DNA barcoding,phylogenetic relationships and speciation of snappers (genus <Emphasis Type="Italic">Lutjanus</Emphasis>)

The phylogenetic relationships of 13 snapper species from the South China Sea have been established using the combined DNA sequences of three full-length mitochondrial genes (COI, COII and CYTB) and two partial nuclear genes (RAG1, RAG2). The 13 species (genus Lutjanus) were selected after DNA barcoding 72 individuals, representing 20 species. Our study suggests that although DNA barcoding aims to develop species identification systems, it may also be useful in the construction of phylogenies by aiding the selection of taxa. Combined mitochondrial and nuclear gene data has an advantage over an individual dataset because of its higher resolving power.     

The formation of Ca<Superscript>2+</Superscript> gradients at the cleavage furrows during cytokinesis of Zebrafish embryos

In dividing embryos, a localized elevation in intracellular Ca²⁺ ([Ca²⁺]_i) at the cleavage furrow has been shown to be essential for cytokinesis. However, the underlying mechanisms for generating and maintaining these [Ca²⁺]_i gradients throughout cytokinesis are not fully understood. In the present study, we analyzed the role of inositol 1,4,5-trisphosphate receptors (IP₃Rs) and endoplasmic reticulum (ER) distribution in determining the intracellular Ca²⁺ gradients in early zebrafish blastomeres. Application of the injected Ca²⁺ indicator, Indo-1, showed that during the first cell division a standing Ca²⁺ gradient was formed ∼35 min after fertilization, with the [Ca²⁺]_i spatially decaying from 500–600 nmol/L at the cleavage furrow to 100–200 nmol/L around the nucleus. While the IP3R immunohistochemical fluorescence was relatively concentrated in the peri-furrow region, ER labeling was relatively enriched in both peri-furrow and peri-nuclear regions. Numeric simulation suggested that a divergence in the spatial distribution of IP3R and the locations of Ca²⁺ uptake within the ER was essential for the formation of a standing Ca²⁺ gradient, and the Ca²⁺ gradient could only be well-established under an optimal stoichiometry of Ca²⁺ uptake and release. Indeed, while inhibition of IP3R Ca²⁺ release blocked the generation of the Ca²⁺ gradient at a lower [Ca²⁺]_i level, both Ca²⁺ release stimulation by inositol 1,4,5-trisphosphate (IP3) injection and ER Ca²⁺ pump inhibition by cyclopiazonic acid also eliminated the Ca²⁺ gradients at higher [Ca²⁺]_i levels. Our results suggest a dynamic relationship between ER-mediated Ca²⁺ release and uptake that underlies the maintenance of the perifurrow Ca²⁺ gradient and is essential for cytokinesis of zebrafish embryos.     

The calculation of information and organismal complexity

Background  

It is difficult to measure precisely the phenotypic complexity of living organisms. Here we propose a method to calculate the minimal amount of genomic information needed to construct organism (effective information) as a measure of organismal complexity, by using permutation and combination formulas and Shannon's information concept.     

Prediction of novel synthetic pathways for the production of desired chemicals

Background  

There have been several methods developed for the prediction of synthetic metabolic pathways leading to the production of desired chemicals. In these approaches, novel pathways were predicted based on chemical structure changes, enzymatic information, and/or reaction mechanisms, but the approaches generating a huge number of predicted results are difficult to be applied to real experiments. Also, some of these methods focus on specific pathways, and thus are limited to expansion to the whole metabolism.     

Spatially complex neighboring relationships among grassland plant species as an effective mechanism of defense against herbivory

Close spatial relationships between plant species are often important for defense against herbivory. The associational plant defense may have important implications for plant community structure, species diversity, and species coexistence. An increasing number of studies have focused on associational plant defense against herbivory at the scale of the individual plant and its nearest neighbors. However, the average neighborhood effects between plant species at the scale of whole plant communities have received almost no attention. The aims of this study were to determine patterns of spatial relationship between different plant species that can provide effective defense against herbivory. We conducted a manipulative experiment using sheep and three native plant species with different palatability. Consumption of palatable plants by herbivores was largest when the three plant species were isolated in three patches and independent of each other. A homogenous and spatially equal neighbor relationship between the three species did not reduce the risk of herbivory of palatable species compared to isolation of these species, but it reduced the total intake of all plant species. The palatable species was subject to less herbivory in a complex spatial neighborhood of several plant species. High complexity of spatial neighborhood resulted in herbivores passively reducing selectivity, thereby reducing the probability of damage to palatable species in the community, or making inaccurate judgments in foraging selectivity between and within patches, thereby reducing the vulnerability of palatable plants and even the whole plant community. We conclude that compelling herbivores to passively reduce the magnitude of foraging selectivity by establishing spatially complex neighborhoods between plant species is a compromise and optimal spatial strategy by plants to defend themselves again herbivory. This may contribute not only to maintenance of plant species diversity but also to a stable coexistence between herbivores and plants in grassland ecosystems.     

Gynostemosides A–E,megastigmane glycosides from Gynostemma pentaphyllum

Megastigmane glycosides (1–5) together with seven (6–12) related known compounds were isolated from the whole plants of Gynostemma pentaphyllum. The structures were elucidated by means of spectroscopic methods, including 2D NMR, HR-ESIMS, and circular dichroism (CD), as well as chemical transformations to be (3R, 4R, 5S, 6S, 7E)-3,4,6-trihydroxymegastigmane-7-en-9-one-3-O-β-d-glucopyranoside (gynostemoside A, 1), (3S, 4S, 5R, 6R, 7E, 9R)-3,4,6,9-tetrahydroxymegastigmane-7-en-3-O-β-d-glucopyranoside (gynostemoside B, 2), (3S, 4S, 5S, 6S, 7E, 9R)-3,4,9-trihydroxymegastigmane-7-en-9-O-β-d-glucopyranoside (gynostemoside C, 3), (3S, 4S, 5S, 6S, 7E, 9R)-3,4,9-trihydroxymegastigmane-7-en-3-O-β-d-glucopyranoside (gynostemoside D, 4), and (3S, 4S, 5S, 6S, 7E, 9R)-3,4,9-trihydroxymegastigmane-7-en-4-O-β-d-glucopyranoside (gynostemoside E, 5), respectively.     

Effects of aqueous root extracts and hydrophobic root exudates of cucumber (Cucumis sativus L.) on nuclei DNA content and expression of cell cycle-related genes in cucumber radicles

Allelopathic interactions implicate the inhibition of cell division by allelochemicals. To examine the effects of autotoxic agents on cell cycle and plant growth, germinated cucumber seeds (Cucumis sativus L.) were incubated in solutions containing the aqueous root extracts of cucumber at 1:100, 1:50, 1:25 and 1:10 (w:v), or the hydrophobic root exudates of cucumber at 25, 50 and 100 mg·L^?1. Aqueous root extracts and hydrophobic root exudates inhibited radicle elongation by 36.47–60.18% and 38.24–62.50%, respectively. The mitosis-specific genes were down-regulated in roots exposed to aqueous root extracts and hydrophobic root exudates. Meanwhile, exposure to either aqueous root extracts or hydrophobic root exudates decreased the proportion of 2C (C-value) and increased the proportion of 8C, leading to an increased mean C-value. We conclude that autotoxic agent-induced inhibition of radicle growth was partly attributed to the down-regulation of cell cycle-related genes and endoreduplication was enhanced under our experimental condition.     

Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection

Association mapping based on the linkage disequilibrium provides a promising tool to identify genes responsible for quantitative variations underlying complex traits. Presented here is a maize association mapping panel consisting of 155 inbred lines with mainly temperate germplasm, which was phenotyped for 34 traits and genotyped using 82 SSRs and 1,536 SNPs. Abundant phenotypic and genetic diversities were observed within the panel based on the phenotypic and genotypic analysis. A model-based analysis using 82 SSRs assigned all inbred lines to two groups with eight subgroups. The relative kinship matrix was calculated using 884 SNPs with minor allele frequency ≥20% indicating that no or weak relationships were identified for most individual pairs. Three traits (total tocopherol content in maize kernel, plant height and kernel length) and 1,414 SNPs with missing data <20% were used to evaluate the performance of four models for association mapping analysis. For all traits, the model controlling relative kinship (K) performed better than the model controlling population structure (Q), and similarly to the model controlling both population structure and relative kinship (Q + K) in this panel. Our results suggest this maize panel can be used for association mapping analysis targeting multiple agronomic and quality traits with optimal association model.     

Silicon enhances growth independent of silica deposition in a low-silica rice mutant, lsi1

To examine whether silica bodies are essential for silicon-enhanced growth of rice seedlings, we investigated the response of rice, Oryza sativa L., to silicon treatment. Silicic acid treatment markedly enhanced the SPAD (soil plant analytical development) values of leaf blades and the growth and development of leaves and lateral roots in cvs. Hinohikari and Oochikara, and a low-silicon mutant, lsi1. Combination of ethanol–benzene displacement and staining with crystal violet lactone enabled more detailed histochemical analysis to visualize silica bodies in the epidermis under bright-field microscopy. Supply of silicon induced the development of motor cells and silica bodies in epidermal cells in Hinohikari and Oochikara but not or marginal in lsi1. X-ray analytical microscopy detected silicon specifically in the leaf sheath, the outermost part of the stem, and the leaf blade midrib, suggesting that silicon is distributed to tissues involved in maintaining rigidity of the plant to prevent lodging, rather than being passively deposited in growing tissues. Silicon supplied at high dose accumulated in all rice seedlings and enhanced growth and SPAD values with or without silica body formation. Silicon accumulated in the cell wall may play an important physiological role different from that played by the silica deposited in the motor cell and silica bodies.