The Dynamics of Conjunctive and Disjunctive Boolean Network Models

For many biological networks, the topology of the network constrains its dynamics. In particular, feedback loops play a crucial role. The results in this paper quantify the constraints that (unsigned) feedback loops exert on the dynamics of a class of discrete models for gene regulatory networks. Conjunctive (resp. disjunctive) Boolean networks, obtained by using only the AND (resp. OR) operator, comprise a subclass of networks that consist of canalyzing functions, used to describe many published gene regulation mechanisms. For the study of feedback loops, it is common to decompose the wiring diagram into linked components each of which is strongly connected. It is shown that for conjunctive Boolean networks with strongly connected wiring diagram, the feedback loop structure completely determines the long-term dynamics of the network. A formula is established for the precise number of limit cycles of a given length, and it is determined which limit cycle lengths can appear. For general wiring diagrams, the situation is much more complicated, as feedback loops in one strongly connected component can influence the feedback loops in other components. This paper provides a sharp lower bound and an upper bound on the number of limit cycles of a given length, in terms of properties of the partially ordered set of strongly connected components.     

Timing of propagule release significantly alters the deposition area of resulting aerial dispersal

Aim The aim of this study is to determine whether changes to the seasonal and circadian timing of propagule release can a have a significant effect on the area covered by resulting aerial dispersal. Location Western Australia. Methods Using the atmospheric pollution model (TAPM), an existing meso‐scale dispersal model, a range of release patterns was simulated and the resulting deposition compared. Comparisons were based on observations of deposition patterns and the calculated area of deposition. Results Small changes to the timing of propagule release were shown to significantly impact on the area experiencing deposition from the resulting aerial dispersal. Main conclusions Simulations performed in this study show that, for small propagules, changes to the timing of release can lead to alternate, clearly differentiable dispersal events. Small changes in both the seasonal and circadian patterns of release can have significant effects on the area that experiences deposition during the resulting dispersal event. This effect is particularly important at the landscape scale and when there is a need to quantify individual dispersal events. Predictive modelling of aerial dispersal needs to be undertaken with an understanding of the manner in which biological and environmental factors that affect the timing of propagule release can influence results. Results presented highlight the need to characterize the epidemiology of pathogenic organisms of importance to biosecurity as much as possible before they arrive.     

Identifying the functional groups and the influence of synthetic chelators on Cd availability and microbial biomass carbon in Cd-contaminated soil

Synthetic chelators play an important role in boosting the microbial biomass carbon (MBC), dissolved organic carbon (DOC), and heavy metal solubility in a contaminated soil toward a sustainability of environment for agricultural crops. Castor plant was grown under different levels of Cd contaminated soil (?Cd and +Cd) following adding three chelating agents, ethylenediaminetetraacetic acid (H₄EDTA), nitriloacetic acid (H₃ NTA), and NH₄ citrate (ammonium citrate) to the soil at rates of 10, 15, and 25 mmol in 5 kg of soil per pot. The highest bioavailable Cd concentrations in soil and castor plant were obtained from NH₄ citrate and H₄EDTA treatments in the contaminated soil. Fourier transform infrared (FTIR) analysis showed that NH₄ citrate was the most effective chelator in Cd-contaminated soil. MBC and DOC contents were significantly increased and reached at 81.98–80.37 and 1.96–1.90 mg kg^?1 respectively, in the (H₃ NTA) and NH₄ citrate treatments in Cd-contaminated soil. Further research is needed to investigate the use of chelators in the phytoextraction of Cd-contaminated soils under field conditions and whether it may be beneficial in accelerating the phytoextraction of Cd through hyperaccumulating plants.     

The potency of lemon (Citrus limon L.) essential oil to control some fungal diseases of grapevine wood

This study aimed to evaluate the in vitro antifungal activity (AA) of the essential oil (EO) of lemon (Citrus limon L.) against three pathogenic fungi attacking grapevine wood. The composition of the EO was also studied. Ten volatile components were identified by gas chromatography–mass spectrometry. The results showed that the EO consists of volatile components where monoterpene hydrocarbons are the most abundant ones. Four major components were identified, which represent 99.9% of the total EO (limonene, neral, ß-pinene, and ?-terpinene). The AA of the EO was evaluated against three pathogenic fungi attacking grapevine wood (Eutypa sp., Botryosphaeria dothidea, and Fomitiporia mediterranea). The results showed that the EO exerts AA against all tested fungi and significantly inhibits their growth. Eutypa sp. is the most sensitive fungus. These results show, for the first time, a new use for the EO of lemon (C. limon L.) to control fungal diseases of grapevine wood.     

MPK9 and MPK12 function in SA-induced stomatal closure in Arabidopsis thaliana

Salicylic acid (SA) induces stomatal closure sharing several components with abscisic acid (ABA) and methyl jasmonate (MeJA) signaling. We have previously shown that two guard cell-preferential mitogen-activated protein kinases (MAPKs), MPK9 and MPK12, positively regulate ABA signaling and MeJA signaling in Arabidopsis thaliana. In this study, we examined whether these two MAPKs are involved in SA-induced stomatal closure using genetic mutants and a pharmacological, MAPKK inhibitor. Salicylic acid induced stomatal closure in mpk9 and mpk12 single mutants but not in mpk9 mpk12 double mutants. The MAPKK inhibitor PD98059 inhibited SA-induced stomatal closure in wild-type plants. Salicylic acid induced extracellular reactive oxygen species (ROS) production, intracellular ROS accumulation, and cytosolic alkalization in the mpk9, mpk12, and mpk9 mpk12 mutants. Moreover, SA-activated S-type anion channels in guard cells of wild-type plants but not in guard cells of mpk9 mpk12 double mutants. These results imply that MPK9 and MPK12 are positive regulators of SA signaling in Arabidopsis guard cells.     

Potato bacterial wilt suppression and plant health improvement after application of different antioxidants

Bacterial wilt caused by Ralstonia solanacearum is a devastating disease that often threatens potato production and exportation. The potential of four antioxidants (seaweed extract (SWE), yeast, chitosan and ascorbic acid (ASA)) in controlling the disease was evaluated in vitro, under glasshouse and field conditions. The field experiment was conducted in two naturally infested locations: Wardan, Giza (sandy soil), and Talia, Minufiya (silty clay soil). Only chitosan showed antibacterial properties against the pathogen in vitro. SWE, yeast and chitosan showed disease suppression under both glasshouse and field conditions. The disease suppression was accompanied by an increase in the ratio of soil copiotrophic to oligotrophic bacteria. The three antioxidants increased plant nitrogen content, decreased soil OM content and decreased C/N ratio. Disease suppression after chitosan application was clearly observed only in Wardan area, which was characterized by a higher soil alkalinity. A high percentage of antagonistic fluorescent strains similar to Pseudomonas putida group were detected for chitosan‐treated plants in Wardan area (sandy soil). ASA drastically decreased the count of the pathogen in soil, but was conducive to the pathogen in plant tissues. A remarkable increase in microbial (bacterial and fungal) soil and rhizosphere diversity as indicated by PCR‐DGGE analysis for bacterial 16S rRNA and fungal 18S rRNA was recorded. In Talia area (silty clay soil), the soil microbial community was more stable and was in general resistant to the disease where the soils were characterized by high electrical conductivity. SWE, yeast and ASA significantly increased crop production in Talia area only.     

<Emphasis Type="Italic">Rubricella aquisinus</Emphasis> gen. nov., sp. nov., a novel member of the family <Emphasis Type="Italic">Rhodobacteraceae</Emphasis>

A Gram-stain negative, ovoid or short rod-shaped, aerobic and non-motile bacterial strain, designated J82^T, was isolated from a seawater sample collected from the coast of Yellow Sea in Qingdao, China. The strain grew at salinities of 1.0–6.0% (w/v) NaCl (optimum, 2.5%). Growth occurred at pH 6.0-8.0 (optimum, pH 7.0) and 10–42 °C (optimum, 28–30 °C). The genomic DNA G + C content was determined to be 57.5 mol%. Q-10 was detected as the respiratory quinone. The major fatty acid (>10%) was Summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). The polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and two unidentified polar lipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain J82^T forms a distinct evolutionary lineage within the family Rhodobacteraceae. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, the strain merits recognition as representative of a novel genus and species within the family Rhodobacteraceae for which the name Rubricella aquisinus gen. nov., sp. nov. is proposed. The type strain of Rubricella aquisinus is J82^T (= DSM 103377^T = CCTCC AB 2016170^T).     

Presaging Critical Residues in Protein interfaces-Web Server (PCRPi-W): A Web Server to Chart Hot Spots in Protein Interfaces

Background

It is well established that only a portion of residues that mediate protein-protein interactions (PPIs), the so-called hot spot, contributes the most to the total binding energy, and thus its identification is an important and relevant question that has clear applications in drug discovery and protein design. The experimental identification of hot spots is however a lengthy and costly process, and thus there is an interest in computational tools that can complement and guide experimental efforts.

Principal Findings

Here, we present Presaging Critical Residues in Protein interfaces-Web server (http://www.bioinsilico.org/PCRPi), a web server that implements a recently described and highly accurate computational tool designed to predict critical residues in protein interfaces: PCRPi. PRCPi depends on the integration of structural, energetic, and evolutionary-based measures by using Bayesian Networks (BNs).

Conclusions

PCRPi-W has been designed to provide an easy and convenient access to the broad scientific community. Predictions are readily available for download or presented in a web page that includes among other information links to relevant files, sequence information, and a Jmol applet to visualize and analyze the predictions in the context of the protein structure.