Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics

Background: Chitosan oligosaccharide (COS), a deacetylated derivative of chitin, is an abundant, and renewable natural polymer. COS has higher antimicrobial properties than chitosan and is presumed to act by disrupting/permeabilizing the cell membranes of bacteria, yeast and fungi. COS is relatively non-toxic to mammals. By identifying the molecular and genetic targets of COS, we hope to gain a better understanding of the antifungal mode of action of COS. Results: Three different chemogenomic fitness assays, haploinsufficiency (HIP), homozygous deletion (HOP), and multicopy suppression (MSP) profiling were combined with a transcriptomic analysis to gain insight in to the mode of action and mechanisms of resistance to chitosan oligosaccharides. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified are involved in processes such as RNA biology (transcription, translation and regulatory mechanisms), membrane functions (e.g. signalling, transport and targeting), membrane structural components, cell division, and proteasome processes. The transcriptomes of control wild type and 5 suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the Ras signal transduction pathway. Down-regulated transcripts included those encoding protein folding components and respiratory chain proteins. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and pre-treatment with these well characterized environmental stressors provided little or any resistance to COS. Conclusions: Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to Amphotericin B, Fluconazole and Terbinafine as the wild type cells and that when COS and Fluconazole are used in combination they act in a synergistic fashion. The gene targets of COS identified in this study indicate that COS’s mechanism of action is different from other commonly studied fungicides that target membranes, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens.

Spatiotemporal characteristics of the Huangtupo landslide in the Three Gorges region (China) constrained by radar interferometry

The Huangtupo landslide is one of the largest in the Three Gorges region, China. The county-seat town of Badong, located on the south shore between the Xiling and Wu gorges of the Yangtze River, was moved to this unstable slope prior to the construction of the Three Gorges Project, since the new Three Gorges reservoir completely submerged the location of the old city. The instability of the slope is affecting the new town by causing residential safety problems. The Huangtupo landslide provides scientists an opportunity to understand landslide response to fluctuating river water level and heavy rainfall episodes, which is essential to decide upon appropriate remediation measures. Interferometric Synthetic Aperture Radar (InSAR) techniques provide a very useful tool for the study of superficial and spatially variable displacement phenomena. In this paper, three sets of radar data have been processed to investigate the Huangtupo landslide. Results show that maximum displacements are affecting the northwest zone of the slope corresponding to Riverside slumping mass I#. The other main landslide bodies (i.e. Riverside slumping mass II#, Substation landslide and Garden Spot landslide) exhibit a stable behaviour in agreement with in situ data, although some active areas have been recognized in the foot of the Substation landslide and Garden Spot landslide. InSAR has allowed us to study the kinematic behaviour of the landslide and to identify its active boundaries. Furthermore, the analysis of the InSAR displacement time-series has helped recognize the different displacement patterns on the slope and their relationships with various triggering factors. For those persistent scatterers, which exhibit long-term displacements, they can be decomposed into a creep model (controlled by geological conditions) and a superimposed recoverable term (dependent on external factors), which appears closely correlated with reservoir water level changes close to the river's edge. These results, combined with in situ data, provide a comprehensive analysis of the Huangtupo landslide, which is essential for its management.

Solubility, Density, Refractive Index, and Viscosity for the Polyhydric Alcohol + CsBr + H2O Ternary Systems at Different Temperatures

The solubility, density, refractive index, and viscosity data for the ethylene glycol + CsBr + H2O, 1,2-propanediol + CsBr + H2O, and glycerin + CsBr + H2O ternary systems have been determined at (288.15, 298.15, and 308.15) K. In all cases, the solubility of CsBr in aqueous solutions was decreased significantly due to the presence of polyhydric alcohol. The liquid–solid equilibrium experimental data were correlated using the NRTL (nonrandom two-liquid) activity coefficient model, considering nondissociation of the dissolved salt in the liquid phase, and new interaction parameters were estimated. The mean deviations between calculated and experimental compositions were low, showing the good descriptive quality and applicability of the NRTL model. The refractive indices, densities, and viscosities for the unsaturated solutions of the three ternary systems have also been measured at three temperatures. Values for all of the properties were correlated with the salt concentrations and proportions of polyhydric alcohol in the solutions.

Real-time monitoring of electrochemically active biofilm developing behavior on bioanode by using EQCM and ATR/FTIR

In the current study, the relationship between current and biomass and bio-adhesion mechanism of electrogenic biofilm on electrode were investigated using EQCM and ATR-SEIRAS linking electrochemistry. The results indicated that cellular biomass of biofilm on QCM-crystal surface showed maximum value of 6.0 μg/cm2 in initial batch and 11.5 μg/cm2 in the second batch on mature biofilm, producing a similar maximum current density of 110 μA/μg. Especially, the optimum cell biomass linking high electricity production ratio (110 μA/μg) occurred before maximum biomass coming, implying that over-growth mature biofilm is not an optimum state for enhancing power output of MFCs. On the other hand, the spectra using ATR-SEIRAS technique linking electrochemistry obviously exhibited water structure adsorption change at early biofilm formation and meanwhile the water adsorption accompanied the adsorbed bacteria and the bound cells population on the electrode increased with time. Meanwhile, the direct contact of bacteria and electrode via outer-membrane protein can be confirmed via a series spectra shift at amide I and amide II modes and water movement from negative bands displacing by adsorbed bacteria. Our study provided supplementary information about the interaction between the microbes and electrode beyond traditional electrochemistry.

Imaging Land Subsidence Induced by Groundwater Extraction in Beijing (China) Using Satellite Radar Interferometry

Beijing is one of the most water-stressed cities in the world. Due to over-exploitation of groundwater, the Beijing region has been suffering from land subsidence since 1935. In this study, the Small Baseline InSAR technique has been employed to process Envisat ASAR images acquired between 2003 and 2010 and TerraSAR-X stripmap images collected from 2010 to 2011 to investigate land subsidence in the Beijing region. The maximum subsidence is seen in the eastern part of Beijing with a rate greater than 100 mm/year. Comparisons between InSAR and GPS derived subsidence rates show an RMS difference of 2.94 mm/year with a mean of 2.41 ± 1.84 mm/year. In addition, a high correlation was observed between InSAR subsidence rate maps derived from two different datasets (i.e., Envisat and TerraSAR-X). These demonstrate once again that InSAR is a powerful tool for monitoring land subsidence. InSAR derived subsidence rate maps have allowed for a comprehensive spatio-temporal analysis to identify the main triggering factors of land subsidence. Some interesting relationships in terms of land subsidence were found with groundwater level, active faults, accumulated soft soil thickness and different aquifer types. Furthermore, a relationship with the distances to pumping wells was also recognized in this work.

An updated evolutionary classification of CRISPR–Cas systems

The evolution of CRISPR–cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR–cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR–Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.