The environmental fate of organic pollutants through the global microbial metabolism

The production of new chemicals for industrial or therapeutic applications exceeds our ability to generate experimental data on their biological fate once they are released into the environment. Typically, mixtures of organic pollutants are freed into a variety of sites inhabited by diverse microorganisms, which structure complex multispecies metabolic networks. A machine learning approach has been instrumental to expose a correlation between the frequency of 149 atomic triads (chemotopes) common in organo-chemical compounds and the global capacity of microorganisms to metabolise them. Depending on the type of environmental fate defined, the system can correctly predict the biodegradative outcome for 73–87% of compounds. This system is available to the community as a web server (http://www.pdg.cnb.uam.es/BDPSERVER). The application of this predictive tool to chemical species released into the environment provides an early instrument for tentatively classifying the compounds as biodegradable or recalcitrant. Automated surveys of lists of industrial chemicals currently employed in large quantities revealed that herbicides are the group of functional molecules more difficult to recycle into the biosphere through the inclusive microbial metabolism

Structure of a Novel Shoulder-to-Shoulder p24 Dimer in Complex with the Broad-Spectrum Antibody A10F9 and Its Implication in Capsid Assembly

10.1371/journal.pone.0061314PLoS ONE84

Development of Photonic Crystal Fiber Based Gas/ Chemical Sensors

The development of highly-sensitive and miniaturized sensors that capable of real-time analytes detection is highly desirable. Nowadays, toxic or colorless gas detection, air pollution monitoring, harmful chemical, pressure, strain, humidity, and temperature sensors based on photonic crystal fiber (PCF) are increasing rapidly due to its compact structure, fast response and efficient light controlling capabilities. The propagating light through the PCF can be controlled by varying the structural parameters and core-cladding materials, as a result, evanescent field can be enhanced significantly which is the main component of the PCF based gas/chemical sensors. The aim of this chapter is to (1) describe the principle operation of PCF based gas/ chemical sensors, (2) discuss the important PCF properties for optical sensors, (3) extensively discuss the different types of microstructured optical fiber based gas/ chemical sensors, (4) study the effects of different core-cladding shapes, and fiber background materials on sensing performance, and (5) highlight the main challenges of PCF based gas/ chemical sensors and possible solutions

Water Solubilization Using Nonionic Surfactants from Renewable Sources in Microemulsion Systems

In this study the effect of temperature, NaCl and oils (hydrocarbons: C8–C16) on the formation and solubilization capacity of the systems of oil/monoacylglycerols (MAG):ethoxylated fatty alcohols (CEO20)/propylene glycol (PG)/water was investigated. The effects of the surfactant mixture on the phase behavior and the concentration of water or oil in the systems were studied at three temperatures (50, 55, 60 °C) and with varied NaCl solutions (0.5; 2; 11%). Electrical conductivity measurement, FTIR spectroscopy and the DSC method were applied to determine the structure and type of the microemulsions formed. The dimension of the microemulsion droplets was characterized by dynamic light scattering. It has been stated that the concentration of CEO20 has a strong influence on the shape and extent of the microemulsion areas. Addition of a nonionic surfactant to the mixture with MAG promotes an increase in the area of microemulsion formation in the phase diagrams, and these areas of isotropic region did not change considerably depending on the temperature, NaCl solution and oil type. It was found that, depending on the concentration of the surfactant mixture, it was possible to obtain U-type microemulsions with dispersed particles size distribution ranging from 25 to 50 nm and consisting of about 30–32% of the water phase in the systems. The conditions under which the microemulsion region was found (electrolyte and temperature—insensitive, comparatively low oil and surfactant concentration) could be highly useful in detergency

Transient Protein-Protein Interaction of the SH3-Peptide Complex via Closely Located Multiple Binding Sites

Protein-protein interactions play an essential role in cellular processes. Certain proteins form stable complexes with their partner proteins, whereas others function by forming transient complexes. The conventional protein-protein interaction model describes an interaction between two proteins under the assumption that a protein binds to its partner protein through a single binding site. In this study, we improved the conventional interaction model by developing a Multiple-Site (MS) model in which a protein binds to its partner protein through closely located multiple binding sites on a surface of the partner protein by transiently docking at each binding site with individual binding free energies. To test this model, we used the protein-protein interaction mediated by Src homology 3 (SH3) domains. SH3 domains recognize their partners via a weak, transient interaction and are therefore promiscuous in nature. Because the MS model requires large amounts of data compared with the conventional interaction model, we used experimental data from the positionally addressable syntheses of peptides on cellulose membranes (SPOT-synthesis) technique. From the analysis of the experimental data, individual binding free energies for each binding site of peptides were extracted. A comparison of the individual binding free energies from the analysis with those from atomistic force fields gave a correlation coefficient of 0.66. Furthermore, application of the MS model to 10 SH3 domains lowers the prediction error by up to 9% compared with the conventional interaction model. This improvement in prediction originates from a more realistic description of complex formation than the conventional interaction model. The results suggested that, in many cases, SH3 domains increased the protein complex population through multiple binding sites of their partner proteins. Our study indicates that the consideration of general complex formation is important for the accurate description of protein complex formation, and especially for those of weak or transient protein complexes

Socioeconomic status and non-fatal injuries among Canadian adolescents: variations across SES and injury measures

BACKGROUND: While research to date has consistently demonstrated that socioeconomic status (SES) is inversely associated with injury mortality in both children and adults, findings have been less consistent for non-fatal injuries. The literature addressing SES and injury morbidity among adolescents has been particularly inconclusive. To explore potential explanations for these discrepant research findings, this study uniquely compared the relationship across different measures of SES and different causes of injury (recreation versus non-recreation injuries) within a sample of Canadian adolescents. METHODS: The sample included adolescent participants (aged 12 to 19 years) in the Canadian 1996–1997 cross-sectional National Population Health Survey (n = 6967). Five SES measures (household income, two neighbourhood-level proxy measures, two parental indicators) were examined in relation to three injury outcomes (total, recreation, and non-recreation injuries) using multivariable logistic regression. RESULTS: Among males, a clear relationship with injury was observed only for a parental SES index, which was positively associated with total and recreation injuries (odds ratios for the highest versus lowest SES category of 1.9 for total and 2.5 for recreation injuries). Among females, there was some evidence of a positive relationship between SES and injuries, particularly for a neighbourhood-level education measure with total and recreation injuries (odds ratios of 1.7 for total and 2.0 for recreation injuries). CONCLUSION: The results suggest that differences related to the measures of SES chosen and the causes of injury under study may both contribute to discrepancies in past research on SES and non-fatal injuries among adolescents. To clarify the potential SES-injury relationship among youth, the findings emphasize a need for a greater understanding of the meaning and relevance of different SES measures for adolescents, and for an exploration of the pathways through which SES may be related to injury risk

Diphenyl Difluoroketone: A Potent Chemotherapy Candidate for Human Hepatocellular Carcinoma

Diphenyl difluoroketone (EF24), a molecule having structural similarity to curcumin, was recently reported to inhibit proliferation of various cancer cells significantly. Here we try to determine the effect and mechanism of EF24 on hepatocellular carcinoma. 2 µM EF24 was found to inhibit the proliferation of PLC/PRF/5, Hep3B, HepG2, SK-HEP-1 and Huh 7 cell lines. However, even 8 µM EF24 treatment did not affect the proliferation of normal liver LO2 cells. Accordingly, 20 mg/kg/d EF24 inhibited the growth of the tumor xenografts conspicuously while causing no apparent change in liver, spleen or body weight. In addition, significant apoptosis and G2/M phase cell cycle arrest were found using flow cytometry. Besides, caspases and PARP activation and features typical of apoptosis including fragmented nuclei with condensed chromatin were also observed. Furthermore, the mechanism was targeted at the reduction of nuclear factor kappa b (NF-κB) pathway and the NF-κB–regulated gene products Bcl-2, COX-2, Cyclin B1. Our study has offered a strategy that EF24 being a therapeutic agent for hepatocellular carcinoma

Regulatory feedback response mechanisms to phosphate starvation in rice

Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding of the molecular mechanisms underlying phosphate uptake by investigating the transcriptional dynamics of two regulators: the Ubiquitin ligase PHO2 and the long non-coding RNA IPS1. Temporal measurements of RNA levels have been integrated into mechanistic mathematical models using advanced statistical techniques. Models based solely on current knowledge could not adequately explain the temporal expression profiles. Further modeling and bioinformatics analysis have led to the prediction of three regulatory features: the PHO2 protein mediates the degradation of its own transcriptional activator to maintain constant PHO2 mRNA levels; the binding affinity of the transcriptional activator of PHO2 is impaired by a phosphate-sensitive transcriptional repressor/inhibitor; and the extremely high levels of IPS1 and its rapid disappearance upon Pi re-supply are best explained by Pi-sensitive RNA protection. This work offers both new opportunities for plant phosphate research that will be essential for informing the development of phosphate efficient crop varieties, and a foundation for the development of models integrating phosphate with other stress responses

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT