Differential Impacts on Bacterial Composition and Abundance in Rhizosphere Compartments between Al-Tolerant and Al-Sensitive Soybean Genotypes in Acidic Soil.

In this study, two soybean genotypes i.e. aluminum-tolerant Baxi 10 (BX10) and aluminum-sensitive Bendi 2 (BD2) were used as plant materials and the acidic red soil was used as growth medium. The soil layers from the inside to the outside of the root are: rhizospheric soil after washing (WRH), rhizospheric soil after brushing (BRH) and rhizospheric soil at two sides (SRH), respectively. The rhizosphere bacterial communities were analyzed by high-throughput sequencing of V4 hypervariable regions of 16S rRNA gene (16S rDNA) amplicons via Illumina MiSeq. The results of alpha diversity showed that the BRH and SRH of BX10 were significantly lower on community richness than that of BD2, while the WRH existed no significant difference between BX10 and BD2. Among the three sampling compartments of the same soybean genotype, WRH had the lowest community richness and diversity while existed the highest coverage. Beta diversity analysis results displayed no significant difference for any compartment between the two genotypes, or among the three different sampling compartments for any same soybean genotype. However, the relative abundance of major bacterial taxa specifically nitrogen-fixating and/or aluminum-tolerant bacteria was significantly different in the compartments of the BRH and/or SRH at phylum and genus levels depicting genotype dependent variations in rhizosphere bacterial community. Strikingly, as compared with BRH and SRH, the WRH within the same genotype (BX10 or BD2) always had an enrichment effect on rhizosphere bacteria associated with nitrogen-fixation.

The extract, LXB-1, from the barks of Liriodendron × hybrid, induced apoptosis via Akt, JNK and ERK1/2 pathways in A549 lung cancer cells.

The effect of LXB-1, an extract from Liriodendron × hybrid, was determined on A549 human lung adenocarcinoma cell lines. Growth inhibition of LXB-1 was analyzed by MTT assay. Cancer cell cycle was measured by flow cytometry. To verify the apoptosis effect of LXB-1 on A549 cells, annexin V/PI double staining assay was performed. The expression levels of proapoptotic proteins were also measured by western blot. The potential mechanisms of LXB-1 inducing apoptosis - the expression and phosphorylation of ERK, p38, JNK and Akt - were investigated by western blot. The IC50 values of LXB-1 on A549 for 24, 48 and 72 h treatment were determined to be 12.97±1.53 µg/mL, 9.55±1.42 µg/mL, and 5.90±0.74 µg/mL, respectively. LXB-1 induced an obvious G2/M cell cycle arrest in A549 cells and resulted in significant cell apoptosis. LXB-1 also increased the cleavage of both caspase-3 and caspase-9, and greatly decreased the protein levels of Bcl-2. Moreover, LXB-1 increased the expression of phosphorylated JNK but decreased the levels of phosphorylated ERK1/2 and Akt. These results suggest that that LXB-1 induced apoptosis through JNK, ERK1/2, and Akt pathways in A549 cells.

(+)- and (-)-liriodenol, a pair of novel enantiomeric lignans from Liriodendron hybrid.

(+)- and (-)-liriodenol, a pair of unprecedented enantiomeric lignans bearing a 1,1-disubstituted olefinic group, were isolated from the barks of Liriodendron hybrid. The structure and relative configurations were determined by comprehensive analysis of MS and NMR spectroscopy. The cytotoxicity of these three lignans ((±)-, (+)-, and (-)-liriodenol) was evaluated in vitro against four selected human tumor cell lines, where (+)-liriodenol showed more significant cytotoxic effects than the (±)- and (-)-liriodenol enantiomers.

[Cloning and expression analysis of differentially expressed genes in Chinese fir stems treated by different concentrations of exogenous IAA].

To reveal the potential genetic mechanisms of indole-3-acetic acid (IAA) that regulate Chinese fir wood formation, cloned the differentially expressed genes via suppress subtractive hybridization (SSH) using the truncated stems treated by 0 and 3 mg IAA/g lanolin as the driver and tester, respectively. A total of 332 unigenes that were involved in cell organization and biosynthesis, developmental processes control, electron transport, stress response, and signal transduction. To further test the results from SSH, we selected those unigenes, whose putative encoding proteins showed significantly homologous with HIRA, PGY1, SMP1, TCT, TRN2, and ARF4, and analyzed their expressed specificity in the wood formative tissues and their response to the secondary developmental changes of vascular cambium stimulated by 0, 1, and 3 mg.IAA/g.lanolin treatment. The results showed that ClHIRA, ClPGY1, and ClARF4, which were specifically expressed in the adaxial zone of stem, were positively response to the activities of cell division and tracheid differentiation stimulated by exogenous IAA treatment. However, ClSMP1, ClTCTP1, and ClTRN2, which were mainly expressed in the abaxial zones of stems, showed negative correlation with the treated levels of exogenous IAA and activities of vascular cambium secondary development at the transcriptional level. This result showed that the differential response of developmental regulatory genes located in different vascular tissues to the level changes of edogenous IAA in stems is likely to be an important molecular mechanism of auxin regulating wood formation.

[Progress on whole genome sequencing in woody plants].

In recent years, the number of sequencing data of plant whole genome have been increasing rapidly and the whole genome sequencing has been also performed widely in woody plants. However, there are a set of obstacles in investigating the whole genome sequencing in woody plants, which include larger genome, complex genome structure, limitations of assembly, annotation, functional analysis, and restriction of the funds for scientific research. Therefore, to promote the efficiency of the whole genome sequencing in woody plants, the development and defect of this field should be analyzed. The three-generation sequencing technologies (i.e., Sanger sequencing, synthesis sequencing, and single molecule sequencing) were compared in our studies. The progress mainly focused on the whole genome sequencing in four woody plants (Populus, Grapevine, Papaya, and Apple), and the application of sequencing results also was analyzed. The future of whole genome sequencing research in woody plants, consisting of material selection, establishment of genetic map and physical map, selection of sequencing technology, bioinformatic analysis, and application of sequencing results, was discussed.

[Comparison of statistical methods for detecting differential expression in microarray data].

DNA microarray is a new tool in biotechnology, which allows simultaneously monitoring thousands of gene expression in cells. The goal of differential gene expression analysis is to detect genes with significant change of gene expression levels arising from experimental conditions. Although various statistical methods have been suggested to confirm differential gene expression, only a few studies compared performance of the statistical methods. This paper presented comparison of statistical methods for finding differentially expressed genes (DEGs) from the microarray data. Using simulated and real datasets (Populus cDNA microarray data), we compared eight methods of identifying differential gene expression. The simulated datasets included four differential distributions (normal distribution, uniform distribution, c2 distribution, and exponential distribution). The results of simulated datasets analysis showed that the eight methods were more preferable with the microarray data of uniform distribution than normal distribution. They were not preferable with the c2 distribution and exponential distribution. Of these eight methods, SAM (Significance Analysis of Microarrays) and Wilcoxon rank sum test performed well in most cases. The results of real cDNA microarray data of Populus showed that there was much similarity of SAM, Samroc, and regression modeling approach. Wilcoxon rank sum test was different from them. Samroc and regression modeling approach were similar in the eight methods. For both simulated and real datasets, SAM, Samroc, and regression modeling approach performed better than other methods.

A preliminary analysis of synonymous codon usage in poplar species.

Poplar is among the most important deciduous tree species in plantations over the world and has been used as an important model system for molecular genetics of trees. The analysis of codon usage may improve the understanding of the mechanism of codon distribution and variation in poplar and the understanding of factors shaping the codon usage patterns. Here, an EN(c) (effective number of codons)-plot method and multivariate statistical method called correspondence analysis (COA) were used to examine the codon usage of 314 genes of poplar. The results show that the main trend was highly negative correlated with the gene expression level assessed by the ''Codon Adaptation Index'' value. Moreover, there were two significant correlations between axis 1 coordinates and GC3(s) content and gene length, we infer that gene nucleotide composition and gene length also play an important role in shaping the codon usage bias in poplar. The result of relative synonymous codon usage (RSCU) analysis shows a high bias of codon usage toward the codon with A or T ending. In addition, we compared the codon preferences among poplar, Arabidopsis thaliana, Oryza sative, Homo sapiens and Escherichia coli, and poplar was found to be most similar to A.thaliana and least similar to E.coli. In this paper, 10 codons defined firstly as optimal codons through an analysis of the high-expression codon in poplar may provide some useful information for genetic engineering of poplar.

[Identification and analysis of differentially expressed genes during wood formation in Chinese fir by SSH].

Wood is an important raw material for the global industry with rapidly increasing demand. To isolate the differentially expressed genes in xylogenesis of Chinese fir [Cunninghamia lanceolata (Lamb.) Hook], a forward subtractive cDNA library was constructed using suppression subtractive hybridization (SSH) method, which was performed using the cDNA from the mutant Dugansha clone as the tester and the cDNA from the normal Jurong 0 clone as the driver. Six hundred and eighteen clones were obtained. Recombinants were identified using PCR with universal T7 and SP6 primers and using EcoR digestion. To further eliminate false positive, dot hybridization was used with four DIG-labeled probes (FSP, RSP, UTP, and UDP). Real-time PCR was performed to confirm the results. A total of 260 unique ESTs were obtained, 60% of the ESTs exhibiting homologies with proteins of known function fell into 4 major classes: metabolism, cell wall biogenesis and remodeling, signal transduction and stress. The systematic analysis of genes involved in wood formation in Chinese fir provides valuable insights into the molecular mechanisms involved in xylem differentiation, is important resources for forest research directed toward understanding the genetic control of wood formation and future endeavors to modify wood and fiber properties for industrial use.

[Efficient plant regeneration in vitro in Pinus massoniana L].

Pinus massoniana L. is one of the important trees for afforestation in South China. The efficient system of plant regeneration from mature zygotic embryos and seedlings of masson pine was established in this study. The influences of basal media, hormones and methods for buds induction, shoots elongation and rooting were studied. The results indicate that DCR medium with 0.5 mg/L BA and 0.05 mg/L IBA shows the highest differentiation rate of adventitious buds. Induction and multiplication of axillary buds take aseptic seedlings as explants. KT has better effect than BA on the axillary buds induction. The best axillary buds induction medium is DCR medium supplemented with 1 mg/L KT and 0.2 mg/L IBA. After culturing on GD medium with 0.1 mg/L BA and 0.2 mg/L IBA for elongation, the buds were transferred on the 1/2 GD medium with 2 mg/L IBA and 0.05 mg/L BA for adventitious roots induction. Paraffin slice indicates that the adventitious buds developed from the meristematic tissue of cotyledonary epicuticula.