Excellent capacitive performance of a three-dimensional hierarchical porous graphene/carbon composite with a superhigh surface area.

Three-dimensional hierarchical porous graphene/carbon composite was successfully synthesized from a solution of graphene oxide and a phenolic resin by using a facile and efficient method. The morphology, structure, and surface property of the composite were investigated intensively by a variety of means such as scanning electron microscopy (SEM), transmission electron microscopy (TEM), N2 adsorption, Raman spectroscopy, and Fourier transform infrared spectroscopy (FTIR). It is found that graphene serves as a scaffold to form a hierarchical pore texture in the composite, resulting in its superhigh surface area of 2034 m(2) g(-1), thin macropore wall, and high conductivity (152 S m(-1)). As evidenced by electrochemical measurements in both EMImBF4 ionic liquid and KOH electrolyte, the composite exhibits ideal capacitive behavior, high capacitance, and excellent rate performance due to its unique structure. In EMImBF4 , the composite has a high energy density of up to 50.1 Wh kg(-1) and also possesses quite stable cycling stability at 100 °C, suggesting its promising application in high-temperature supercapacitors. In KOH electrolyte, the specific capacitance of this composite can reach up to an unprecedented value of 186.5 F g(-1), even at a very high current density of 50 A g(-1), suggesting its prosperous application in high-power applications.

[Genome-scale sequence data processing and epigenetic analysis of DNA methylation].

A new approach recently developed for detecting cytosine DNA methylation (mC) and analyzing the genome-scale DNA methylation profiling, is called BS-Seq which is based on bisulfite conversion of genomic DNA combined with next-generation sequencing. The method can not only provide an insight into the difference of genome-scale DNA methylation among different organisms, but also reveal the conservation of DNA methylation in all contexts and nucleotide preference for different genomic regions, including genes, exons, and repetitive DNA sequences. It will be helpful to under-stand the epigenetic impacts of cytosine DNA methylation on the regulation of gene expression and maintaining silence of repetitive sequences, such as transposable elements. In this paper, we introduce the preprocessing steps of DNA methylation data, by which cytosine (C) and guanine (G) in the reference sequence are transferred to thymine (T) and adenine (A), and cytosine in reads is transferred to thymine, respectively. We also comprehensively review the main content of the DNA methylation analysis on the genomic scale: (1) the cytosine methylation under the context of different sequences; (2) the distribution of genomic methylcytosine; (3) DNA methylation context and the preference for the nucleotides; (4) DNA- protein interaction sites of DNA methylation; (5) degree of methylation of cytosine in the different structural elements of genes. DNA methylation analysis technique provides a powerful tool for the epigenome study in human and other species, and genes and environment interaction, and founds the theoretical basis for further development of disease diagnostics and therapeutics in human.

Genome sequencing and identification of gene function in rice.

Rice is known to be one of the most important crops for human consumption. As the model cereal crop, large-scale sequencing of rice genome must play quite important roles both in theoretical research and practical application in rice breeding, which announces the opening of another new way to resolve the world food crisis. At present, the emphasis of rice genome research has been transferred from structure genomics to functional analysis. The discovery of new genes and annotation of gene function was believed to be an important issue in functional genomics research. In this article, the sequencing and functional research of the rice genome were reviewed. These results may provide some useful clues for rice genetic engineering and breeding practices.

[Genomic analysis of serine carboxypeptidase-like protein family of Arabidopsis thaliana].

Based on hidden Markov models (HMM), the paper utilized reported SCP (Serine Carboxypeptidases) protein sequences as datasets to build HMM profile. To search Arabidopsis thaliana whole proteome,and identified 54 SCPL (Serine Carboxypeptidase-Like) proteins coding genes. The intron-exon structure, the chromosome mapping and the characteristic of coded protein sequences of those 54 putative genes were analyzed in details, revealing seven gene clusters probably resulted from recent gene duplication. This implied that a remarkable number of Arabidopsis thaliana SCPL genes are harboring alternative splice sites. Phylogenetics evolution analysis suggested 88.9% proteins encoded by Arabidopsis genes belong to two string subfamily of carboxypeptidase, I or II, while only 11.1% proteins fall into single string carboxypeptidase III subfamily. Our results indicated besides the facts that all enzymes of this family contained a central catalytic domain of unique topology and three dimensional structure designated as "alpha/beta hydrolase fold", the DNA and their encoded protein sequences also gave clues to phylogentics studies.

[Gene cloning and structure characterization of CMS/Rf system in plants].

It has achieved great success in plant heterosis by using cytoplasmic male sterility and fertility restorer (CMS/Rf) system. In order to elucidate the action mechanism of Rf gene in this system, many researchers have been contributing themselves to map and clone fertility restorer genes in recent years. Four Rf genes were recently cloned successfully. Here we presented the overview of plant CMS fertility restorer gene mapping, cloning and its molecular mechanism. It was also discussed on utilization of fertility restorer genes in the molecular breeding in plants.

[Comparison study on the methods for finding borders between coding and non-coding DNA regions in rice].

Entropy-based divergence measures have provided an impelling tool in evaluating sequence complexity, predicting CpG island, and detecting borders between coding and non-coding DNA regions etc. In this paper, two new divergence measures: the alpha-KL divergence and the alpha-Jensen-Shannon divergence were defined and a coarse-graining vector of amino acids- corresponding codons was proposed according to codons GC-content, in order to improve the computational approach to finding borders between coding and non-coding in rice. A comparison of the accuracies gained by different vectors (the Jensen-Shannon divergence, the Jensen-Renyi divergence, the alpha-KL divergence and the alpha-Jensen -Shannon divergence) showed that recognition efficiency based on the new information measures with the vector coarse-graining increase by 4-5 times than that of Bernaola's method in the 'stop codon' of coding regions in rice.

Cloning and Sequencing of the Genome Segment S9 of Rice Black-streaked Dwarf Virus.

Genome segment S9's of rice black-streaked dwarf virus (RBSDV) of three Chinese isolates were amplified by RT-PCR and sequenced, and were found to be consisted of 1 900 nt (RBSDV-Zj S9 EMBL accession number AJ297430),1 898 nt (RBSDV-Heb S9 EMBL accession number AJ297429) and 1 900 nt (RBSDV-Hub S9 EMBL accession number AJ291706), respectively. Genome segment S9's of three Chinese Isolates shared 98.5%--98.8% sequence homology and all contained two open reading frames (ORF), which encoded two polypeptides with moleclular weights of 40 kD and 24 kD, respectively. Amino acid sequence comparison of the polypeptides encoded by the second ORF of the corresponding genomic segment of five isolates, including three Chinese isolates, Japanese isolate, and Italian MRDV (maize rough dwarf virus), were highly conserved.

[The structure and regulation of plant proteinase inhibitor genes and their strategy in pest control].

The diverse plant proteinase inhibitors (PIs) genes from different plant species have been isolated and their products with one or more genes are targeted at different biochemical and physiological process with the insect, and well played a potent defensive role against insects and pathogens. The use of recombinant PIs and synergistic activation to protect plants has been incorporated in integrated pest management program. Though they may not replace the use of chemical pesticides in the near future, but effectively complement it. Currently, the role and mechanism of action for most of these inhibitors are being studied in detail. This article describes the structure of PIs genes, their regulation and expression, and discusses the strategy to develop transgenic plants against phytophagous insects.

[Comparative phylogenetic analysis of the rice and Arabidopsis PHD-finger proteins].

PHD-finger (plant homeodomain finger), a unique Cys4-His-Cys3 pattern zinc-containing domain, is widely found in many transcriptional regulation proteins from plants or animals. This protein has many different family members distributing in plant or animal proteome,and plays key roles in the development. Here, we identified 44 different putative PHD-finger proteins in the rice (Oryza sativa) genome and performed a phylogenetic analysis with 45 Arabidopsis thaliana proteins. The analysis led to a classification of the 89 proteins into two major groups based on the number of PHD-fingers. Phylogentic analysis of these proteins indicated that there are common ancestors in both plant and human genomes, from which two or three PHD-finger containing proteins might duplicate.

[Synonymous codon usage bias in the rice cultivar 93-11 (Oryza sativa L. ssp. indica)].

By using the whole genome sequences and EST data from the indica rice cultivar 93-11, a detailed relative analysis is made of the effect of some impact factors on synonymous codon usage. The results showed that the gene expression level assessed by mRNA abundance is positive relative to the "codon adaptation index" (CAI, 0.227**), and "codon preference parameter" (CPP, 0.145**), but negative relative to "effective number of codons" (ENC, -0.147**), indicating that genes with higher expression showed more significant variation in codon usage. There are significant negative correlations between gene length and CAI, CPP (r = -0.413** and -0.480** respectively), but a positive correlation between gene length and ENC(r = 0.210**), which suggested a tendency of shorter genes to higher expression of the transcriptional activity in 93-11. From the results that a higher negative correlation between GC content and ENC(r = -0.740**), but higher positive correlations between GC content and CAI, CPP (r = 0.877** and 0.832**, respectively), we can concluded that the GC content in coding region gave far more contribution to codon usage bias than that mRNA abundance and gene length. Four kinds of bases showed a three-period distribution in the translation initiation region, the bias at the first codon sites, which located +4, and +6, in the downstream of ATG being the largest. That suggested that there was a strong action of natural selection on these specific positions in the 93-11 genome. In this paper twenty-five codons defined firstly as "optimal codons" in 93-11 may provide some more useful information for rice gene-transformation.

[Physiological and genetic analysis of lesion resembling disease mutants (lrd) of Oryza sativa L].

Ten indica rice and eight japonica rice mutants with lesion resembling disease (lrd27-44) were obtained by gamma-ray mutagenesis of the whole genomes. These mutants exhibited diverse lesion mimic phenotypes under different growth environments, could be accordingly classified two types, sensitive and insensitive to environments. Basing on difference in development of lesion mimics, they can be divided into three categories: whole life lesion mimics (WLLM), vegetative initiation lesion mimics (VILM), and reproductive initiation lesion mimics (RILM). Lesion mimics resulted from the programmed cell death and were triggered by light, but not by wounding. The genetic analysis showed that four mutants, lrd32, lrd39, lrd40 and lrd42, were controlled by one or two recessive loci. Among the 18 lrd mutants, lrd37 and lrd40 conferred non-race-specific resistance to Xanthomonas oryzae pv. oryzae. Gene mapping and cloning of Lrd32 and Lrd40 are under way.

[Mapping by molecular markers showing segregation distortion].

The comparative analysis of segregation distortions of the codominant markers data presented in software MAPMAKER are made, where five RFLPs markers involve in a mouse F2 population with 333 individuals. The successive chi(2) test begins with the determinations of gametic or zygotic selection types, followed by the estimation of recombination fractions between two markers with the Newton-Raphson iteration method. It is better to use the molecular marker showing segregation distortion for constructing a genetic map, in the case of seriously skew segregation between both the adjoining markers. The successive chi(2) test provides better accuracy than that of classical chi(2) test for the estimation of the recombination values in F2 population with segregation distortion.

Fine mapping and candidate gene prediction of the photoperiod and thermo-sensitive genic male sterile gene pms1(t) in rice.

Pei'ai64S, an indica sterile variety with photoperiod and thermo-sensitive genic male sterile (PTGMS) genes, has been widely exploited for commercial seed production for "two-line" hybrid rice in China. One PTGMS gene from Pei'ai64S, pms1(t), was mapped by a strategy of bulked-extreme and recessive-class approach with simple sequence repeat (SSR) and insert and deletion (In-Del) markers. Using linkage analysis for the F(2) mapping population consisting of 320 completely male sterile individuals derived from a cross between Pei'ai64S and 93-11 (indica restorer) lines, the pms1(t) gene was delimited to the region between the RM21242 (0.2 cM) and YF11 (0.2 cM) markers on the short arm of chromosome 7. The interval containing the pms1(t) locus, which was co-segregated with RM6776, is a 101.1 kb region based on the Nipponbare rice genome. Fourteen predicted loci were found in this region by the Institute for Genomic Research (TIGR) Genomic Annotation. Based on the function of the locus LOC_Os07g12130 by bioinformatics analysis, it is predicted to encode a protein containing a Myb-like DNA-binding domain, and may process the transcript with thermosensory response. The reverse transcription-polymerase chain reaction (RT-PCR) results revealed that the mRNA levels of LOC_Os07g12130 were altered in different photoperiod and temperature treatments. Thus, the LOC_Os07g12130 locus is the most likely candidate gene for pms1(t). These results may facilitate not only using the molecular marker assisted selection of PTGMS genes, but also cloning of the pms1(t) gene itself.

Transgenic Brassica chinensis plants expressing a bacterial codA gene exhibit enhanced tolerance to extreme temperature and high salinity.

Transgenic Brassica compestris L. spp. chinensis plants expressing a choline oxidase (codA) gene from Arthrobacter globiformis were obtained through Agrobacterium tumefaciens-mediated transformation. In the transgenic plants, codA gene expression and its product transportation to chloroplasts were detected by the enzyme-linked immunosorbent assay (ELISA) examination, immunogold localization, and (1)H-nuclear magnetic resonance ((1)H-NMR). Stress tolerance was evaluated in the T(3) plants under extreme temperature and salinity conditions. The plants of transgenic line 1 (L1) showed significantly higher net photosynthetic rate (P(n)) and P(n) recovery rate under high (45 °C, 4 h) and low temperature (1 °C, 48 h) treatments, and higher photosynthetic rate under high salinity conditions (100, 200, and 300 mmol/L NaCl, respectively) than the wild-type plants. The enhanced tolerance to high temperature and high salinity stresses in transgenic plants is associated with the accumulation of betaine, which is not found in the wild-type plants. Our results indicate that the introduction of codA gene from Arthrobacter globiformis into Brassica compestris L. spp. chinensis could be a potential strategy for improving the plant tolerance to multiple stresses.