Expanded flux variability analysis on metabolic network of Escherichia coli

Flux balance analysis, based on the mass conservation law in a cellular organism, has been extensively employed to study the interplay between structures and functions of cellular metabolic networks. Consequently, the phenotypes of the metabolism can be well elucidated. In this paper, we introduce the Expanded Flux Variability Analysis （EFVA） to characterize the intrinsic nature of metabolic reactions, such as flexibility, modularity and essentiality, by exploring the trend of the range, the maximum and the minimum flux of reactions. We took the metabolic network of Escherichia coli as an example and analyzed the variability of reaction fluxes under different growth rate constraints. The average variability of all reactions decreases dramatically when the growth rate increases. Consider the noise effect on the metabolic system, we thus argue that the microorganism may practically grow under a suboptimal state. Besides, under the EFVA framework, the reactions are easily to be grouped into catabolic and anabolic groups. And the anabolic groups can be further assigned to specific biomass constitute. We also discovered the growth rate dependent essentiality of reactions.     

Inductive transfer learning for unlabeled target-domain via hybrid regularization

Recent years have witnessed an increasing interest in transfer learning. This paper deals with the classification problem that the target-domain with a different distribution from the source-domain is totally unlabeled, and aims to build an inductive model for unseen data. Firstly, we analyze the problem of class ratio drift in the previous work of transductive transfer learning, and propose to use a normalization method to move towards the desired class ratio. Furthermore, we develop a hybrid regularization framework for inductive transfer learning. It considers three factors, including the distribution geometry of the target-domain by manifold regularization, the entropy value of prediction probability by entropy regularization, and the class prior by expectation regularization. This framework is used to adapt the inductive model learnt from the source-domain to the target-domain. Finally, the experiments on the real-world text data show the effectiveness of our inductive method of transfer learning. Meanwhile, it can handle unseen test points.     

Phylogenetic relationships and divergence times of the family Araucariaceae based on the DNA sequences of eight genes

Araucariaceae is one of the most primitive families of the living conifers, and its phylogenetic relationships and divergence times are critically important issues. The DNA sequences of 8 genes, i.e., nuclear ribosomal 18S and 26S rRNA, chloroplast 16S rRNA, rbcL, matK and rps4, and mitochondrial coxl and atpl, obtained from this study and GenBank were used for constructing the molecular phylogenetic trees of Araucariaceae, indicating that the phyiogenetic relationships among the three genera of this family should be （（Wollemia, Agathis）, Araucaria）. On the basis of the fossil calibrations of Wollemia and the two tribes Araucaria and Eutacta of the genus Araucaria, the divergence time of Araucariaceae was estimated to be （308± 53） million years ago, that is, the origin of the family was in the Late Carboniferous rather than Triassic as a traditional view. With the same gene combination, the diver- gence times of the genera Araucaria and Agathis were （246 ± 47） and （61 ±15） Ma, respectively. Statis- tical analyses on the phylogenetic trees generated by using different genes and comparisons of the divergence times estimated by using those genes suggested that the chloroplast matK and rps4 genes are most suitable for investigating the phylogenetic relationships and divergence times of the family Araucariaceae.     

Evolution of the serum resistance-associated SRA gene in African trypanosomes

Serum resistance-associated (SRA) protein, a protein unique for Trypanosoma brucei rhodesiense, is responsible for resistance of this parasite to the lysis by normal human serum (NHS) and is a vital molecular marker to distinguish this species from other African trypanosomes. We cloned and sequenced the SRA basic copy (SRAbc) gene from T. b. rhodesiense and related species and found that this gene is confined to the subgenus Trypanozoon. The average 82% identity among the sequenced SRAbc genes indicates that they may have a common origin and are highly conserved. Since SRAbc coexists in the T. b. rhodesiense genome with SRA, we propose that SRAbc might be the ‘donor VSG’, which after duplication became inserted into the expression site by recombination. Under natural selection, SRAbc could reform into SRA following mosaic formation. Supported by National Natural Science Foundation of China (Grant Nos. 30570245, 30670275), Changjiang Scholars and Innovative Research Team in University (Grant No. DPCKSCU/IRT0447), International Foundation for Science of Sweden (Grant No. B/4318-1), Grant Agency of the Czech Republic (Grant No. Z60220518) and Education Foundation of the Czech Republic (Grant No. 2B06129)     

Functional characterization and mapping of two MADS box genes from peach （Prunus persica）

Previously an AGAMOUS gene homologue PpMADS4 and a FRUITFULL gene homologue PpMADS6 were isolated from peach （Prunus persica）, and both genes were shown to express in the developing floral and fruits. To gain insight into their function, the two genes were constitutively expressed in Arabidopsis thaliana and their effects on plant growth and floral organ development were studied in this work. The transgenic plants all displayed early flowering and conversion of inflorescence to floral meristem. However, the two genes had different effects on the floral organ structures in A. thaliana. The transgenic plants overexpressing PpMADS4 displayed homeotic conversion of floral organs, and particularly the perianth abscission was inhibited. The plants overexpressing PpMADS6 showed early flowering, produced higher number of carpels, petals, and stamens than nontransgenic plants, and pod shatter was prevented; significantly, the transgenic plants yielded more than one siliques from a single flower. A SSR molecular marker was developed for PpMADS4, and it was then assigned into the G5 linkage group of Prunus sp. Both PpMADS4 and PpMADS6 genes were located at the same region in the G5 linkage group. Our results showed the potential application of these two MADS box genes for crop and fruit tree improvement.     

Two-port network model and startup criteria for thermoacoustic oscillators

The startup process of a thermoacoustic engine is a self-excited oscillation process generated in inhomogeneous acoustic media. To reveal these coupling relations between various influential factors is an important task of basic research on thermoacoustics. In this paper thermoacoustic engines are regarded as thermoacoustic oscillators consisting of the active network and the passive network. Accordingly, the two-port Y-parameter for relevant component is derived, and standing wave and traveling wave thermoacoustic engine are described by the negative-resistance and feedback model, respectively. The relevant two-port network topology is given as well. The startup criteria for thermoacoustic oscillators are obtained by using Nyquist instability criterion. The model prediction of startup parameters, particularly, startup frequency and mode characteristic are in agreement with that of experimental results reported in the literature. Moreover, with topological graphs it is verified that standing wave engines would start up in a negative-resistance state and there would exist high frequency modes in thermoacoustic-Stirling engines. By investigating into the frequency response of thermoacoustic system, this method proposed can achieve such an objective that these effects of operating and structural parameters of engine on startup modes and startup temperature can be revealed in an analytical way. Thus this approach to test and check thermal stability can be provided in a design phase, instead of using empirical frequency to design thermoacoustic systems. Electronic Supplementary Material  Supplementary material is available for this article at and is accessible for authorized users. Supported by National Natural Science Foundation of China (Grant Nos. 50576024 and 51076013)     

System reliability analysis for kinematic performance of planar mechanisms

Based on the reliability and mechanism kinematic accuracy theories, we propose a general methodology for system reliability analysis of kinematic performance of planar mechanisms. The loop closure equations are used to estimate the kinematic performance errors of planar mechanisms. Reliability and system reliability theories are introduced to develop the limit state functions （LSF） for failure of kinematic performance qualities. The statistical fourth moment method and the Edgeworth series technique are used on system reliability analysis for kinematic performance of planar mechanisms, which relax the restrictions of probability distribution of design variables. Finally, the practicality, efficiency and accuracy of the proposed method are demonstrated by numerical examples.     

Evidence and modeling study of droughts in China during 4―2 ka BP

Four periods with predominated droughts are identified in 4-2 ka BP according to documentary data, namely 3.6-3.5, 3.1-3.0, 2.8-2.7, and 2.45-2.35 ka BP. Palaeo-environmental data indicated that droughts were predominated in 4-2 ka BP in the south of Northeast China, Inner-Mongolia, east of Qinghai-Tibetan Plateau, and South China. Modeling study shows that precession may be responsible for the occurrence of droughts in 4-2 ka BP, integrating the GCM with forcing of insolation.     

Estimating divergence times among subfamilies in Nymphalidae

The mitochondrial cytochrome oxidase subunit Ⅰ （COⅠ） gene and the nuclear elongation factor 1α （EF-1α） gene were sequenced from 13 species of Nymphalidae. Phylogenetic trees of Nymphalidae, which is the largest family in butterflies, were constructed based on the sequences determined from 13 species sequenced in our laboratory and an additional 43 species obtained from GenBank using the maximum likelihood （ML） and Bayesian methods. Relative-rate tests between lineages in these phylogenetic trees were performed. On the basis of the results of the relative-rate tests and fossil information of Satyrinae, Nymphalinae and Biblidinae, the average divergence times among the subfamilies are estimated as 44.2-87.1 million years ago （Ma）. These results will be helpful for better understanding of the origin and evolution of this family, as well as the divergence time of butterflies and other complex taxa.     

SCFP,a novel fiber-specific promoter in cotton

To investigate the expression pattern of GhSCFP which was isolated from cotton fiber cDNA library, a 1006 bp upstream fragment of the gene was cloned by chromosome walking and fused to GUSand GFP respectively. Histochemical GUS and GFP fluorescence analysis revealed that the expression of the report genes driven by the promoter sequence was detectable only in outer layer cells during the seed development in the transgentic tobaccos. In transgenic cotton, strong GUS activity was observed in spherical protrusions on 0 dpa （days post anthesis） ovule surface, and in the 2-36 dpa fiber cells, while no GUS signals were detected in the root, leaves, stem, corolla, anther and stigma. Our data demonstrated that GhSCFP upstream sequence is a cotton fiber-specific promoter and this promoter will be useful in the molecular research on fiber cell development and in cotton fiber improvements by genetic modification.     

Transfer of a eubacteria-type cell division site-determining factor CrldfnD 8ene to the nucleus from the chloroplast genome in Chlamydomonas reinhardtii

MinD is a ubiquitous ATPase that plays a crucial role in selection of the division site in eubacteria, chloroplasts, and probably Archaea. In four green algae, MesosUgma viride, Nephroselmis olivacea, Chlorella vulgaris and Prototheca wickerhamii, MinD homologues are encoded in the plastid genome. However, in Arabidopsis, MinD is a nucleus-encoded, chloroplast-targeted protein involved in chloroplast division, which suggests that MinD has been transferred to the nucleus in higher land plants. Yet the lateral gene transfer （LGT） of MinD from plastid to nucleus during plastid evolution remains poorly understood. Here, we identified a nucleus-encoded MinD homologue from unicellular green alga Chlamydomonas reinhardtii, a basal species in the green plant lineage. Overexpression of CrMinD in wild type E. coil inhibited cell division and resulted in the filamentous cell formation, clearly demonstrated the conservation of the MinD protein during the evolution of photosynthetic eukaryotes. The transient expression of CrMinD-egfp confirmed the role of CrMinD protein in the regulation of plastid division. Searching all the published plastid genomic sequences of land plants, no MinD homologues were found, which suggests that the transfer of MinD from plastid to nucleus might have occurred before the evolution of land plants.     

Proteomic analysis of long-term salinity stress-responsive proteins in <Emphasis Type="Italic">Thellungiella halophila</Emphasis> leaves

Salinity is one of the most severe environmental factors that may impair crop productivity. A proteomic study based on two-dimensional gel electrophoresis is performed in order to analyze the long-term salinity stress response of Thellungiella halophila, an Arabidopsis-related halophyte. Four-week-old seedlings are exposed to long-term salinity treatment. The total crude proteins are extracted from leaf blades, separated by 2-DE, stained with Coomassie Brilliant Blue, and differentially displayed spots are identified by MALDI-TOF MS or QTOF MS/MS. Among 900 protein spots reproducibly detected on each gel, 30 spots exhibit significant change and some of them are identified. The identified proteins include not only some previously characterized stress-responsive proteins such as TIR-NBS-LRR class disease resistance protein, ferritin-1, and pathogenesis-related protein 5, but also some proteins related to energy pathway, metabolism, RNA processing and protein degradation, as well as proteins with unknown functions. The possible functions of these proteins in salinity tolerance of T. halophila are discussed and it is suggested that the long-term salinity tolerance of T. halophila is achieved, at least partly, by enhancing defense system, adjusting energy and metabolic pathway and maintaining RNA structure.     

Stamen specification and anther development in rice

Male reproductive development is a complex biological process which includes the formation of the stamen with differentiated anther tissues, in which microspores/pollens are generated, then anther dehiscence and subsequently pollination. Stamen specification and anther development involve a number of extraordinary events such as meristem transition, cell division and differentiation, cell to cell communication, etc., which need the cooperative interaction of sporophytic and gametophytic genes. The advent of various tools for rice functional gene identification, such as complete genome sequence, genome-wide microarrays, collections of mutants, has greatly facilitated our understanding of mechanisms of rice stamen specification and anther development. Male sterile lines are critical for hybrid rice breeding, therefore understanding these processes will not only contribute greatly to the basic knowledge of crop developmental biology, but also to the development of new varieties for hybrid rice breeding in the future.     

The Escherichia coli O157:H7 DNA detection on a gold nanoparticle-enhanced piezoelectric biosensor

This paper presents development of a quartz crystal microbalance （QCM） biosensor for real-time detection of E. coil O157：H7 DNA based on nanogold particles amplification. Many inner Au nanoparticles were immobilized onto the thioled surface of the Au electrode, then more specific thiolated sin- gle-stranded DNA （ssDNA） probes could be fixed through Au-SH bonding. The hybridization was induced by exposing the ssDNA probe to the complementary target DNA of E. coli O157：H7 gene eaeA, then resulted in a mass change and corresponding frequency shifts （ △f ） of the QCM. The outer avidin-coated Au nanoparticles could combine with the target DNA to increase the mass. The electrochemical techniques, cyclic voltammetry （CV） and electrochemical impedance spectroscopy （EIS） were adopted to manifest and character each step. The target DNA corresponding to 2.0×10^3 colony forming unit （CFU）/mL E. coil O157：H7 cells can be detected by this biosensor, so it is practical to develop a sensitive and effective QCM biosensor for pathogenic bacteria detection based on specific DNA analysis. The piezoelectric biosensing system has potential for further applications, such as food safety and environment monitoring, and this approach lays the groundwork for incorporating the method into an integrated system for in-field bacteria detection.     

Identification of a novel tillering dwarf mutant and fine mapping of the TDDL（T） gene in rice （Oryza sativa L.）

Rice plant architecture is an important agronomic trait that affects the grain yield. To understand the molecular mechanism that controls plant architecture, a tillering dwarf mutant with darker-green leaves derived from an indica cultivar IR64 treated with EMS is characterized. The mutant, designated as tddl（t）, is nonallelic to the known tiilering dwarf mutants. It is controlled by one recessive nuclear gene, TDDL（T）, and grouped into the dn-type dwarfism according to Takeda＇s definition. The dwarfism of the mutant is independent of gibberellic acid based on the analyses of two GA-mediated processes. The independence of brassinosteroid （BR） and naphthal-3-acetic acid （NAA） of the tddl（t） mutant, together with the decreased size of parenchyma cells in the vascular bundle, indicates that the TDDL（7） gene might participate in another hormone pathway. TDDL（T） is fine mapped within an 85.51 kb region on the long arm of rice chromosome 4, where 20 ORFs are predicted by RiceGAAS （http：//ricegaas.dna.affrc. go.jp/rgadb/）. Further cloning of TDDL（T） will benefit both marker assisted selection （MAS） of plant architecture and dissection of the molecular mechanism underlying tillering dwarf in rice.     

Divisional and hierarchical innervations of G. gecko’s toes to motion and reception

As a member of robot families, climbing robots have become one of the research hot-spots in the robotic field recently and Gekko gecko （G. gecko） has been broadly seen as an ideal model for climbing robot development. But for gecko-mimic robots, one of the key problems is how to design the robot＇s foot. In this paper, （1） high-speed camera recording and electrophysiological method are used to observe motion patterns of G. gecko＇s foot when it climbs on different oriented surfaces; （2） nerve innervations of gecko＇s toes to motion and reception are studied. It is found that the five toes of the G. gecko can be divided into two motion and reception divisions, and also its motion and reception are modulated and controlled hierarchically. The results provide important information and exclusive ideas for the foot design and control algorithm of gecko-mimic robots.     

Investisations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 （Tetraodontiformes,Tetraodontidae）

The phylogenetic relationships within the genus Takifugu Abe, 1949 （Tetraodontiformes, Tetraodontidae） remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsi- mony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that （1） the genus Takifugu is a monophyletic assemblage; （2） the genus is divided into 6 subgroups based on the moecular data; and （3） there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.