean length and root-mean-square length were 10.6 and 10.8 cm, respectively. The mean TS of anchovy in the 10–45-m layer was estimated to be –50.9 dB, with a 95% confidence interval of (–51.0, –50.8) dB. The TS data showed, however, a clear depth-dependence that was very close to and not significantly different from what might be expected according to Boyle’s law. The TS model was estimated to be TS = 20 log L − 71.6 for the conventional relationship between TS and length, but TS = 20 log L− (20/3) log (1+z/10) − 67.6 when the depth (z, m) effect was included according to Boyle’s law. These results may have a significant influence on abundance estimates of anchovy derived from acoustic surveys, both in the Yellow Sea and in other parts of the world. [ABSTRACT FROM PUBLISHER]

In this study, the full mitochondrial genome of a basidiomycete fungus, Pleurotus ostreatus, was sequenced and analyzed. It is a circular DNA molecule of 73 242 bp and contains 44 known genes encoding 18 proteins and 26 RNA genes. The protein-coding genes include 14 common mitochondrial genes, one ribosomal small subunit protein 3 gene, one RNA polymerase gene and two DNA polymerase genes. In addition, one RNA and one DNA polymerase genes were identified in a mitochondrial plasmid. These two genes show relatively low similarities to their homologs in the mitochondrial genome but they are nearly identical to the known mitochondrial plasmid genes from another Pleurotus ostreatus strain. This suggests that the plasmid may mediate the horizontal gene transfer of the DNA and RNA polymerase genes into mitochondrial genome, and such a transfer may be an ancient event. Phylogenetic analysis based on the cox1 ORFs verified the traditional classification of Pleurotus ostreatus among fungi. However, the discordances were observed in the phylogenetic trees based on the six cox1 intronic ORFs of Pleurotus ostreatus and their homologs in other species, suggesting that these intronic ORFs are foreign DNA sequences obtained through HGT. In summary, this analysis provides valuable information towards the understanding of the evolution of fungal mtDNA. [ABSTRACT FROM AUTHOR]

We undertook a chemical genetics screen to identify chemical inhibitors of brassinosteroid (BR) action. From a chemical library of 10,000 small molecules, one compound was found to inhibit hypocotyl length and activate the expression of a BR-repressed reporter gene (CPD::GUS) in Arabidopsis, and it was named brassinopride (BRP). These effects of BRP could be reversed by co-treatment with brassinolide, suggesting that BRP either directly or indirectly inhibits BR biosynthesis. Interestingly, the compound causes exaggerated apical hooks, similar to that caused by ethylene treatment. The BRP-induced apical hook phenotype can be blocked by a chemical inhibitor of ethylene perception or an ethylene-insensitive mutant, suggesting that, in addition to inhibiting BR, BRP activates ethylene response. Analysis of BRP analogs provided clues about structural features important for its effects on two separate targets in the BR and ethylene pathways. Analyses of the responses of various BR and ethylene mutants to BRP, ethylene, and BR treatments revealed modes of cross-talk between ethylene and BR in dark-grown seedlings. Our results suggest that active downstream BR signaling, but not BR synthesis or a BR gradient, is required for ethylene-induced apical hook formation. The BRP-related compounds can be useful tools for manipulating plant growth and studying hormone interactions. [ABSTRACT FROM PUBLISHER]

PHO1 was previously identified in Arabidopsis (Arabidopsis thaliana) as a protein involved in loading inorganic phosphate (Pi) into the xylem of roots and its expression was associated with the vascular cylinder. Seven genes homologous to AtPHO1 (PpPHO1;1-PpPHO1;7) have been identified in the moss Physcomitrella patens. The corresponding proteins harbor an SPX tripartite domain in the N-terminal hydrophilic portion and an EXS domain in the conserved C-terminal hydrophobic portion, both common features of the plant PHO1 family. Northern-blot analysis showed distinct expression patterns for the PpPHO1 genes, both at the tissue level and in response to phosphate deficiency. Transgenic P. patens expressing the β-glucuronidase reporter gene under three different PpPHO1 promoters revealed distinct expression profiles in various tissues. Expression of PpPHO1;1 and PpPHO1;7 was specifically induced by Pi starvation. P. patens homologs to the Arabidopsis PHT1, DGD2, SQD1, and APSI genes also responded to Pi deficiency by increased mRNA levels. Morphological changes associated with Pi deficiency included elongation of caulonemata with inhibition of the formation of side branches, resulting in colonies with greater diameter, but reduced mass compared to Pi-sufficient plants. Under Pi-deficient conditions, P. patens also increased the synthesis of ribonucleases and of an acid phosphatase, and increased the ratio of sulfolipids over phospholipids. These results indicate that P. pa tens and higher plants share some common strategies to adapt to Pi deficiency, although morphological changes are distinct, and that the PHO1 proteins are well conserved in bryophyte despite the lack of a developed vascular system. [ABSTRACT FROM AUTHOR]

Knowledge of the variation of crustal thickness is essential in many applications, such as forward dynamic modelling, numerical heat flow calculations, seismologic applications and geohistory reconstructions. We present a 3-D model of the Moho undulations over the entire Tibetan plateau derived from gravity inversion. The gravity field has been obtained by using the Gravity Recovery and Climate Experiment (GRACE) potential field development which has been integrated with terrestrial data, and is presently the best available in the studied area. For the effective use of the global geopotential model that has no height information of observation stations, upward continuation is applied. The Moho model is characterized by a sequence of troughs and ridges with a semi-regular pattern, which could reflect the continent–continent collision between the Indian and Eurasian plates. The three deep Moho belts (troughs) and shallow Moho belts (ridges) between them are clearly found to have an E–W directional trend parallel to the border of the plateau and tectonic lines, while variation of the directionality is observed in central to southeast Tibet. To describe the distinctive shape of the Moho troughs beneath Tibet, we introduce the term, ‘Moho ranges’. The most interesting aspects of the Moho ranges are (1) that they run in parallel with the border and tectonic sutures of the plateau, (2) that the distances between ranges are found at regular distances of about 330 km except in northeast Tibet and (3) that the splitting of the ranges into two branches is found as the distance between them is increasing. From our study, we conclude that the distinctive undulations of the Tibetan Moho have been formed by buckling in a compressional environment, superimposed on the regional increase in crustal thickness. According to our analysis, the GRACE satellite-only data turns out to have good enough resolution for being used to determine the very deep Moho beneath Tibet. Our Moho model is the first one that covers the entire plateau. [ABSTRACT FROM AUTHOR]

A fast algorithm for computing the non-parametric maximum likelihood estimate of a mixing distribution is presented. At each iteration, the algorithm adds new important points to the support set as guided by the gradient function, updates all mixing proportions via a quadratically convergent method and discards redundant support points straightaway. With its convergence being theoretically established, numerical studies show that it is very fast and stable, compared with several other algorithms that are available in the literature. [ABSTRACT FROM AUTHOR]

Upland cotton (Gossypium hirsutum) produces the most widely used natural fibers, yet the regulatory mechanisms governing fiber cell elongation are not well understood. Through sequencing of a cotton fiber cDNA library and subsequent microarray analysis, we found that ethylene biosynthesis is one of the most significantly upregulated biochemical pathways during fiber elongation. The 1-Aminocyclopropane-1-Carboxylic Acid Oxidase1-3 (ACO1-3) genes responsible for ethylene production were expressed at significantly higher levels during this growth stage. The amount of ethylene released from cultured ovules correlated with ACO expression and the rate of fiber growth. Exogenously applied ethylene promoted robust fiber cell expansion, whereas its biosynthetic inhibitor L-(2-aminoethoxyvinyl)-glycine (AVG) specifically suppressed fiber growth. The brassinosteroid (BR) biosynthetic pathway was modestly upregulated during this growth stage, and treatment with BR or its biosynthetic inhibitor brassinazole (BRZ) also promoted or inhibited, respectively, fiber growth. However, the effect of ethylene treatment was much stronger than that of BR, and the inhibitory effect of BRZ on fiber cells could be overcome by ethylene, but the AVG effect was much less reversed by BR. These results indicate that ethylene plays a major role in promoting cotton fiber elongation. Furthermore, ethylene may promote cell elongation by increasing the expression of sucrose synthase, tubulin, and expansin genes. [ABSTRACT FROM AUTHOR]

Hydrogen peroxide (H2O2) as a widespread molecule plays an important role in plant stress responses. Here, we showed that an Arabidopsis line overexpressing hemoglobin 1 (AtGLB1) can enhance its tolerance to severe hypoxic stress. In our research, Arabidopsis lines with different hemoglobin levels were employed to study the relationship between H2O2 level and the tolerance to hypoxic stress. The relatively low endogenous H2O2 level of AtGLB1-overexpressing plants could be one of the main factors for the increased tolerance of plants to hypoxic stress. Further investigation indicated that the activity of the antioxidant system involved in scavenging H2O2 increased in all three lines examined during hypoxic treatment, while only the line overexpressing AtGLB1 could retain these relatively high levels up to 48 h of the treatment, suggesting that the antioxidant system might play a role in the low H2O2 level of Arabidopsis overexpressing AtGLB1. [ABSTRACT FROM AUTHOR]

Ethylene controls multiple physiological processes in plants, including cell elongation. Consequently, ethylene synthesis is regulated by internal and external signals. We show that a light-entrained circadian clock regulates ethylene release from unstressed, wild-type Arabidopsis (Arabidopsis thaliana) seedlings, with a peak in the mid-subjective day. The circadian clock drives the expression of multiple ACC SYNTHASE genes, resulting in peak RNA levels at the phase of maximal ethylene synthesis. Ethylene production levels are tightly correlated with ACC SYNTHASE 8 steady-state transcript levels. The expression of this gene is controlled by light, by the circadian clock, and by negative feedback regulation through ethylene signaling. In addition, ethylene production is controlled by the TIMING OF CAB EXPRESSION 1 and CIRCADIAN CLOCK ASSOCIATED 1 genes, which are critical for all circadian rhythms yet tested in Arabidopsis. Mutation of ethylene signaling pathways did not alter the phase or period of circadian rhythms. Mutants with altered ethylene production or signaling also retained normal rhythmicity of leaf movement. We conclude that circadian rhythms of ethylene production are not critical for rhythmic growth. [ABSTRACT FROM AUTHOR]

PHO1 has been recently identified as a protein involved in the loading of inorganic phosphate into the xylem of roots in Arabidopsis. The genome of Arabidopsis contains 11 members of the PHO1 gene family. The cDNAs of all PHO1 homologs have been cloned and sequenced. All proteins have the same topology and harbor a SPX tripartite domain in the N-terminal hydrophilic portion and an EXS domain in the C-terminal hydrophobic portion. The SPX and EXS domains have been identified in yeast (Saccharomyces cerevisiae) proteins involved in either phosphate transport or sensing or in sorting proteins to endomembranes. The Arabidopsis genome contains additional proteins of unknown function containing either a SPX or an EXS domain. Phylogenetic analysis indicated that the PHO1 family is subdivided into at least three clusters. Reverse transcription-PCR revealed a broad pattern of expression in leaves, roots, stems, and flowers for most genes, although two genes are expressed exclusively in flowers. Analysis of the activity of the promoter of all PHO1 homologs using promoter-βglucuronidase fusions revealed a predominant expression in the vascular tissues of roots, leaves, stems, or flowers. β-Glucuronidase expression is also detected for several promoters in nonvascular tissue, including hydathodes, trichomes, root tip, root cortical/epidermal cells, and pollen grains. The expression pattern of PHO1 homologs indicates a likely role of the PHO1 proteins not only in the transfer of phosphate to the vascular cylinder of various tissues but also in the acquisition of phosphate into cells, such as pollen or root epidermal/cortical cells. [ABSTRACT FROM AUTHOR]

Background: Dendritic cells (DCs) play a central role in immune responses and may be useful adjuvants for tumor vaccine therapy. We previously reported that F4/80[sup -]B220[sup -] CD11c[sup +] DC precursors expressing the CC chemokine receptors CCR1 and CCR5 are mobilized rapidly into the circulation in mice injected with Propionibacterium acnes and are recruited into inflammatory tissue by macrophage inflammatory protein 1α (MIP-1α), which binds to CCR1 and CCR5. Here we investigate the mechanisms of DC precursor mobilization and the antitumor effect of these cells in mice. Methods: Numbers of DC precursors in peripheral blood were determined in P. acnes-treated mice (groups of 10 C57BL/B6 [B6] wild-type mice, CCR1[sup -/-] mice, CCR5[sup -/-] mice, and B6 mice treated with antibody to MIP-1α or control antibody) and in B6 mice injected with recombinant MIP-1α. MIP-1α-mobilized DC precursors matured by treatment with granulocyte-macrophage colony-stimulating factor, interleukin 4, and tumor necrosis factor-α and pulsed with B16 melanoma lysates were assayed for their ability to confer protective immunity against tumor challenge in vivo and to induce cytotoxic T lymphocytes against B16 tumor cells in vitro. Results: The recruitment of DC precursors into the circulation by P. aches administration was higher in B6 mice (12.6%, 95% confidence interval [CI] = 9.1% to 16.1%) than in CCR1[sup -/-] (9.0%, 95% CI = 7.5% to 10.5%), CCR5[sup -/-] (6.3%, 95% CI = 5.2% to 7.3%), or anti-MIP-1α antibody-treated (6.6%, 95% CI = 5.7% to 7.5%) mice. Injection of MIP-1α also mobilized DC precursors into the circulation (13.1%, 95% CI = 10.8% to 15.6%). Matured MIP-α-mobilized-DC precursors pulsed with B16 tumor lysates elicited B16-specific antitumor immunity in vitro and in vivo. Conclusions: MIP-1α and its receptors are important in recruiting DC precursors into the circulation. DC precursors mobilized rapidly by MIP-1α may provide sufficient useful DC precursors for DC-based vaccination in cancer treatment. [ABSTRACT FROM AUTHOR]

Presents a study that compared consistency of species richness and relative abundance data collected concurrently using mist netting and point counts during landbird migration in riparian habitats along the middle Rio Grande of central New Mexico. Methodology; Point counts; Mist netting.

This article investigates the effects of a type of sub-optimal behavior on financial markets. Considerable evidence suggests that the notion of market efficiency fails to predict some strong empirical regularities on financial markets. The reconciliation of those empirical findings has led many economists to reconsider the assumption of unbounded rationality behind the efficient market hypothesis. The model demonstrates that near-rational agents gradually modify their decisions, and their behavior approaches the rational behavior asymptotically. The introduction of near-rational agents sheds some light on a variety of anomalous phenomena on financial markets, including excess price volatility, persistent price deviations from fundamental values, and mean-reverting behavior of asset prices.

The article discusses a study which examines the effective methods of measuring humic acids in nucleic acid samples for molecular biological analysis. It explores the sensitivity of each approach and the effects of DNA/RNA and proteins on the evaluation. Findings of the study reveal that real-time polymerase chain reaction (RT-PCR) is more sensitive to humic acids than the PCR method.

Examines the generation of reactive oxygen species (ROS) from hinokitiol, 4-isopropyltropolone from Japanese cypress and western red cedar, under near-ultraviolet irradiation. Distinct electron spin resonance signal characteristic of the adduct of 5,5-dimethyl-1-pyrroline-N-oxide; Generation of ROS during photochemical reaction of hinokitiol.

A letter to the editor is presented in response to the article about the fear of the threat posed by resistant microbial strains and by the use of antibiotics worldwide as the New Delhi metallo-beta-lactamase-1 emerges in India, Pakistan and Great Britain.

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010. [ABSTRACT FROM PUBLISHER]

Motivation: Inferring the relationships between transcription factors (TFs) and their targets has utmost importance for understanding the complex regulatory mechanisms in cellular systems. However, the transcription factor activities (TFAs) cannot be measured directly by standard microarray experiment owing to various post-translational modifications. In particular, cooperative mechanism and combinatorial control are common in gene regulation, e.g. TFs usually recruit other proteins cooperatively to facilitate transcriptional reaction processes. Results: In this article, we propose a novel method for inferring transcriptional regulatory networks (TRN) from gene expression data based on protein transcription complexes and mass action law. With gene expression data and TFAs estimated from transcription complex information, the inference of TRN is formulated as a linear programming (LP) problem which has a globally optimal solution in terms of L1 norm error. The proposed method not only can easily incorporate ChIP-Chip data as prior knowledge, but also can integrate multiple gene expression datasets from different experiments simultaneously. A unique feature of our method is to take into account protein cooperation in transcription process. We tested our method by using both synthetic data and several experimental datasets in yeast. The extensive results illustrate the effectiveness of the proposed method for predicting transcription regulatory relationships between TFs with co-regulators and target genes. Availability: The software TRNinfer is available from http://intelligent.eic.osaka-sandai.ac.jp/chenen/TRNinfer.htm Contact: chen@eic.osaka-sandai.ac.jp and zxs@amt.ac.cn Supplementry information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Motivation: With more and more data on molecular networks (e.g. protein interaction networks, gene regulatory networks and metabolic networks) available, the discovery of conserved patterns or signaling pathways by comparing various kinds of networks among different species or within a species becomes an increasingly important problem. However, most of the conventional approaches either restrict comparative analysis to special structures, such as pathways, or adopt heuristic algorithms due to computational burden. Results: In this article, to find the conserved substructures, we develop an efficient algorithm for aligning molecular networks based on both molecule similarity and architecture similarity, by using integer quadratic programming (IQP). Such an IQP can be relaxed into the corresponding quadratic programming (QP) which almost always ensures an integer solution, thereby making molecular network alignment tractable without any approximation. The proposed framework is very flexible and can be applied to many kinds of molecular networks including weighted and unweighted, directed and undirected networks with or without loops. Availability: Matlab code and data are available from http://zhangroup.aporc.org/bioinfo/MNAligner or http://intelligent.eic.osaka-sandai.ac.jp/chenen/software/MNAligner, or upon request from authors. Contact: zxs@amt.ac.cn, chen@eic.osaka-sandai.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Ethylene controls multiple physiological processes in plants, including cell elongation. Consequently, ethylene synthesis is regulated by internal and external signals. We show that a light-entrained circadian clock regulates ethylene release from unstressed, wild-type Arabidopsis (Arabidopsis thaliana) seedlings, with a peak in the mid-subjective day. The circadian clock drives the expression of multiple ACC SYNTHASE genes, resulting in peak RNA levels at the phase of maximal ethylene synthesis. Ethylene production levels are tightly correlated with ACC SYNTHASE 8 steady-state transcript levels. The expression of this gene is controlled by light, by the circadian clock, and by negative feedback regulation through ethylene signaling. In addition, ethylene production is controlled by the TIMING OF CAB EXPRESSION 1 and CIRCADIAN CLOCK ASSOCIATED 1 genes, which are critical for all circadian rhythms yet tested in Arabidopsis. Mutation of ethylene signaling pathways did not alter the phase or period of circadian rhythms. Mutants with altered ethylene production or signaling also retained normal rhythmicity of leaf movement. We conclude that circadian rhythms of ethylene production are not critical for rhythmic growth. [ABSTRACT FROM AUTHOR]