Criticality Is an Emergent Property of Genetic Networks that Exhibit Evolvability

Accumulating experimental evidence suggests that the gene regulatory networks of living organisms operate in the critical phase, namely, at the transition between ordered and chaotic dynamics. Such critical dynamics of the network permits the coexistence of robustness and flexibility which are necessary to ensure homeostatic stability (of a given phenotype) while allowing for switching between multiple phenotypes (network states) as occurs in development and in response to environmental change. However, the mechanisms through which genetic networks evolve such critical behavior have remained elusive. Here we present an evolutionary model in which criticality naturally emerges from the need to balance between the two essential components of evolvability: phenotype conservation and phenotype innovation under mutations. We simulated the Darwinian evolution of random Boolean networks that mutate gene regulatory interactions and grow by gene duplication. The mutating networks were subjected to selection for networks that both (i) preserve all the already acquired phenotypes (dynamical attractor states) and (ii) generate new ones. Our results show that this interplay between extending the phenotypic landscape (innovation) while conserving the existing phenotypes (conservation) suffices to cause the evolution of all the networks in a population towards criticality. Furthermore, the networks produced by this evolutionary process exhibit structures with hubs (global regulators) similar to the observed topology of real gene regulatory networks. Thus, dynamical criticality and certain elementary topological properties of gene regulatory networks can emerge as a byproduct of the evolvability of the phenotypic landscape.     

A Putative Gene sbe3-rs for Resistant Starch Mutated from SBE3 for Starch Branching Enzyme in Rice (Oryza sativa L.)

Foods high in resistant starch (RS) are beneficial to prevent various diseases including diabetes, colon cancers, diarrhea and chronic renal or hepatic diseases. Elevated RS in rice is important for public health since rice is a staple food for half of the world population. A japonica mutant ‘Jiangtangdao 1’ (RS = 11.67%) was crossed with an indica cultivar ‘Miyang 23’ (RS = 0.41%). The mutant sbe3-rs that explained 60.4% of RS variation was mapped between RM6611 and RM13366 on chromosome 2 (LOD = 36) using 178 F₂ plants genotyped with 106 genome-wide polymorphic SSR markers. Using 656 plants from four F_3∶4 families, sbe3-rs was fine mapped to a 573.3 Kb region between InDel 2 and InDel 6 using one STS, five SSRs and seven InDel markers. SBE3 which codes for starch branching enzyme was identified as a candidate gene within the putative region. Nine pairs of primers covering 22 exons were designed to sequence genomic DNA of the wild type for SBE3 and the mutant for sbe3-rs comparatively. Sequence analysis identified a missense mutation site where Leu-599 of the wild was changed to Pro-599 of the mutant in the SBE3 coding region. Because the point mutation resulted in the loss of a restriction enzyme site, sbe3-rs was not digested by a CAPS marker for SpeI site while SBE3 was. Co-segregation of the digestion pattern with RS content among 178 F₂ plants further supported sbe3-rs responsible for RS in rice. As a result, the CAPS marker could be used in marker-assisted breeding to develop rice cultivars with elevated RS which is otherwise difficult to accurately assess in crops. Transgenic technology should be employed for a definitive conclusion of the sbe3-rs.     

Usefulness of combined in vivo skin comet assay and in vivo skin micronucleus test

We have already found that the in vivo skin comet assay is useful for the evaluation of primary DNA damage induced by genotoxic chemicals in epidermal skin cells. The aim of the present study was to evaluate the sensitivity and specificity of the combined in vivo skin comet assay and in vivo skin micronucleus (MN) test using the same animal to explore the usefulness of the new test method. The combined alkaline comet assay and MN test was carried out with three chemicals: 4-nitroquinoline-1-oxide (4NQO), N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) and benzo[a]pyrene (B[a]P). In the first experiment, we compared DNA- and chromosome-damaging effects of 3 [72, 24 and 3 hours (h) before sacrifice] and 4 applications (72, 48, 24 and 3h before sacrifice) of 4NQO, which induces dermal irritancy. The animals were euthanized and their skin was sampled for the combination test. As a result, the 4-application method was able to detect both DNA- and chromosome-damaging potential with a lower concentration; therefore, in the second experiment, MNNG and B[a]P were topically applied four times, respectively. The animals were euthanized, and then their skins were sampled for combination tests. In the alkaline comet assay, significant differences in the percent of DNA (%DNA) in the tail were observed in epidermal skin cells treated with MNNG and B[a]P. In the MN test, an increased frequency of MN cells (%MN) cells was observed by treatment with MNNG; however, there were no significant increases. In contrast, significant differences in %MN were observed by treatment with B[a]P. From these results, we conclude that the combined in vivo skin comet assay and in vivo MN test was useful because it can detect different genotoxicity with the same sampling time and reduce the number of animals used.     

Effects of drought stress on phosphorus and potassium uptake dynamics in summer maize (Zea mays) throughout the growth cycle

The effects of drought stress on the phosphorus (P) and potassium (K) uptake dynamics of summer maize (Zea mays L.) throughout the growth cycle were studied. Field trials were conducted under a completely randomized design with three field water capacity (FC) regimes: 75?% FC was well watered and considered to be the control, 55?% FC represented moderate stress (MS), and 35?% FC represented severe stress (SS). The water regimes were applied from the third leaf stage until maturity. Drought stress induced sharp decreases in total K and P uptake of maize organs at different developmental stages and, in particular, detrimentally affected the nutrient uptake capability of roots. SS caused more deleterious effect than MS on both total K and P uptake by plant organs. The results suggested maize plants differ in their ability to maintain nutrient uptake under drought stress, and it is highly dependent on the intensity and duration of drought stress and the developmental stage. The decrease in total K and P uptake caused by both MS and SS was accompanied by reduction in biomass production in drought-stressed tissues. The biomass allocation patterns in response to drought stress fluctuated strong mostly because of competitive changes in the shoot and roots at different stages, thus the root:shoot ratio increased at some stages and decreased at other stages. SS induced a dramatic reduction in the harvest index (HI), whereas MS slightly decreased HI. Thus, water limitation caused lower K and P uptake and HI.     

Screening for a single-chain variable-fragment antibody that can effectively neutralize the cytotoxicity of the Vibrio parahaemolyticus thermolabile hemolysin

Vibrio parahaemolyticus is a halophilic bacterium that is widely distributed in water resources. The bacterium causes lethal food-borne diseases and poses a serious threat to human and animal health all over the world. The major pathogenic factor of V. parahaemolyticus is thermolabile hemolysin (TLH), encoded by the tlh gene, but its toxicity mechanisms are unknown. A high-affinity antibody that can neutralize TLH activity effectively is not available. In this study, we successfully expressed and purified the TLH antigen and discovered a high-affinity antibody to TLH, named scFv-LA3, by phage display screening. Cytotoxicity analysis showed that scFv-LA3 has strong neutralization effects on TLH-induced cell toxicity.     

A novel series of pyrazolylpiperidine N-type calcium channel blockers

Selective blockers of the N-type calcium channel have proven to be effective in animal models of chronic pain. However, even though intrathecally delivered synthetic ω-conotoxin MVIIA from Conus magnus (ziconotide [Prialt®]) has been approved for the treatment of chronic pain in humans, its mode of delivery and narrow therapeutic window have limited its usefulness. Therefore, the identification of orally active, small-molecule N-type calcium channel blockers would represent a significant advancement in the treatment of chronic pain. A novel series of pyrazole-based N-type calcium channel blockers was identified by structural modification of a high-throughput screening hit and further optimized to improve potency and metabolic stability. In vivo efficacy in rat models of inflammatory and neuropathic pain was demonstrated by a representative compound from this series.     

Study on population genetic diversity of Camellia japonica in 5 islands between China and Japan

运用ISSR分子标记法对中、日两国5个岛屿天然山茶种群共150个个体进行遗传多样性分析.结果表明:筛选出的20条引物扩增得到205条清晰条带,其中183条为多态性条带,多态位点百分比(PPB)为89.27％.经POPGENE软件分析,山茶种群平均多态位点百分比(PPB)为72.00％,Nei's基因多样性指数(HE)为0.2743,Shannon信息多态性指数(H)为0.4023,种群水平遗传多样性较高.基因分化系数Gst=0.2033,表明遗传变异主要存在于种群内个体间.Mantel检验(r=0.7989,P＜0.05)和UPGMA聚类表明岛屿地理隔离对山茶种群遗传分化具有重要影响.基于岛屿山茶种群遗传结构的分析,建议加强我国岛屿自然种群的就地保护力度.