Coordinated surface activities in Variovorax paradoxus EPS

<p>Abstract</p> <p>Background</p> <p><it>Variovorax paradoxus </it>is an aerobic soil bacterium frequently associated with important biodegradative processes in nature. Our group has cultivated a mucoid strain of <it>Variovorax paradoxus </it>for study as a model of bacterial development and response to environmental conditions. Colonies of this organism vary widely in appearance depending on agar plate type.</p> <p>Results</p> <p>Surface motility was observed on minimal defined agar plates with 0.5% agarose, similar in nature to swarming motility identified in <it>Pseudomonas aeruginosa </it>PAO1. We examined this motility under several culture conditions, including inhibition of flagellar motility using Congo Red. We demonstrated that the presence of a wetting agent, mineral, and nutrient content of the media altered the swarming phenotype. We also demonstrated that the wetting agent reduces the surface tension of the agar. We were able to directly observe the presence of the wetting agent in the presence and absence of Congo Red, and found that incubation in a humidified chamber inhibited the production of wetting agent, and also slowed the progression of the swarming colony. We observed that swarming was related to both carbon and nitrogen sources, as well as mineral salts base. The phosphate concentration of the mineral base was critical for growth and swarming on glucose, but not succinate. Swarming on other carbon sources was generally only observed using M9 salts mineral base. Rapid swarming was observed on malic acid, d-sorbitol, casamino acids, and succinate. Swarming at a lower but still detectable rate was observed on glucose and sucrose, with weak swarming on maltose. Nitrogen source tests using succinate as carbon source demonstrated two distinct forms of swarming, with very different macroscopic swarm characteristics. Rapid swarming was observed when ammonium ion was provided as nitrogen source, as well as when histidine, tryptophan, or glycine was provided. Slower swarming was observed with methionine, arginine, or tyrosine. Large effects of mineral content on swarming were seen with tyrosine and methionine as nitrogen sources. Biofilms form readily under various culture circumstances, and show wide variance in structure under different conditions. The amount of biofilm as measured by crystal violet retention was dependent on carbon source, but not nitrogen source. Filamentous growth in the biofilm depends on shear stress, and is enhanced by continuous input of nutrients in chemostat culture.</p> <p>Conclusion</p> <p>Our studies have established that the beta-proteobacterium <it>Variovorax paradoxus </it>displays a number of distinct physiologies when grown on surfaces, indicative of a complex response to several growth parameters. We have identified a number of factors that drive sessile and motile surface phenotypes. This work forms a basis for future studies using this genetically tractable soil bacterium to study the regulation of microbial development on surfaces.</p

Phosphorus and Nitrogen Transport in the Binational Great Lakes Basin Estimated Using SPARROW Watershed Models

AbstractEutrophication problems in the Great Lakes are caused by excessive nutrient inputs (primarily phosphorus, P, and nitrogen, N) from various sources throughout its basin. In developing protection and restoration plans, it is important to know where and from what sources the nutrients originate. As part of a binational effort, Midcontinent SPARROW (SPAtially Referenced Regression On Watershed attributes) models were developed and used to estimate P and N loading from throughout the entire basin based on nutrient inputs similar to 2002; previous SPARROW models only estimated U.S. contributions. The new models have a higher resolution (~2‐km2 catchments) enabling improved descriptions of where nutrients originate and the sources at various spatial scales. The models were developed using harmonized geospatial datasets describing the stream network, nutrient sources, and environmental characteristics affecting P and N delivery. The models were calibrated using loads from sites estimated with ratio estimator and regression techniques and additional statistical approaches to reduce spatial correlation in the residuals and have all monitoring sites equally influence model development. SPARROW results, along with interlake transfers and direct atmospheric inputs, were used to quantify the entire P and N input to each lake and describe the importance of each nutrient source. Model results can be used to compare loading and yields from various tributaries and jurisdictions

Biopolymer additives to reduce erosion-induced soil losses during irrigation

A series of biopolymers added to irrigation water were tested for their efficacy in reducing shear-induced erosion in a laboratory-scale mini-furrow. Suspensions of chitosan, starch xanthate, cellulose xanthate, and acid-hydrolyzed cellulose microfibrils, at concentrations of 20, 80, 80, and 120 ppm, respectively, reduced suspended solids by more than 80%. None of these biopolymers, however, exhibited the > 90% runoff sediment reduction shown by the present industry standard, synthetic polyacrylamide polymers, PAM. PAM is effective at concentrations as low as 5 ppm. In field tests, chitosan solutions were only marginally effective in reducing runoff from the end of a 137 m long furrow, with indications that results were dependent on the length of the furrow. Sediment runoff of some clay-rich Northern California soils was reduced by up to 85% by increasing the concentration of exchangeable calcium to > 2.5mM. Calcium improved the sedimentation of the polyelectrolytic polymers in this study

Polymer additives in irrigation water to reduce erosion and better manage water infiltration

Water-soluble polyacrylamide (PAM) was identified as an environmentally safe and highly effective erosion preventing and infiltration-enhancing polymer when applied in furrow irrigation water at 1-10 g m-3, i.e. 1-10 ppm. The agricultural use of polyacrylamide, PAM, as an additive in irrigation water has grown rapidly since commercial introduction in 1995 because it improves water infiltration and reduces erosion-induced soil losses up to 97%, saving tons of topsoil per hectare per year. Various polymers and biopolymers have long been recognized as viable soil conditioners because they stabilize soil surface structure and pore continuity. The new strategy of adding the conditioner, high molecular weight anionic PAM, to the irrigation water in the first several hours of irrigation enables a significant costs savings over traditional application methods of tilling soil conditoner into the entire (15 cm deep) soil surface layer. By adding PAM to the irrigation water, soil structure is Unproved in the all-important 1-5 mm thick layer at the soil/water interface of the 25 to 30% of field surface contacted by flowing water. Recent studies with biopolymers such as chitosan, charged polysaccharides, whey, and industrial cellulose derivatives show potential as biopolymer alternatives to PAM. Their success will depend on production economics

Long-range vibrational dynamics are directed by Watson-Crick base-pairing in duplex DNA

Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation leads to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. Based on observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramo-lecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single and double-stranded DNA

Preventing soil erosion with polymer additives

The agricultural use of polyacrylamide, PAM, as an additive in irrigation water has grown rapidly since commercial introduction in 1995, with over l million acres treated in 1998. PAM provides both economic and environmental benefits by improving water infiltration and reducing up to 98% of erosion-induced soil losses — a yearly saving of tons of topsoil per acre. With as little as 5 ppm of PAM in the first irrigation water to run across the field, soil cohesion increases enough to prevent particle detachment and erosion. Stable soil/polymer flocs result from PAM's high molecular weight (typically > 12 million) and its affinity to soil via coulombic and Van der Waals attraction. Although water soluble linear PAM is the only class of commercial polymer presently used to reduce erosion during irrigation, other polymer additives have shown some potential. Biopolymers such as chitosan, starch xanthate, cellulose xanthate, and acid-hydrolyzed cellulose microfibrils reduce shear-induced erosion; however concentrations at least 6-10 times higher than PAM are required to obtain the > 90% runoff sediment reduction shown by commercial PAM. The application of PAM in agricultural irrigation water and potential biopolymer alternatives to PAM are discusse

Antagonism of STAT3 signalling by Ebola virus

Many viruses target signal transducers and activators of transcription (STAT) 1 and 2 to antagonise antiviral interferon signalling, but targeting of signalling by other STATs/cytokines, including STAT3/interleukin 6 that regulate processes important to Ebola virus (EBOV) haemorrhagic fever, is poorly defined. We report that EBOV potently inhibits STAT3 responses to interleukin-6 family cytokines, and that this is mediated by the interferon-antagonist VP24. Mechanistic analysis indicates that VP24 effects a unique strategy combining distinct karyopherin-dependent and karyopherin-independent mechanisms to antagonise STAT3-STAT1 heterodimers and STAT3 homodimers, respectively. This appears to reflect distinct mechanisms of nuclear trafficking of the STAT3 complexes, revealed for the first time by our analysis of VP24 function. These findings are consistent with major roles for global inhibition of STAT3 signalling in EBOV infection, and provide new insights into the molecular mechanisms of STAT3 nuclear trafficking, significant to pathogen-host interactions, cell physiology and pathologies such as cancer

Wet scavenging of soluble gases in DC3 deep convective storms using WRF-Chem simulations and aircraft observations

We examine wet scavenging of soluble trace gases in storms observed during the Deep Convective Clouds and Chemistry (DC3) field campaign. We conduct high-resolution simulations with the Weather Research and Forecasting model with Chemistry (WRF-Chem) of a severe storm in Oklahoma. The model represents well the storm location, size, and structure as compared with Next Generation Weather Radar reflectivity, and simulated CO transport is consistent with aircraft observations. Scavenging efficiencies (SEs) between inflow and outflow of soluble species are calculated from aircraft measurements and model simulations. Using a simple wet scavenging scheme, we simulate the SE of each soluble species within the error bars of the observations. The simulated SEs of all species except nitric acid (HNO_3) are highly sensitive to the values specified for the fractions retained in ice when cloud water freezes. To reproduce the observations, we must assume zero ice retention for formaldehyde (CH_2O) and hydrogen peroxide (H_2O_2) and complete retention for methyl hydrogen peroxide (CH_3OOH) and sulfur dioxide (SO_2), likely to compensate for the lack of aqueous chemistry in the model. We then compare scavenging efficiencies among storms that formed in Alabama and northeast Colorado and the Oklahoma storm. Significant differences in SEs are seen among storms and species. More scavenging of HNO_3 and less removal of CH_3OOH are seen in storms with higher maximum flash rates, an indication of more graupel mass. Graupel is associated with mixed-phase scavenging and lightning production of nitrogen oxides (NO_x), processes that may explain the observed differences in HNO_3 and CH_3OOH scavenging

An analysis of fast photochemistry over high northern latitudes during spring and summer using in-situ observations from ARCTAS and TOPSE

Observations of chemical constituents and meteorological quantities obtained during the two Arctic phases of the airborne campaign ARCTAS (Arctic Research of the Composition of the Troposphere from Aircraft and Satellites) are analyzed using an observationally constrained steady state box model. Measurements of OH and HO2 from the Penn State ATHOS instrument are compared to model predictions. Forty percent of OH measurements below 2 km are at the limit of detection during the spring phase (ARCTAS-A). While the median observed-to-calculated ratio is near one, both the scatter of observations and the model uncertainty for OH are at the magnitude of ambient values. During the summer phase (ARCTAS-B), model predictions of OH are biased low relative to observations and demonstrate a high sensitivity to the level of uncertainty in NO observations. Predictions of HO2 using observed CH2O and H2O2 as model constraints are up to a factor of two larger than observed. A temperature-dependent terminal loss rate of HO2 to aerosol recently proposed in the literature is shown to be insufficient to reconcile these differences. A comparison of ARCTAS-A to the high latitude springtime portion of the 2000 TOPSE campaign (Tropospheric Ozone Production about the Spring Equinox) shows similar meteorological and chemical environments with the exception of peroxides; observations of H2O2 during ARCTAS-A were 2.5 to 3 times larger than those during TOPSE. The cause of this difference in peroxides remains unresolved and has important implications for the Arctic HOx budget. Unconstrained model predictions for both phases indicate photochemistry alone is unable to simultaneously sustain observed levels of CH2O and H2O2; however when the model is constrained with observed CH2O, H2O2 predictions from a range of rainout parameterizations bracket its observations. A mechanism suitable to explain observed concentrations of CH2O is uncertain. Free tropospheric observations of acetaldehyde (CH3CHO) are 2–3 times larger than its predictions, though constraint of the model to those observations is sufficient to account for less than half of the deficit in predicted CH2O. The box model calculates gross O3 formation during spring to maximize from 1–4 km at 0.8 ppbv d−1, in agreement with estimates from TOPSE, and a gross production of 2–4 ppbv d−1 in the boundary layer and upper troposphere during summer. Use of the lower observed levels of HO2 in place of model predictions decreases the gross production by 25–50%. Net O3 production is near zero throughout the ARCTAS-A troposphere, and is 1–2 ppbv in the boundary layer and upper altitudes during ARCTAS-B

Effect of oligomer length on vibrational coupling and energy relaxation in double-stranded DNA

The effect of oligomer length on the vibrational mode coupling and energy relaxation mechanisms of AT-rich DNA oligomers in double- and single-stranded conformations has been investigated using two-dimensional infrared spectroscopy. Vibrational coupling of modes of the DNA bases to the symmetric stretching vibration of the backb one phosphate group was observed for oligomers long enough to form duplex-DNA structures. The coupling was lost upon melting of the duplex. No significant effect of oligomer length or DNA secondary structure was found on either the timescale for vibrational relaxation of the base modes or the mechanism, which was consistent with a cascade process from base modes to intermediate modes, some of which are located on the deoxyribose group, and subsequently to the phosphate backbone. The study shows that vibrational coupling between base and backbone requires formation of the double-helix structure while vibrational energy management is an inherent property of the nucleotide