Chemokines in neuroectodermal cancers: the crucial growth signal from the soil.

Although chemokines and their receptors were initially identified as regulators of cell trafficking during inflammation and immune response, they have emerged as crucial players in all stages of tumor development, primary growth, migration, angiogenesis, and establishment as metastases in distant target organs. Neuroectodermal tumors regroup neoplasms originating from the embryonic neural crest cells, which display clinical and biological similarities. These tumors are highly malignant and rapidly progressing diseases that disseminate to similar target organs such as bone marrow, bone, liver and lungs. There is increasing evidence that interaction of several chemokine receptors with corresponding chemokine ligands are implicated in the growth and invasive characteristics of these tumors. In this review we summarize the current knowledge on the role of CXCL12 chemokine and its CXCR4 and CXCR7 receptors in the progression and survival of neuroectodermal tumors, with particular emphasis on neuroblastoma, the most typical and enigmatic neuroectodermal childhood tumor.

Persistence and cell culturability of biocontrol strain Pseudomonas fluorescens CHA0 under plough pan conditions in soil and influence of the anaerobic regulator gene anr.

Certain fluorescent pseudomonads can protect plants from soil-borne pathogens, and it is important to understand how these biocontrol agents survive in soil. The persistence of the biocontrol strain Pseudomonas fluorescens CHA0-Rif under plough pan conditions was assessed in non-sterile soil microcosms by counting total cells (immunofluorescence microscopy), intact cells (BacLight membrane permeability test), viable cells (Kogure's substrate-responsiveness test) and culturable cells (colony counts on selective plates) of the inoculant. Viable but non-culturable cells of CHA0-Rif (106 cells g-1 soil) were found in flooded microcosms amended with fermentable organic matter, in which the soil redox potential was low (plough pan conditions), in agreement with previous observations of plough pan samples from a field inoculated with CHA0-Rif. However, viable but non-culturable cells were not found in unamended flooded, amended unflooded or unamended unflooded (i.e. control) microcosms, suggesting that such cells resulted from exposure of CHA0-Rif to a combination of low redox potential and oxygen limitation in soil. CHA0-Rif is strictly aerobic. Its anaerobic regulator ANR is activated by low oxygen concentrations and it controls production of the biocontrol metabolite hydrogen cyanide under microaerophilic conditions. Under plough pan conditions, an anr-deficient mutant of CHA0-Rif and its complemented derivative displayed the same persistence pattern as CHA0-Rif, indicating that anr was not implicated in the formation of viable but non-culturable cells of this strain at the plough pan.

Igneous garnet and amphibole fractionation in the roots of island arcs: experimental constraints on andesitic liquids

To evaluate the role of garnet and amphibole fractionation at conditions relevant for the crystallization of magmas in the roots of island arcs, a series of experiments were performed on a synthetic andesite at conditions ranging from 0.8 to 1.2 GPa, 800-1,000 degrees C and variable H2O contents. At water undersaturated conditions and fO(2) established around QFM, garnet has a wide stability field. At 1.2 GPa garnet ? amphibole are the high-temperature liquidus phases followed by plagioclase at lower temperature. Clinopyroxene reaches its maximal stability at H2O-contents <= 9 wt% at 950 degrees C and is replaced by amphibole at lower temperature. The slopes of the plagioclase-in boundaries are moderately negative in T-XH2O space. At 0.8 GPa, garnet is stable at magmatic H2O contents exceeding 8 wt% and is replaced by spinel at decreasing dissolved H2O. The liquids formed by crystallization evolve through continuous silica increase from andesite to dacite and rhyolite for the 1.2 GPa series, but show substantial enrichment in FeO/MgO for the 0.8 GPa series related to the contrasting roles of garnet and amphibole in fractionating Fe-Mg in derivative liquids. Our experiments indicate that the stability of igneous garnet increases with increasing dissolved H2O in silicate liquids and is thus likely to affect trace element compositions of H2O-rich derivative arc volcanic rocks by fractionation. Garnet-controlled trace element ratios cannot be used as a proxy

Biological control of soil-borne pathogens by fluorescent pseudomonads.

Particular bacterial strains in certain natural environments prevent infectious diseases of plant roots. How these bacteria achieve this protection from pathogenic fungi has been analysed in detail in biocontrol strains of fluorescent pseudomonads. During root colonization, these bacteria produce antifungal antibiotics, elicit induced systemic resistance in the host plant or interfere specifically with fungal pathogenicity factors. Before engaging in these activities, biocontrol bacteria go through several regulatory processes at the transcriptional and post-transcriptional levels.

The mycorrhizal contribution to plant productivity, plant nutrition and soil structure in experimental grassland.

Previous studies have shown that arbuscular mycorrhizal fungi (AMF) can influence plant diversity and ecosystem productivity. However, little is known about the effects of AMF and different AMF taxa on other important community properties such as nutrient acquisition, plant survival and soil structure. We established experimental grassland microcosms and tested the impact of AMF and of different AMF taxa on a number of grassland characteristics. We also tested whether plant species benefited from the same or different AMF taxa in subsequent growing seasons. AMF enhanced phosphorus acquisition, soil aggregation and survival of several plant species, but AMF did not increase total plant productivity. Moreover, AMF increased nitrogen acquisition by some plant species, but AMF had no effect on total N uptake by the plant community. Plant growth responses to AMF were temporally variable and some plant species obtained the highest biomass with different AMF in different years. Hence the results indicate that it may be beneficial for a plant to be colonized by different AMF taxa in different seasons. This study shows that AMF play a key role in grassland by improving plant nutrition and soil structure, and by regulating the make-up of the plant community.

Persistence of a biocontrol Pseudomonas inoculant as high populations of culturable and non-culturable cells in 200-cm-deep soil profiles

Little is known about the ecology of soil inoculants used for pathogen biocontrol, biofertilization and bioremediation under field conditions. We investigated the persistence and the physiological states of soil-inoculated Pseudomonas protegens (previously Pseudomonas fluorescens) CHA0 (108 CFU g−1 surface soil) in different soil microbial habitats in a planted ley (Medicago sativa L.) and an uncovered field plot. At 72 days, colony counts of the inoculant were low in surface soil (uncovered plot) and earthworm guts (ley plot), whereas soil above the plow pan (uncovered plot), and the rhizosphere and worm burrows present until 1.2 m depth (ley plot) were survival hot spots (105-106 CFU g−1 soil). Interestingly, strain CHA0 was also detected in the subsoil of both plots, at 102-105 CFU g−1 soil between 1.8 and 2 m depth. However, non-cultured CHA0 cells were also evidenced based on immunofluorescence microscopy. Kogure's direct viable counts of nutrient-responsive cells showed that many more CHA0 cells were in a viable but non-culturable (VBNC) or a non-responsive (dormant) state than in a culturable state, and the proportion of cells in those non-cultured states depended on soil microbial habitat. At the most, cells in a VBNC state amounted to 34% (above the plow pan) and those in a dormant state to 89% (in bulk soil between 0.6 and 2 m) of all CHA0 cells. The results indicate that field-released Pseudomonas inoculants may persist at high cell numbers, even in deeper soil layers, and display a combination of different physiological states whose prevalence fluctuates according to soil microbial habitats.

Identification of opsA, a gene involved in solute stress mitigation and survival in soil, in the polycyclic aromatic hydrocarbon-degrading bacterium Novosphingobium sp. strain LH128.

The aim of this study was to identify genes involved in solute and matric stress mitigation in the polycyclic aromatic hydrocarbon (PAH)-degrading Novosphingobium sp. strain LH128. The genes were identified using plasposon mutagenesis and by selection of mutants that showed impaired growth in a medium containing 450 mM NaCl as a solute stress or 10% (wt/vol) polyethylene glycol (PEG) 6000 as a matric stress. Eleven and 14 mutants showed growth impairment when exposed to solute and matric stresses, respectively. The disrupted sequences were mapped on a draft genome sequence of strain LH128, and the corresponding gene functions were predicted. None of them were shared between solute and matric stress-impacted mutants. One NaCl-affected mutant (i.e., NA7E1) with a disruption in a gene encoding a putative outer membrane protein (OpsA) was susceptible to lower NaCl concentrations than the other mutants. The growth of NA7E1 was impacted by other ions and nonionic solutes and by sodium dodecyl sulfate (SDS), suggesting that opsA is involved in osmotic stress mitigation and/or outer membrane stability in strain LH128. NA7E1 was also the only mutant that showed reduced growth and less-efficient phenanthrene degradation in soil compared to the wild type. Moreover, the survival of NA7E1 in soil decreased significantly when the moisture content was decreased but was unaffected when soluble solutes from sandy soil were removed by washing. opsA appears to be important for the survival of strain LH128 in soil, especially in the case of reduced moisture content, probably by mitigating the effects of solute stress and retaining membrane stability.

Functionally and phylogenetically diverse plant communities key to soil biota

Recent studies assessing the role of biological diversity for ecosystem functioning indicate that the diversity of functional traits and the evolutionary history of species in a community, not the number of taxonomic units, ultimately drives the biodiversity-ecosystem-function relationship. Here, we simultaneously assessed the importance of plant functional trait and phylogenetic diversity as predictors of major trophic groups of soil biota (abundance and diversity), six years from the onset of a grassland biodiversity experiment. Plant functional and phylogenetic diversity were generally better predictors of soil biota than the traditionally used species or functional group richness. Functional diversity was a reliable predictor for most biota, with the exception of soil microorganisms, which were better predicted by phylogenetic diversity. These results provide empirical support for the idea that the diversity of plant functional traits and the diversity of evolutionary lineages in a community are important for maintaining higher abundances and diversity of soil communities.

The roles of flux- and decompression melting and their respective fractionation lines for continental crust formation: Evidence from the Kohistan arc

Delamination and foundering of the lower continental crust (LCC) into the mantle is part of the crust-forming mechanism. However, knowledge of the composition and mineralogy of the preserved or delaminated LCC over geological timescales remains scarce. We provide a synopsis of recent research within the Kohistan arc (Pakistan) and demonstrate that hydrous and less hydrous liquid lines of descent related to flux assisted and decompression mantle melting, respectively, produce compositionally different lower crustal rocks. The argument refers to two lower crustal sections exposed in Kohistan, the older Southern Plutonic Complex (SPC) and the younger Chilas Complex. The SPC typifies a hydrous, high-pressure fractionation sequence of olivine-pyroxenes-garnet-Fe/Ti-oxide-amphibole-plagioclase. The Chilas Complex illustrates a less hydrous fractionation sequence of olivine-clinopyroxene-orthopyroxene-plagioclase-amphibole. Despite the similarity of the Chilas Complex rocks to proposed lower crust compositions, the less hydrous fractionation results in unrealistically small volumes of silica-rich rocks, precluding the Chilas Complex gabbros to represent the magmatic complement to the upper crust. The composition of the SPC lower crust differs markedly from bulk lower crust estimates, but is complementary to silica-rich rocks exposed along this section and in the Kohistan batholith. These observations inspire a composite model for the formation of continental crust (CC) where the negatively buoyant delaminated and the buoyant preserved lower continental crusts (LCC) differ in genesis, mineralogy, and composition. We propose that the upper, non-sedimentary subsequent removal of the complementary, negatively buoyant garnet-pyroxene-amphibole-plagioclase-rich cumulates. In contrast, the LCC, which is buoyant and preserved over geological timescales, is formed by less hydrous parental mantle melts. We suggest that the bulk continental crust composition is related to mixing of these petrologically not directly related end members. Published by Elsevier B.V.

Simultaneous determination of Pu and Am radioisotopes in environmental samples: a tool for determining origin and release date

A radiochemical procedure was developed for the sequential determination of Pu and Am radioisotopes in environmental samples. The radioisotope activities were then used to assess the origin and release date of the environmental plutonium. The radioanalytical procedure is based on the separation of Pu and Am on selective extraction chromatographic resins (Eichrom TEVA and DGA). Alpha sources were prepared by electrodeposition on stainless steel discs, and the alpha emitting radionuclides (238Pu, 239,240Pu and 241Am) were measured by alpha spectrometry. For the determination of the beta emitting 241Pu, the Pu alpha source was leached in hot concentrated nitric acid and the Pu fraction further purified by extraction chromatography on a small column of TEVA resin (100 μg of resin in a pipette tip). 241Pu is then measured by ultra low level liquid scintillation counting. Due to the lack of reference material for 241Pu, the proposed radiochemical method was nevertheless validated using four IAEA reference sediments with information values of 241Pu. The proposed method was then used to determine the 238Pu, 239,240Pu, 241Pu and 241Am activity concentrations in alpine soils of France and Switzerland. The soil is the primary receptor of the atmospheric radioactive fallout and, because of the strong binding interaction with soils particles, the isotopes are little fractionated. Therefore, the activity ratios 241Pu/239+240Pu and 238Pu/239,240Pu in soil samples were used to determine the origin (source) and date of the Pu contamination in the investigated alpine sites. The 241Pu/239,240Pu and 238Pu/239,240Pu activity ratios confirmed that the main origin of Pu in the alpine soils was the global fallout from the nuclear bomb tests (NBT) in the fifties and sixties. Furthermore, the 241Pu/241Am activity ratios were used to determine the age of the Pu contamination, which is also an important data for distinguishing the Pu sources. The estimation of the date of the contamination, by the 241Pu/241Am age-dating method, further confirmed the NBT as the Pu source. However, the 241Pu/241Am dating method was limited to samples where Pu-Am fractionation was insignificant. If any, the contribution of the Chernobyl accident in the studied sites is negligible.

Heated Optical Fiber for Distributed Soil-Moisture Measurements: A Lysimeter Experiment

An Actively Heated Fiber Optics (AHFO) method to estimate soil moisture is tested and the analysis technique improved on. The measurements were performed in a lysimeter uniformly packed with loam soil with variable water content profiles. In the first meter of the soil profi le, 30 m of fiber optic cable were installed in a 12 loops coil. The metal sheath armoring the fiber cable was used as an electrical resistance heater to generate a heat pulse, and the soil response was monitored with a Distributed Temperature Sensing (DTS) system. We study the cooling following three continuous heat pulses of 120 s at 36 W m(-1) by means of long-time approximation of radial heat conduction. The soil volumetric water contents were then inferred from the estimated thermal conductivities through a specifically calibrated model relating thermal conductivity and volumetric water content. To use the pre-asymptotic data we employed a time correction that allowed the volumetric water content to be estimated with a precision of 0.01-0.035 (m(3) m(-3)). A comparison of the AHFO measurements with soil-moisture measurements obtained with calibrated capacitance-based probes gave good agreement for wetter soils [discrepancy between the two methods was less than 0.04 (m(3) m(-3))]. In the shallow drier soils, the AHFO method underestimated the volumetric water content due to the longertime required for the temperature increment to become asymptotic in less thermally conductive media [discrepancy between the two methods was larger than 0.1 (m(3) m(-3))]. The present work suggests that future applications of the AHFO method should include longer heat pulses, that longer heating and cooling events are analyzed, and, temperature increments ideally be measured with higher frequency.

Enantioselective transformation of alpha-hexachlorocyclohexane by the dehydrochlorinases LinA1 and LinA2 from the soil bacterium Sphingomonas paucimobilis B90A.

Sphingomonas paucimobilis B90A contains two variants, LinA1 and LinA2, of a dehydrochlorinase that catalyzes the first and second steps in the metabolism of hexachlorocyclohexanes (R. Kumari, S. Subudhi, M. Suar, G. Dhingra, V. Raina, C. Dogra, S. Lal, J. R. van der Meer, C. Holliger, and R. Lal, Appl. Environ. Microbiol. 68:6021-6028, 2002). On the amino acid level, LinA1 and LinA2 were 88% identical to each other, and LinA2 was 100% identical to LinA of S. paucimobilis UT26. Incubation of chiral alpha-hexachlorocyclohexane (alpha-HCH) with Escherichia coli BL21 expressing functional LinA1 and LinA2 S-glutathione transferase fusion proteins showed that LinA1 preferentially converted the (+) enantiomer, whereas LinA2 preferred the (-) enantiomer. Concurrent formation and subsequent dissipation of beta-pentachlorocyclohexene enantiomers was also observed in these experiments, indicating that there was enantioselective formation and/or dissipation of these enantiomers. LinA1 preferentially formed (3S,4S,5R,6R)-1,3,4,5,6-pentachlorocyclohexene, and LinA2 preferentially formed (3R,4R,5S,6S)-1,3,4,5,6-pentachlorocyclohexene. Because enantioselectivity was not observed in incubations with whole cells of S. paucimobilis B90A, we concluded that LinA1 and LinA2 are equally active in this organism. The enantioselective transformation of chiral alpha-HCH by LinA1 and LinA2 provides the first evidence of the molecular basis for the changed enantiomer composition of alpha-HCH in many natural environments. Enantioselective degradation may be one of the key processes determining enantiomer composition, especially when strains that contain only one of the linA genes, such as S. paucimobilis UT26, prevail.

Soil tillage affects the community structure of mycorrhizal fungi in maize roots

In this study we tested whether communities of arbuscular mycorrhizal fungi (AMF) colonizing the roots of maize (Zea mays L.) were affected by soil tillage practices (plowing, chiseling, and no-till) in a long-term field experiment carried out in Tanikon (Switzerland). AMF were identified in the roots using specific polymerase chain reaction (PCR) markers that had been developed for the AMF previously isolated from the soils of the studied site. A nested PCR procedure with primers of increased specificity (eukaryotic, then, fungal, then AMF species or. species-grouop specific) was used. Sequencing of amplified DNA confirmed that the DNA obtained from the maize roots was of AMF origin. Presence of particular AMF species or species-group was scored as a presence of a DNA product after PCR with specific primers. We also used single-strand conformation polymorphism analysis (SSCP), of amplified DNA samples to-check if the amplification of the DNA from maize roots matched the expected profile for a particular AMF isolate with a given specific primer pair. Presence of the genus Scutellospora, in maize roots was strongly reduced in plowed and chiseled soils. Fungi from the suborder Glomineae were more prevalent colonizers of maize roots growing in plowed soils, but were also present in the roots from other tillage treatments. These changes in community of AMF colonizing maize roots might be due to (1), the differences in tolerance to the tillage-induced disruption of the hyphae among the different AMF species, (2) changes in nutrient content of the soil, (3) changes in microbial activity, or (4) changes in weed populations in response to soil tillage. This is the first report on community composition of AMF in the roots of a field-grown crop plant (maize) as affected by soil tillage.

Speciation of naturally-accumulated uranium in an organic-rich soil of an alpine region (Switzerland)

Very high concentrations of uranium (up to 4000 ppm) were found in a natural soil in the Dischma valley, an alpine region in the Grisons canton in Switzerland. The goal of this study was to examine the redox state and the nature of uranium binding in the soil matrix in order to understand the accumulation mechanism. Pore water profiles collected from Dischma soil revealed the establishment of anoxic conditions with increasing soil depth. A combination of chemical extraction methods and spectroscopy was applied to characterize the redox state and binding environment of uranium in the soil. Bicarbonate extraction under anoxic conditions released most of the uranium indicating that uranium occurs predominantly in the hexavalent form. Surprisingly, the uranium redox state did not vary greatly as a function of depth. X-ray absorption near edge spectroscopy (XANES), confirmed that uranium was present as a mixture of U(VI) and U(IV) with U(VI) dominating. Sequential extractions of soil samples showed that the dissolution of solid organic matter resulted in the simultaneous release of the majority of the soil uranium content (>95%). Extended X-ray absorption fine structure (EXAFS) spectroscopy also revealed that soil-associated uranium in the soil matrix was mainly octahedrally coordinated, with an average of 1.7 axial (at about 1.76 Å) and 4.6 to 5.3 equatorial oxygen atoms (at about 2.36 Å) indicating the dominance of a uranyl-like (UO22+) structure presumably mixed with some U(IV). An additional EXAFS signal (at about 3.2 Å) identified in some spectra suggested that uranium was also bound (via an oxygen atom) to a light element such as carbon, phosphorus or silicon. Gamma spectrometric measurements of soil profiles failed to identify uranium long-life daughter products in the soil which is an indication that uranium originates elsewhere and was transported to its current location by water. Finally, it was found that the release of uranium from the soil was significantly promoted at very low pH values (pH 2) and increased with increasing pH values (between pH 5 and 9).