Nitrogen addition alleviates water loss of Moso bamboo (Phyllostachys edulis) under drought by affecting light-induced stomatal responses.

The combined climate-change-evoked drought and nitrogen (N) deposition have severely affected plant carbon and water relations governed by stomata. However, the interplay between steady-state and dynamic stomatal behavior responses to light remains unclear regarding its impact on plant water and carbon relations. The objective here was to investigate whether light-induced stomatal dynamics could mitigate the adverse effects of steady-state gas exchange on water conservation or photosynthesis under drought and N addition conditions. We conducted a manipulative experiment to investigate the impacts of throughfall reduction, N addition, and their combination on light-induced stomatal and photosynthetic dynamics in a Moso bamboo (Phyllostachys edulis) forest. We determined the influence of stomal response rate on water loss and photosynthesis, and further assessed whether it mitigated the effects of steady-state gas exchange (gs). We found that Moso bamboo decreased gs under throughfall reduction, while accelerated stomatal opening and biochemical activation when irradiance increased, which reduced the lag in photosynthesis during the induction period. In contrast, under the combined throughfall reduction and N addition condition, Moso bamboo increased gs but showed faster stomatal closure, which decreased the percentage of transpiration following a decrease in light intensity. Our findings indicate that stomatal dynamic behavior may depend on the effects of steady-state gas exchange on water conservation and carbon uptake under different soil water and N conditions. These discoveries contribute to our understanding of the coupling mechanisms of plant water use and carbon uptake in the context of global changes.

Crystal Plane Regulation Promotes the Oriented Conversion of Radicals in Heterogeneous Persulfate Catalyzed Oxidation Process.

In heterogeneous persulfate-catalyzed oxidation systems, the mechanism underlying the crystal plane effects of the catalyst on the selective conversion of reactive oxygen species (ROS) remains ambiguous. In this study, nano-Co3 O4 catalysts with varying crystallinity and exposure levels of (111) crystal planes are prepared via a hydrothermal method. Compared to low crystalline catalysts, high crystallinity catalysts predominantly expose (111) planes containing higher concentrations of Co2+ and oxygen vacancies (Ov), resulting in an increase degradation efficiency of p-nitrobenzaldehyde (4-NBA) from 74.5% to 100%. Radical quenching experiments and EPR characterization reveal that the degradation of 4-NBA occurs through a radical pathway, and quantification of radicals demonstrates that increasing exposure levels of (111) planes effectively promote radical yield (CSO4•- increase from 18.2 to 172.8 µm and C•OH increase from 1 to 58.9 µm). Furthermore, XPS and DFT calculations indicate that high crystallinity catalyst possesses more Ov active sites on (111) planes. The presence of Ov not only facilitates the adsorption of PMS molecules but also enhances electron transfer from Co2+ to PMS, leading to directed formation and efficient transformation of radicals. This study presents a novel strategy for promoting efficient radical formation in persulfate-activated systems.

Case report: Successful outcome of a young patient with rhabdomyolysis and shock caused by diquat poisoning.

The widespread use of diquat as a substitute for paraquat has led to an increase in poisoning deaths. A successful case of diquat poisoning complicated with rhabdomyolysis and shock was lacking. A 13-year-old previously healthy girl ingested 40 ml of diquat solution in a suicide attempt. The concentration of diquat in serum was 436.2 ug/L at 10 h after poisoning. The clinical course was characterized by progressive multi-organ dysfunction, particularly rhabdomyolysis and shock. The main treatments included intensive hemoperfusion combined with continuous renal replacement therapy (CRRT), drainage, and activated carbon adsorption. Meanwhile, accurate dilatation under the model of pulse indicator continuous cardiac output (PICCO) was essential for the successful treatment of shock. The serum concentration of diquat declined to 20 ug/L after 96 h of treatments. The patient was discharged from the hospital after 3 weeks of treatment without obvious symptoms. So far, this was the first successful case of diquat poisoning complicated with rhabdomyolysis and shock, which would enrich the experience of diquat poisoning treatment.

The effects of genetic distance, nutrient conditions, and recognition ways on outcomes of kin recognition in Glechoma longituba.

Kin recognition might help plants decrease competitive cost and improve inclusive fitness with close genes; thus it might interact with environmental factors to affect communities. Whether and how various factors, such as the genetic distance of neighbors, environmental stressors, or the way a plant recognizes its neighbors, might modify plant growth strategies remains unclear. To answer these questions, we conducted experiments in which ramets of a clonal plant, Glechoma longituba, were grown adjacent to different genetically related neighbors (clone kin / close kin / distant kin) in different nutrient conditions (high / medium / low), or with only root exudates from pre-treatment in culture solution. By comparing competitive traits, we found that: (1) kin recognition in G. longituba was enhanced with closer genetic distance; (2) the outcomes of kin recognition were influenced by the extent of nutrient shortage; (3) kin recognition helped to alleviate the nutrient shortage effect; (4) kin recognition via root exudates affected only below-ground growth. Our results provide new insights on the potential for manipulating the outcome of kin recognition by altering neighbor genetic distance, nutrient conditions and recognition ways. Moreover, kin recognition can help plants mitigate the effects of nutrient shortage, with potential implications in agricultural research.

Predictability of parental ultraviolet-B environment shapes the growth strategies of clonal Glechoma longituba.

Although there is an increasing debate about ecological consequences of environmental predictability for plant phenotype and fitness, the effect of predictability of parental environments on the offspring is still indefinite. To clarify the role of environmental predictability in maternal effects and the growth strategy of clonal offspring, a greenhouse experiment was conducted with Glechoma longituba. The parental ramets were arranged in three ultraviolet-B (UV-B) conditions, representing two predictable environments (regular and enhanced UV-B) and an unpredictable environment (random UV-B), respectively. The offspring environments were the same as their parent or not (without UV-B). At the end of experiment, the growth parameters of offspring were analyzed. The results showed that maternal effects and offspring growth were regulated by environmental predictability. Offspring of unpredictable environmental parents invested more resources in improving defense components rather than in rapid growth. Although offspring of predictable parents combined two processes of defense and growth, there were still some differences in the strategies between the two offspring, and the offspring of regular parent increased the biomass allocation to roots (0.069 g of control vs. 0.092 g of regular), but that of enhanced parent changed the resource allocation of nitrogen in roots and phosphorus in blade. Moreover, when UV-B environments of parent and offspring were matched, it seemed that maternal effects were not adaptive, while the growth inhibition in the predictable environment was weaker than that in unpredictable environment. In the predictable environment, the recovered R/S and the increased defense substances (flavonoid and anthocyanin) contributed to improving offspring fitness. In addition, when UV-B environments of parent and offspring were mismatched, offspring growth was restored or improved to some extent. The offspring performance in mismatched environments was controlled by both transgenerational effect and within-generational plasticity. In summary, the maternal effects affected growth strategies of offspring, and the differences of strategies depended on the predictability of parental UV-B environments, the clone improved chemical defense to cope with unpredictable environments, while the growth and defense could be balanced in predictable environments. The anticipatory maternal effects were likely to improve the UV-B resistance.

Enhancing effects of dissolved and media surface-bound organic matter on titanium dioxide nanoparticles transport in iron oxide-coated porous media under acidic conditions.

Natural organic matter (NOM) and iron oxides have been proved to be crucial factors controlling the behaviors of nanoparticles in heterogenous environment. Here, we conducted experimental and modeling study on the transport of titanium dioxide nanoparticles (TiO2 NPs) in iron oxide-coated quartz in the presence of NOM under acidic conditions. Results showed the antagonistic effects of iron oxides and NOM on TiO2 NPs mobility. The inhibition of iron oxides coated on quartz was crystal form-dependent other than quantity-dependent. Amorphous ferric oxyhydroxide with higher specific surface area brought more positive charge and favorable deposition sites onto quartz, and induced more retention of nanoparticles than two crystalline iron oxides, goethite and hematite. Dissolved organic matter (DOM) facilitated TiO2 NPs transport in iron oxide-coated quartz. In comparation with the limited enhancing effects of DOM, the NOM coatings on media surface partially or largely offset the inhibition of goethite on nanoparticles mobility through direct occupation of attachment sites and sites screening due to the steric repulsion of the macromolecules. Owing to the higher steric hindrance, humic acid, both in dissolved and media surface-bound states, exerted stronger facilitating effects on TiO2 NPs mobility relative to fulvic acid.

Effects of foreign metal doping on the step-by-step oxidation process in M-OMS-2 catalyzed activation of PMS.

Various metal cations M (M = Mg2+, Ca2+, Zn2+, Cu2+, Fe3+) were doped into the tunnel of manganese octahedral molecular sieve (OMS-2). Redox-inactive metal (Ca, Mg and Zn) doped OMS-2 exhibited better peroxymonosulfate (PMS) catalytic activity than redox metal-doped Cu-OMS-2 and Fe-OMS-2. Redox-inactive metals doping improves the conductivity and reducibility of the catalyst, while transition metal doping reduces the dispersion of manganese. More importantly, the degradation of ACE can be divided into two stages. In the first stage, ACE was oxidized dominantly through mediated electron transfer process. Subsequently, singlet oxygen (1O2) gradually dominated oxidative degradation in the second stage, which was derived from the reaction between superoxide radical (O2•-) and metastable manganese intermediates. The long half-life of O2•- on the surface of OMS-2 ensured the delay generation of 1O2. This study not only provides a new idea for improving the efficiency of heterogeneous catalysts activation of PMS, but also meaningful for the in-depth study of multiple reaction mechanisms in PMS activation processes.

Density-dependence tips the change of plant-plant interactions under environmental stress.

Facilitation studies typically compare plants under differential stress levels with and without neighbors, while the density of neighbors has rarely been addressed. However, recent empirical studies indicate that facilitation may be density-dependent too and peak at intermediate neighbor densities. Here, we propose a conceptual model to incorporate density-dependence into theory about changes of plant-plant interactions under stress. To test our predictions, we combine an individual-based model incorporating both facilitative response and effect, with an experiment using salt stress and Arabidopsis thaliana. Theoretical and experimental results are strikingly consistent: (1) the intensity of facilitation peaks at intermediate density, and this peak shifts to higher densities with increasing stress; (2) this shift further modifies the balance between facilitation and competition such that the stress-gradient hypothesis applies only at high densities. Our model suggests that density-dependence must be considered for predicting plant-plant interactions under environmental change.

Dataset for characterization of dissolved organic matter extracted from organic wastes and their effects on the transport of titanium dioxide nanoparticles in acidic saturated porous media in the presence of monovalent electrolyte.

This dataset is related to the research article in Chemosphere, entitled 'The limited facilitating effect of dissolved organic matter extracted from organic wastes on the transport of titanium dioxide nanoparticles in acidic saturated porous media' [1]. The data summarised the characterization of dissolved organic matter (DOM) extracted from organic wastes and their effects on the transport of titanium dioxide nanoparticles (TiO2 NPs) in acidic saturated porous media in the presence of monovalent electrolyte. Three types of dissolved organic matter were extracted from organic materials, including swine manure, sludge, and sediment, using deionized water, and were characterized with UV-Vis, FTIR and elementary analysis. The adsorption of DOM onto TiO2 NPs was evaluated in the presence of NaCl, and zeta potentials of TiO2 NPs were also determined. Breakthrough column experiments were conducted to quantify the effects of the extracted DOM on the transport behaviours of TiO2 NPs in acidic porous media compared with humic acid. Moreover, the interaction energy between nanoparticles and between nanoparticles and quartz media was calculated according to the classical DLVO theory. The dataset could be used as a reference for the evaluation and prediction of the environmental fate and subsequent risk of engineered nanomaterials.

The limited facilitating effect of dissolved organic matter extracted from organic wastes on the transport of titanium dioxide nanoparticles in acidic saturated porous media.

The complexity of natural dissolved organic matter (DOM) motivates the determination of how DOM from diverse sources affects the environmental behaviors of engineered nanoparticles. Here, three types of DOM, DOM extracted from swine manure (SWDOM), sludge (SLDOM) and sediment (SEDOM), were characterized, and their effects on the transport of titanium dioxide nanoparticles (TiO2 NPs, 30 nm in diameter) were evaluated and compared with those of humic acid (HA). Characterization tests showed differences in the aromaticity and weight-average molecular weight (Mw) properties among the three extracted DOM solutions, and greater distinctions were found between the extracted DOM and HA. All the extracted DOM facilitated TiO2 NPs transport in acidic porous media. Nevertheless, the enhancing effects varied among the different extracted DOM types. SWDOM had a promoting effect on TiO2 NPs mobility that was equivalent to that of SEDOM and much higher than that of SLDOM. However, the facilitating effects of all three extracted DOM types were limited compared to that of HA. Based on the combined analysis of DOM properties and TiO2 NPs transport behaviors, it could be concluded that aromaticity and Mw were the key properties determining the limited promoting effects of DOM on TiO2 NPs mobility, and the specific UV absorbance at 280 nm (normalized by concentration, SUVA280) was a facile and useful indicator of the DOM-promoted transport of TiO2 NPs. These findings revealed that transport potential in the presence of DOM would be overestimated if either HA or fulvic acid were chosen as the DOM model in studies.

Soil Abiotic Properties and Plant Functional Traits Mediate Associations Between Soil Microbial and Plant Communities During a Secondary Forest Succession on the Loess Plateau.

In the context of secondary forest succession, aboveground-belowground interactions are known to affect the dynamics and functional structure of plant communities. However, the links between soil microbial communities, soil abiotic properties, plant functional traits in the case of semi-arid and arid ecosystems, are unclear. In this study, we investigated the changes in soil microbial species diversity and community composition, and the corresponding effects of soil abiotic properties and plant functional traits, during a ≥150-year secondary forest succession on the Loess Plateau, which represents a typical semi-arid ecosystem in China. Plant community fragments were assigned to six successional stages: 1-4, 4-8, 8-15, 15-50, 50-100, and 100-150 years after abandonment. Bacterial and fungal communities were analyzed by high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene and the internal transcribed spacer (ITS2) region of the rRNA operon, respectively. A multivariate variation-partitioning approach was used to estimate the contributions of soil properties and plant traits to the observed microbial community composition. We found considerable differences in bacterial and fungal community compositions between the early (S1-S3) and later (S4-S6) successional stages. In total, 18 and 12 unique families were, respectively, obtained for bacteria and fungi, as indicators of microbial community succession across the six stages. Bacterial alpha diversity was positively correlated with plant species alpha diversity, while fungal diversity was negatively correlated with plant species diversity. Certain fungal and bacterial taxa appeared to be associated with the occurrence of dominant plant species at different successional stages. Soil properties (pH, total N, total C, NH4-N, NO3-N, and PO4-P concentrations) and plant traits explained 63.80% and 56.68% of total variance in bacterial and fungal community compositions, respectively. These results indicate that soil microbial communities are coupled with plant communities via the mediation of microbial species diversity and community composition over a long-term secondary forest succession in the semi-arid ecosystem. The bacterial and fungal communities show distinct patterns in response to plant community succession, according to both soil abiotic properties and plant functional traits.

Facilitation from an intraspecific perspective - stress tolerance determines facilitative effect and response in plants.

Plant-plant interactions are reciprocal and include effects on and response to neighbours. Distinct traits confer competitive effect and response ability, but how specific traits determine effect and response in facilitative interactions has not been studied experimentally. We utilized the model species Arabidopsis thaliana to test for trait dependence of facilitative interactions. Salt-sensitive (sos) mutants or salt-tolerant wild-types were exposed to an experimental salinity gradient with and without intraspecific neighbours and the intensity of plant-plant interactions was measured for three performance variables. We tested whether salt tolerance can predict facilitative effect and response and whether a tradeoff exists between competitive ability and tolerance to stress. Interactions shifted very clearly from negative to positive with increasing stress. Salt-sensitive genotypes were less negatively affected by competition but more dependent on facilitation than were wild-types, indicating a tradeoff between competitive ability and stress tolerance. Surprisingly, sensitive genotypes imposed stronger facilitative effects, despite being much smaller under stress, probably because they retrieved more salt from the soil. Stress tolerance defined facilitative effect and response via distinct mechanisms. We advocate more controlled experiments with model species to advance our understanding of the trait dependence of biotic interactions and their consequences for community organization.

Understanding Electrocatalytic Hydrodechlorination of Chlorophenols on Palladium-Modified Cathode in Aqueous Solution.

This work aimed at investigating electrocatalytic hydrodechlorination (ECH) mechanisms of chlorophenols (CPs) on a Pd-modified cathode. Experiments on the ECH of 2,4-dichlorophenol were conducted under extreme test conditions, i.e., with various buffer solutions and several sodium salt solutions as supporting electrolytes. Buffer solutions promote dechlorination due to their property of retarding the alkalinity of a solution. ECH was found to be significantly inhibited by sulfite. Experimental results showed that sulfite poisoning on Pd catalysts was reversible. Protonation may account, at least in part, for the observed high pH dependency of ECH, which proceeded rapidly, with lower apparent activation energy (E a) in the acidic electrolyte. In addition, pH influenced the selectivity of dechlorination of CPs. It was inferred that the ECH of CPs on the Pd-modified electrode was a preactivated electrocatalytic reaction.

Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process.

Quantifying the drivers underlying the distribution of biodiversity during succession is a critical issue in ecology and conservation, and also can provide insights into the mechanisms of community assembly. Ninety plots were established in the Loess Plateau region of northern Shaanxi in China. The taxonomic and phylogenetic (alpha and beta) diversity were quantified within six succession stages. Null models were used to test whether phylogenetic distance observed differed from random expectations. Taxonomic beta diversity did not show a regular pattern, while phylogenetic beta diversity decreased throughout succession. The shrub stage occurred as a transition from phylogenetic overdispersion to clustering either for NRI (Net Relatedness Index) or betaNRI. The betaNTI (Nearest Taxon Index) values for early stages were on average phylogenetically random, but for the betaNRI analyses, these stages were phylogenetically overdispersed. Assembly of woody plants differed from that of herbaceous plants during late community succession. We suggest that deterministic and stochastic processes respectively play a role in different aspects of community phylogenetic structure for early succession stage, and that community composition of late succession stage is governed by a deterministic process. In conclusion, the long-lasting evolutionary imprints on the present-day composition of communities arrayed along the succession gradient.

Plant functional traits suggest a change in novel ecological strategies for dominant species in the stages of forest succession.

In forest succession, the ecological strategies of the dominant species that are based on functional traits are important in the determination of both the mechanisms and the potential directions of succession. Thirty-one plots were established in the Loess Plateau region of northern Shaanxi in China. Fifteen leaf traits were measured for the 31 dominant species that represented the six stages of succession, and the traits included four that were related to morphology, seven to stoichiometry and four to physiological ecology. The species from the different successional stages had different patterns of distribution of the traits, and different key traits predicted the turnover of the species during succession. The ash and the cellulose contents were key regulatory factors of species turnover in the early successional communities, and the trait niche forces in sugar and leaf dry mass content might become more important with the progression of succession. When only the three herb stages were considered, a progressive replacement of the ruderal by the competitive-ruderal species occurred in the intermediate stages of succession, which was followed by the stress-tolerant-competitive or the competitive-stress tolerant-ruderal strategists late in the succession. Thus, the different species that occurred in the different stages of succession shared different trait-based ecological strategies. Additionally, these differences occurred concomitantly with a shift toward competitive-stress tolerant-ruderal strategies.

Decolorization characteristics of a newly isolated salt-tolerant Bacillus sp. strain and its application for azo dye-containing wastewater in immobilized form.

Strain CICC 23870 capable of decolorization of various azo dyes under high saline conditions was isolated from saline-alkali soil. The oxygen-insensitive azoreductase in crude extracts exhibited a wide substrate adaptively in the presence of NADH as a cofactor. The decolorization process by free cells followed first-order kinetics, with a high Methyl Orange (MO) tolerance concentration up to 100 mg l(-1) estimated by Haldane model. The average decolorization rate of free cell system was 26.30 mg g(-1) h(-1) at initial MO concentration of 32.7 mg l(-1). However, the values for the systems of immobilized cells (4 mm) in alginate, alginate and nano-TiO2, and alginate and powered activated carbon (PAC) were 6.83, 4.64, and 11.34 mg g(-1) h(-1), respectively. The effective diffusion factors in the tree different matrices were calculated by diffusion-based mathematic model. The diffusion step controls the overall decolorization rate, and the effective diffusion coefficients varied with internal structure of the bead matrices. The diffusion coefficients were increased from 4.98 × 10(-9) to 2.25 × 10(-8) cm(2) s(-1) when PAC was added, but decreased to 6.62 × 10(-10) cm(2) s(-1) when nano-TiO2 was added. The immobilized matrices could be reused for at least three cycles but with a decreased decolorization rate, possibly due to the breakage of beads at the end of each cycle, which led to the loss of immobilized bacteria.

Exploiting topic modeling to boost metagenomic reads binning.

BACKGROUND: With the rapid development of high-throughput technologies, researchers can sequence the whole metagenome of a microbial community sampled directly from the environment. The assignment of these metagenomic reads into different species or taxonomical classes is a vital step for metagenomic analysis, which is referred to as binning of metagenomic data. RESULTS: In this paper, we propose a new method TM-MCluster for binning metagenomic reads. First, we represent each metagenomic read as a set of "k-mers" with their frequencies occurring in the read. Then, we employ a probabilistic topic model -- the Latent Dirichlet Allocation (LDA) model to the reads, which generates a number of hidden "topics" such that each read can be represented by a distribution vector of the generated topics. Finally, as in the MCluster method, we apply SKWIC -- a variant of the classical K-means algorithm with automatic feature weighting mechanism to cluster these reads represented by topic distributions. CONCLUSIONS: Experiments show that the new method TM-MCluster outperforms major existing methods, including AbundanceBin, MetaCluster 3.0/5.0 and MCluster. This result indicates that the exploitation of topic modeling can effectively improve the binning performance of metagenomic reads.

Phytotoxicity of ZnO nanoparticles and the released Zn(II) ion to corn (Zea mays L.) and cucumber (Cucumis sativus L.) during germination.

Toxicity of engineered nanoparticles on organisms is of concern worldwide due to their extensive use and unique properties. The impacts of ZnO nanoparticles (ZnO NPs) on seed germination and root elongation of corn (Zea mays L.) and cucumber (Cucumis sativus L.) were investigated in this study. The role of seed coats of corn in the mitigation toxicity of nanoparticles was also evaluated. ZnO NPs (1,000 mg L(-1)) reduced root length of corn and cucumber by 17 % (p < 0.05) and 51 % (p < 0.05), respectively, but exhibited no effects on germination. In comparison with Zn(2+), toxicity of ZnO NPs on the root elongation of corn could be attributed to the nanoparticulate ZnO, while released Zn ion from ZnO could solely contribute to the inhibition of root elongation of cucumber. Zn uptake in corn exposed to ZnO NPs during germination was much higher than that in corn exposed to Zn(2+), whereas Zn uptake in cucumber was significantly correlated with soluble Zn in suspension. It could be inferred that Zn was taken up by corn and cucumber mainly in the form of ZnO NPs and soluble Zn, respectively. Transmission electron microscope confirmed the uptake of ZnO NPs into root of corn. Although isolation of the seed coats might not be the principal factor that achieved avoidance from toxicity on germination, seed coats of corn were found to mitigate the toxicity of ZnO NPs on root elongation and prevent approximately half of the Zn from entering into root and endosperm.

Nitric oxide is involved in integration of UV-B absorbing compounds among parts of clonal plants under a heterogeneous UV-B environment.

In nature, ultraviolet-B (UV-B) radiation is highly heterogeneous, both spatially and temporally. Plants exposed to UV-B radiation produce UV-B absorbing compounds that function as a protective filter. For clonal plants under heterogeneous UV-B radiation conditions, integration among ramets can allow irradiated ramets to benefit un-irradiated ramets by causing them to increase their UV-B absorbing compounds content. In this study, we evaluated integration between pairs of clonal ramets of Glechoma longituba under heterogeneous or homogeneous UV-B conditions. We determined the levels of UV-B absorbing compounds, nitric oxide (NO) and hydrogen peroxide (H2 O2 ) and measured the activity of phenylalanine ammonia-lyase (PAL) in connected ramet pairs under homogeneous or heterogeneous UV-B conditions. Under heterogeneous UV-B conditions, the UV-B absorbing compounds content increased in leaves of irradiated and un-irradiated ramets, but not in the connecting stolons. The NO content increased in irradiated and un-irradiated leaves and stolons, but the H2 O2 content did not. Application of NO synthesis inhibitors and an NO blocker to irradiated ramets blocked the increase in UV-B absorbing compounds and PAL activity in un-irradiated ramets. These results suggested that NO is involved in the integration process for UV-B absorbing compounds among ramets. Our findings suggested that a UV-B-induced increase in NO transmits a signal to un-irradiated ramets via the stolon, leading to an increase in PAL activity and UV-B absorbing compounds content. The internal translocation of signal enables members of clonal networks to function as a whole unit and to mount an efficient defensive response to localized UV-B radiation.

A comparative evaluation on prediction methods of nucleosome positioning.

Nucleosome positioning plays an essential role in cellular processes by modulating accessibility of DNA to proteins. Many computational models have been developed to predict genome-wide nucleosome positions from DNA sequences. Comparative analysis of predicted and experimental nucleosome positioning maps facilitates understanding the regulatory mechanisms of transcription and DNA replication. Therefore, a comprehensive evaluation of existing computational methods is important and useful for biologists to choose appropriate ones in their research. In this article, we carried out a performance comparison among eight widely used computational methods on four species including yeast, fruitfly, mouse and human. In particular, we compared these methods on different regions of each species such as gene sequences, promoters and 5'UTR exons. The experimental results show that the performances of the two latest versions of the thermodynamic model are relatively steadier than the other four methods. Moreover, these methods are workable on four species, but their performances decrease gradually from yeast to human, indicating that the fundamental mechanism of nucleosome positioning is conserved through the evolution process, but more and more factors participate in the determination of nucleosome positions, which leads to sophisticated regulation mechanisms.