Electrostatic Energetics of Bacillus subtilis Ribonuclease P Protein Determined by Nuclear Magnetic Resonance-Based Histidine pKa Measurements.

The pKa values of ionizable groups in proteins report the free energy of site-specific proton binding and provide a direct means of studying pH-dependent stability. We measured histidine pKa values (H3, H22, and H105) in the unfolded (U), intermediate (I), and sulfate-bound folded (F) states of RNase P protein, using an efficient and accurate nuclear magnetic resonance-monitored titration approach that utilizes internal reference compounds and a parametric fitting method. The three histidines in the sulfate-bound folded protein have pKa values depressed by 0.21 ± 0.01, 0.49 ± 0.01, and 1.00 ± 0.01 units, respectively, relative to that of the model compound N-acetyl-l-histidine methylamide. In the unliganded and unfolded protein, the pKa values are depressed relative to that of the model compound by 0.73 ± 0.02, 0.45 ± 0.02, and 0.68 ± 0.02 units, respectively. Above pH 5.5, H22 displays a separate resonance, which we have assigned to I, whose apparent pKa value is depressed by 1.03 ± 0.25 units, which is ∼0.5 units more than in either U or F. The depressed pKa values we observe are consistent with repulsive interactions between protonated histidine side chains and the net positive charge of the protein. However, the pKa differences between F and U are small for all three histidines, and they have little ionic strength dependence in F. Taken together, these observations suggest that unfavorable electrostatics alone do not account for the fact that RNase P protein is intrinsically unfolded in the absence of ligand. Multiple factors encoded in the P protein sequence account for its IUP property, which may play an important role in its function.

Contribution of bacterial outer membrane vesicles to innate bacterial defense.

BACKGROUND: Outer membrane vesicles (OMVs) are constitutively produced by Gram-negative bacteria throughout growth and have proposed roles in virulence, inflammation, and the response to envelope stress. Here we investigate outer membrane vesiculation as a bacterial mechanism for immediate short-term protection against outer membrane acting stressors. Antimicrobial peptides as well as bacteriophage were used to examine the effectiveness of OMV protection. RESULTS: We found that a hyper-vesiculating mutant of Escherichia coli survived treatment by antimicrobial peptides (AMPs) polymyxin B and colistin better than the wild-type. Supplementation of E. coli cultures with purified outer membrane vesicles provided substantial protection against AMPs, and AMPs significantly induced vesiculation. Vesicle-mediated protection and induction of vesiculation were also observed for a human pathogen, enterotoxigenic E. coli (ETEC), challenged with polymyxin B. When ETEC with was incubated with low concentrations of vesicles concomitant with polymyxin B treatment, bacterial survival increased immediately, and the culture gained resistance to polymyxin B. By contrast, high levels of vesicles also provided immediate protection but prevented acquisition of resistance. Co-incubation of T4 bacteriophage and OMVs showed fast, irreversible binding. The efficiency of T4 infection was significantly reduced by the formation of complexes with the OMVs. CONCLUSIONS: These data reveal a role for OMVs in contributing to innate bacterial defense by adsorption of antimicrobial peptides and bacteriophage. Given the increase in vesiculation in response to the antimicrobial peptides, and loss in efficiency of infection with the T4-OMV complex, we conclude that OMV production may be an important factor in neutralizing environmental agents that target the outer membrane of Gram-negative bacteria.

Geochemical and isotopic evidence for seawater contamination of the hydrothermal system of Taal volcano, Luzon, the Philippines

The hydrologic structure of Taal Volcano has favored development of an extensive hydrothermal system whose prominent feature is the acidic Main Crater Lake (pH<3) lying in the center of an active vent complex, which is surrounded by a slightly alkaline caldera lake (Lake Taal). This peculiar situation makes Taal prone to frequent, and sometimes catastrophic, hydrovolcanic eruptions. Fumaroles, hot springs, and lake waters were sampled in 1991, 1992, and 1995 in order to develop a geochemical model for the hydrothermal system. The low-temperature fumarole compositions indicate strong interaction of magmatic vapors with the hydrothermal system under relatively oxidizing conditions. The thermal waters consist of highly, moderately, and weakly mineralized solutions, but none of them corresponds to either water-rock equilibrium or rock dissolution. The concentrated discharges have high Na contents (>3500 mg/kg) and low SO4/Cl ratios (<0.3). The Br/Cl ratio of most samples suggests incorporation of seawater into the hydrothermal system. Water and dissolved sulfate isotopic compositions reveal that the Main Crater Lake and spring discharges are derived from a deep parent fluid (T≃300°C), which is a mixture of seawater, volcanic water, and Lake Taal water. The volcanic end member is probably produced in the magmatic-hydrothermal environment during absorption of high-temperature gases into groundwater. Boiling and mixing of the parent water give rise to the range of chemical and isotopic characteristics observed in the thermal discharges. Incursion of seawater from the coastal region to the central part of the volcano is supported by the low water levels of the lakes and by the fact that Lake Taal was directly connected to the China sea until the sixteenth century. The depth to the seawater-meteoric water interface is calculated to be 80 and 160 m for the Main Crater Lake and Lake Taal, respectively. Additional data are required to infer the hydrologic structure of Taal. Geochemical surveillance of the Main Crater Lake using the SO4/Cl, Na/K, or Mg/Cl ratio cannot be applied straightforwardly due to the presence of seawater in the hydrothermal system.

Evaluación de la fertilización con sulfato de magnesio durante el período de llenado en trigo duro (Trititicum durum) bajo riego

p.443-448

Chitosan derivatives alter release profiles of model compounds from calcium phosphate implants

The aim of the current study was to evaluate the impact of chitosan derivatives, namely N-octyl-chitosan and N-octyl-O-sulfate chitosan, incorporated in calcium phosphate implants to the release profiles of model drugs. The rate and extent of calcein (on M.W. 650 Da) ED, and FITC-dextran (M.W. 40 kDa) on in vitro release were monitored by fluorescence spectroscopy. Results show that calcein release is affected by the type of chitosan derivative used. A higher percentage of model drug was released when the hydrophilic polymer N-octyl-sulfated chitosan was present in the tablets compared with the tablets containing the hydrophobic polymer N-octyl-chitosan. The release profiles of calcein or FD from tablets containing N-octyl-O-sulfate revealed a complete release for FD after 120 h compared with calcein where 20% of the drug was released over the same time period. These results suggest that the difference in the release profiles observed from the implants is dependent on the molecular weight of the model drugs. These data indicate the potential of chitosan derivatives in controlling the release profile of active compounds from calcium phosphate implants. (C) 2009 Elsevier Ltd. All rights reserved.

Water transport in zinc oxy-chloride cements

The water uptake and water loss behaviour in three different formulations of zinc oxy-chloride cement have been studied in detail. Specimens of each material were subjected to a high humidity atmosphere (93% RH) over saturated aqueous sodium sulfate, and a low humidity desiccating atmosphere over concentrated sulfuric acid. In high humidity, the cement formulated from the nominal 75% ZnCl2 solutions gained mass, eventually becoming too sticky to weigh further. The specimens at 25% and 50% ZnCl2 by contrast lost mass by a diffusion process, though by 1 week the 50% cement had stated to gain mass and was also too sticky to weigh. In low humidity, all three cements lost mass, again by a diffusion process. Both water gain and water loss followed Fick's law for a considerable time. In the case of water loss under desiccating conditions, this corresponded to values of Mt/MĄ well above 0.5. However, plots did not go through the origin, showing that there was an induction period before true diffusion began. Diffusion coefficients varied from 1.56 x 10-5 (75% ZnCl2) to 2.75 x 10-5 cm2/s (50% ZnCl2), and appeared to be influenced not simply by composition. The drying of the 25% and 50% ZnCl2 cements in high humidity conditions occurred at a much lower rate, with a value of D of 2.5 x 10-8 cm2/s for the 25% ZnCl2 cement. This cement was found to equilibrate slowly, but total water loss did not differ significantly from that of the cements stored under desiccating conditions. Equilibration times for water loss in desiccating conditions were of the order of 2-4 hours, depending on ZnCl2 content; equilibrium water losses were respectively 28.8 [25% ZnCl2], 16.2 [50%] and 12.4 [75%] which followed the order of ZnCl2 content. It is concluded that the water transport processes are strongly influenced by the ZnCl2 content of the cement.

Ocean acidification has different effects on the production of DMS and DMSP measured in cultures of Emiliania huxleyi and a mesocosm study: a comparison of laboratory monocultures and community interactions

The human-induced rise in atmospheric carbon dioxide since the industrial revolution has led to increasing oceanic carbon uptake and changes in seawater carbonate chemistry, resulting in lowering of surface water pH. In this study we investigated the effect of increasing CO2 partial pressure (pCO2) on concentrations of volatile biogenic dimethylsulfide (DMS) and its precursor dimethylsulfoniopropionate (DMSP), through monoculture studies and community pCO2 perturbation. DMS is a climatically important gas produced by many marine algae: it transfers sulfur into the atmosphere and is a major influence on biogeochemical climate regulation through breakdown to sulfate and formation of subsequent cloud condensation nuclei (CCN). Overall, production of DMS and DMSP by the coccolithophore Emiliania huxleyi strain RCC1229 was unaffected by growth at 900 matm pCO2, but DMSP production normalised to cell volume was 12% lower at the higher pCO2 treatment. These cultures were compared with community DMS and DMSP production during an elevated pCO2 mesocosm experiment with the aim of studying E. huxleyi in the natural environment. Results contrasted with the culture experiments and showed reductions in community DMS and DMSP concentrations of up to 60 and 32% respectively at pCO2 up to 3000 matm, with changes attributed to poorer growth of DMSP-producing nanophytoplankton species, including E. huxleyi, and potentially increased microbial consumption of DMSand dissolvedDMSPat higher pCO2.DMSandDMSPproduction differences between culture and community likely arise from pH affecting the inter-species responses between microbial producers and consumers.

Global oceanic emission of ammonia: Constraints from seawater and atmospheric observations

Current global inventories of ammonia emissions identify the ocean as the largest natural source. This source depends on seawater pH, temperature, and the concentration of total seawater ammonia (NHx(sw)), which reflects a balance between remineralization of organic matter, uptake by plankton, and nitrification. Here we compare [NHx(sw)] from two global ocean biogeochemical models (BEC and COBALT) against extensive ocean observations. Simulated [NHx(sw)] are generally biased high. Improved simulation can be achieved in COBALT by increasing the plankton affinity for NHx within observed ranges. The resulting global ocean emissions is 2.5 TgN a−1, much lower than current literature values (7–23 TgN a−1), including the widely used Global Emissions InitiAtive (GEIA) inventory (8 TgN a−1). Such a weak ocean source implies that continental sources contribute more than half of atmospheric NHx over most of the ocean in the Northern Hemisphere. Ammonia emitted from oceanic sources is insufficient to neutralize sulfate aerosol acidity, consistent with observations. There is evidence over the Equatorial Pacific for a missing source of atmospheric ammonia that could be due to photolysis of marine organic nitrogen at the ocean surface or in the atmosphere. Accommodating this possible missing source yields a global ocean emission of ammonia in the range 2–5 TgN a−1, comparable in magnitude to other natural sources from open fires and soils.

CYSTATIN RELATED EPIDIDYMAL SPERMATOGENIC PROTEIN RESIDES IN THE OUTER DENSE FIBRES AND LIKELY TRANSIENTLY ASSOCIATES WITH THE SURFACE OF EPIDIDYMAL MOUSE SPERMATOZOA

Cystatin Related Epididymal Spermatogenic protein (CRES) is expressed in both the testis and epididymis and found associated with spermatozoa. It appears as non-glycosylated (14 and 12 kDa) and glycosylated isoforms (19 and 17 kDa). The role of CRES is enigmatic and dependent on localization of its isoforms, which is the objective of this study. The initial approach was to investigate testicular and epididymal origins of these isoforms by immunohistochemistry and immunogold cytochemistry. To further pinpoint CRES localization we then selectively extracted and fractionated epididymal spermatozoa in order to find by immunoblotting which sperm fractions contained CRES isoforms. Immunohistochemical analysis of mouse spermatogenesis showed that CRES was expressed in the tail cytoplasm of elongating spermatids from step 9-16, with a pattern reminiscent of outer dense fibre (ODF) proteins. Ultrastructural immunocytochemistry revealed that the immunogold label was concentrated over growing ODFs and mitochondrial sheath in the testes which persisted in spermatozoa through the epididymis. Sequential extractions of isolated sperm tails with Triton X-100-dithiothreitol (DTT) to remove the mitochondrial sheath, whose extract contained an unrelated 66 kDa immunoreactive band, followed by either sodium dodecyl sulfate (SDS)-DTT or urea-DTT to solubilise accessory fibres of the tail revealed a 14 kDa immunoreactive band associated with the ODF. In addition, Western blots revealed glycosylated and non-glycosylated CRES isoforms in nonyl phenoxylpolyethoxylethanol (NP40) extracts of the caput, but not cauda, sperm. Immunohistochemical analysis of the caput and cauda epithelium showed that CRES is secreted by the Golgi apparatus of the ii initial segment, fills the proximal caput lumen, and disappears by mid caput. Western blots of caput and cauda tissue and luminal fluid revealed 14 and 19 kDa immunoreactive bands in caput tissues and luminal fluid, but not in the cauda. This study concludes that there are two origins of CRES, one arising in the testis and the other in the epididymis. Testicular CRES is ionically and covalently associated with the ODF while epididymal CRES is detergent soluble and is most likely associated temporarily with the surface of caput epididymal sperm.

Arteriolar and venular patterning in retinas of mice selectively expressing VEGF isoforms.

The murine VEGF gene is alternatively transcribed to yield the VEGF120, VEGF164, and VEGF188 isoforms, which differ in their potential to bind to heparan sulfate and neuropilin-1 and to stimulate endothelial growth. Here, their role in retinal vascular development was studied in mice selectively expressing single isoforms. VEGF164/164 mice were normal, healthy, and had normal retinal angiogenesis. In contrast, VEGF120/120 mice exhibited severe defects in vascular outgrowth and patterning, whereas VEGF188/188 mice displayed normal venular outgrowth but impaired arterial development. It is noteworthy that neuropilin-1, a receptor for VEGF164, was predominantly expressed in retinal arterioles. These findings reveal distinct roles of the various VEGF isoforms in vascular patterning and arterial development in the retina.

Microbiological characteristics in a zero-valent iron reactive barrier

Zero-valent iron (Fe0)-based permeable reactive barriertreatment has been generating great interest for passivegroundwater remediation, yet few studies have paid particularattention to the microbial activity and characteristics withinand in the vicinity of the Fe0-barrier matrix. The presentstudy was undertaken to evaluate the microbial population andcommunity composition in the reducing zone of influence byFe0 corrosion in the barrier at the Oak Ridge Y-12 Plantsite. Both phospholipid fatty acids and DNA analyses were usedto determine the total microbial population and microbialfunctional groups, including sulfate-reducing bacteria,denitrifying bacteria, and methanogens, in groundwater andsoil/iron core samples. A diverse microbial community wasidentified in the strongly reducing Fe0 environment despitea relatively high pH condition within the Fe0 barrier (up topH 10). In comparison with those found in the backgroundsoil/groundwater samples, the enhanced microbial populationranged from 1 to 3 orders of magnitude and appeared to increase from upgradient of the barrier to downgradient soil. Inaddition, microbial community composition appeared to change overtime, and the bacterial types of microorganismsincreased consistently as the barrier aged. DNA analysisindicated the presence of sulfate-reducing and denitrifyingbacteria in the barrier and its surrounding soil. However, theactivity of methanogens was found to be relatively low,presumably as a result of the competition by sulfate/metal-reducing bacteria and denitrifying bacteria because of the unlimited availability of sulfate and nitrate in the site groundwater. Results of this study provide evidenceof a diverse microbial population within and in the vicinity ofthe iron barrier, although the important roles of microbial activity, either beneficially or detrimentally, on the longevityand enduring efficiency of the Fe0 barriers are yet to be evaluated.

Low-frequency electrical response to microbial induced sulfide precipitation

We investigated the sensitivity of low-frequency electrical measurements to microbe-induced metal sulfide precipitation. Three identical sand-packed monitoring columns were used; a geochemical column, an electrical column and a control column. In the first experiment, continuous upward flow of nutrients and metals in solution was established in each column. Cells of Desulfovibrio vulgaris (D. vulgaris) were injected into the center of the geochemical and electrical columns. Geochemical sampling and post-experiment destructive analysis showed that microbial induced sulfate reduction led to metal precipitation on bacteria cells, forming motile biominerals. Precipitation initially occurred in the injection zone, followed by chemotactic migration of D. vulgaris and ultimate accumulation around the nutrient source at the column base. Results from this experiment conducted with metals show (1) polarization anomalies, up to 14 mrad, develop at the bacteria injection and final accumulation areas, (2) the onset of polarization increase occurs concurrently with the onset of lactate consumption, (3) polarization profiles are similar to calculated profiles of the rate of lactate consumption, and (4) temporal changes in polarization and conduction correlate with a geometrical rearrangement of metal-coated bacterial cells. In a second experiment, the same biogeochemical conditions were established except that no metals were added to the flow solution. Polarization anomalies were absent when the experiment was replicated without metals in solution. We therefore attribute the polarization increase observed in the first experiment to a metal-fluid interfacial mechanism that develops as metal sulfides precipitate onto microbial cells and form biominerals. Temporal changes in polarization and conductivity reflect changes in (1) the amount of metal-fluid interfacial area, and (2) the amount of electronic conduction resulting from microbial growth, chemotactic movement and final coagulation. This polarization is correlated with the rate of microbial activity inferred from the lactate concentration gradient, probably via a common total metal surface area effect.

Geophysical imaging of stimulated microbial biomineralization

Understanding how microorganisms influence the physical and chemical properties of the subsurface is hindered by our inability to observe microbial dynamics in real time and with high spatial resolution. Here, we investigate the use of noninvasive geophysical methods to monitor biomineralization at the laboratory scale during stimulated sulfate reduction under dynamic flow conditions. Alterations in sediment characteristics resulting from microbe-mediated sulfide mineral precipitation were concomitant with changes in complex resistivity and acoustic wave propagation signatures. The sequestration of zinc and iron in insoluble sulfides led to alterations in the ability of the pore fluid to conduct electrical charge and of the saturated sediments to dissipate acoustic energy. These changes resulted directly from the nucleation, growth, and development of nanoparticulate precipitates along grain surfaces and within the pore space. Scanning and transmission electron microscopy (SEM and TEM) confirmed the sulfides to be associated with cell surfaces, with precipitates ranging from aggregates of individual 3-5 nm nanocrystals to larger assemblages of up to 10-20 m in diameter. Anomalies in the geophysical data reflected the distribution of mineral precipitates and biomass over space and time, with temporal variations in the signals corresponding to changes in the aggregation state of the nanocrystalline sulfides. These results suggest the potential for using geophysical techniques to image certain subsurface biogeochemical processes, such as those accompanying the bioremediation of metal-contaminated aquifers.

A group contribution method for viscosity estimation of ionic liquids

Based on experimental viscosity data collected from the literature and using density data obtained from a predictive method previously proposed by the authors, a group contribution method is proposed to estimate viscosity of imidazolium-, pyridinium-, and pyrrolidinium-based ILs containing hexafluorophosphate (PF6), tetrafluoroborate (BF4), bis(trifluoromethanesulfonyl) amide (Tf2N), chloride (Cl), acetate (CH3COO), methyl sulfate (MeSO4), ethyl sulfate (EtSO4), and trifluoromethanesulfonate (CF3SO3) anions, covering wide ranges of temperature, 293–393 K and viscosity, 4–21,000 cP. It is shown that a good agreement with literature data is obtained. For circa 500 data points of 29 ILs studied, a mean percent deviation (MPD) of 7.7% with a maximum deviation smaller than 28% was observed. 71.1% of the estimated viscosities present deviations smaller than 10% of the experimental values while only 6.4% have deviations larger than 20%. The group contribution method here developed can thus be used to evaluate the viscosity of new ionic liquids in wide ranges of temperatures at atmospheric pressure and, as data for new groups of cations and anions became available, can be extended to a larger range of ionic liquids.

PURIFICATION AND PARTIAL CHARACTERIZATION OF AN ENDO-POLYGALACTURONASE FROM ASPERGILLUS NIGER

A pectinase was identified and isolated from a commercial Aspergillus niger pectinase preparation. The crude enzyme preparation, which was prepared by precipitation of the water extract of the culture of A. niger with ammonium sulfate, was further fractionated by three steps of chromatography, i. e., cation exchange, hydrophobic interaction and onion exchange, to obtain an electrophoretically homogeneous pectinase. The molecular weight of the purified enzyme was estimated by SDS-PAGE to be about 40.4 kDa under both nonreducing and reducing conditions, with the optimum pH at 5.0 and the optimum temperature at 36C. The enzyme was stable at temperatures below 35C. The partial N-terminal ammo acid sequence data analysis of the first 19 amina acids of the obtained pectinase revealed 94.7% and 89.5% homology with two reported pectinases from A. niger.