bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isorenieratene Biosynthesis in Green Sulfur Bacteria Requires the Cooperative Actions of Two Carotenoid Cyclases
Authors: Maresca Julia A. , Romberger Steven P. , Bryant Donald A. 
Published: August 2008

ABSTRACT

The cyclization of lycopene to γ- or β-carotene is a major branch point in the biosynthesis of carotenoids in photosynthetic bacteria. Four families of carotenoid cyclases are known, and each family includes both mono- and dicyclases, which catalyze the formation of γ- and β-carotene, respectively. Green sulfur bacteria (GSB) synthesize aromatic carotenoids, of which the most commonly occurring types are the monocyclic chlorobactene and the dicyclic isorenieratene. Recently, the
cruA
gene, encoding a conserved hypothetical protein found in the genomes of all GSB and some cyanobacteria, was identified as a lycopene cyclase. Further genomic analyses have found that all available fully sequenced genomes of GSB encode an ortholog of
cruA
. Additionally, the genomes of all isorenieratene-producing species of GSB encode a
cruA
paralog, now named
cruB
. The
cruA
gene from the chlorobactene-producing GSB species
Chlorobaculum tepidum
and both
cruA
and
cruB
from the brown-colored, isorenieratene-producing GSB species
Chlorobium phaeobacteroides
strain DSM 266
T
were heterologously expressed in lycopene- and neurosporene-producing strains of
Escherichia coli
, and the
cruB
gene of
Chlorobium clathratiforme
strain DSM 5477
T
was also heterologously expressed in
C. tepidum
by inserting the gene at the
bchU
locus. The results show that CruA is probably a lycopene monocyclase in all GSB and that CruB is a γ-carotene cyclase in isorenieratene-producing species. Consequently, the branch point for the synthesis of mono- and dicyclic carotenoids in GSB seems to be the modification of γ-carotene, rather than the cyclization of lycopene as occurs in cyanobacteria.
Dual Promoters Control Expression of theBacillus anthracisVirulence Factor AtxA
Authors: Bongiorni Cristina , Fukushima Tatsuya , Wilson Adam C. , Chiang Christina , Mansilla M. Cecilia , Hoch James A. , Perego Marta 
Published: August 2008

ABSTRACTThe AtxA virulence regulator ofBacillus anthracisis required for toxin and capsule gene expression. AtxA is a phosphotransferase system regulatory domain-containing protein whose activity is regulated by phosphorylation/dephosphorylation of conserved histidine residues. Here we report that transcription of theatxAgene occurs from two independent promoters, P1 (previously described by Dai et al. [Z. Dai, J. C. Sirard, M. Mock, and T. M. Koehler, Mol. Microbiol.16:1171-1181, 1995]) and P2, whose transcription start sites are separated by 650 bp. Both promoters have −10 and −35 consensus sequences compatible with recognition by σA-containing RNA polymerase, and neither promoter depends on the sporulation sigma factor SigH. The dual promoter activity and the extended untranslated mRNA suggest that as-yet-unknown regulatory mechanisms may act on this region to influence the level of AtxA in the cell.
The CorA Mg2+Channel Is Required for the Virulence ofSalmonella entericaSerovar Typhimurium
Authors: Papp-Wallace Krisztina M. , Nartea Margaret , Kehres David G. , Porwollik Steffen , McClelland Michael , Libby Stephen J. , Fang Ferric C. , Maguire Michael E. 
Published: August 2008

ABSTRACTCorA is the primary Mg2+channel inSalmonella entericaserovar Typhimurium. AcorAmutant is attenuated in mice and defective for invasion of and replication within epithelial cells. Microarray studies show that several virulence effectors are repressed in acorAmutant strain, which ultimately manifests itself as a decrease in virulence.
The Stable, Functional Core of DdrA from
Deinococcus radiodurans
R1 Does Not Restore Radioresistance In Vivo
Authors: Harris Dennis R. , Ngo Khanh V. , Cox Michael M. 
Published: August 2008

ABSTRACT

DdrA protein binds to and protects 3′ DNA ends and is essential for preserving the genome integrity of
Deinococcus radiodurans
following treatment by gamma radiation in an environment lacking nutrients. Limited proteolysis was used to identify a stable and functional protein core, designated DdrA157, consisting of the first 157 residues of the protein. In vitro, the biochemical differences between wild-type and mutant proteins were modest. DdrA exhibits a strong bias in binding DNA with 3′ extensions but not with 5′ extensions. The mutant DdrA157 exhibited a greater affinity for 5′ DNA ends but still bound to 3′ ends more readily. However, when we replaced the wild-type
ddrA
gene with the mutant gene for
ddrA157
, the resulting
D. radiodurans
strain became almost as sensitive to gamma radiation as the
ddrA
knockout strain. These results suggest that while the stable protein core DdrA157 is functional for DNA binding and protection assays in vitro, the carboxyl terminus is required for important functions in vivo. The C terminus may therefore be required for protein or DNA interactions or possibly as a regulatory region for DNA binding or activities not yet identified.
Phage-Associated Mutator Phenotype in Group A Streptococcus
Authors: Scott Julie , Thompson-Mayberry Prestina , Lahmamsi Stephanie , King Catherine J. , McShan W. Michael 
Published: August 2008

ABSTRACT

Defects in DNA mismatch repair (MMR) occur frequently in natural populations of pathogenic and commensal bacteria, resulting in a mutator phenotype. We identified a unique genetic element in
Streptococcus pyogenes
strain SF370 that controls MMR via a dynamic process of prophage excision and reintegration in response to growth. In
S. pyogenes
,
mutS
and
mutL
are organized on a polycistronic mRNA under control of a common promoter. Prophage SF370.4 is integrated between the two genes, blocking expression of the downstream gene (
mutL
) and resulting in a mutator phenotype. However, in rapidly growing cells the prophage excises and replicates as an episome, allowing
mutL
to be expressed. Excision of prophage SF370.4 and expression of MutL mRNA occur simultaneously during early logarithmic growth when cell densities are low; this brief window of MutL gene expression ends as the cell density increases. However, detectable amounts of MutL protein remain in the cell until the onset of stationary phase. Thus, MMR in
S. pyogenes
SF370 is functional in exponentially growing cells but defective when resources are limiting. The presence of a prophage integrated into the 5′ end of
mutL
correlates with a mutator phenotype (10
−7
to 10
−8
mutation/generation, an approximately a 100-fold increase in the rate of spontaneous mutation compared with prophage-free strains [10
−9
to 10
−10
mutation/generation]). Such genetic elements may be common in
S. pyogenes
since 6 of 13 completed genomes have related prophages, and a survey of 100 strains found that about 20% of them are positive for phages occupying the SF370.4
attP
site. The dynamic control of a major DNA repair system by a bacteriophage is a novel method for achieving the mutator phenotype and may allow the organism to respond rapidly to a changing environment while minimizing the risks associated with long-term hypermutability.
Sensitivity of the Present-Day Climate to Freshwater Forcing Associated with Antarctic Sea Ice Loss
Authors: Aiken Christopher M. , England Matthew H. 
Published: August 2008

Abstract
The role played by Southern Hemisphere sea ice in the global climate system is explored using an earth system climate model of intermediate complexity. An ensemble of experiments is analyzed in which freshwater forcing equivalent to a complete 100-yr meltback of Southern Hemisphere sea ice is applied to a model run that simulates the present climate. This freshwater forcing acts to mildy subdue Southern Ocean deep overturning, reducing mean Antarctic Bottom Water (AABW) export by 0.5 Sv (1 Sv ≡ 106 m3 s−1) in the ensemble average. The decreased convective overturning cools the surface waters, thereby increasing sea ice volume and thus forming a negative feedback that stabilizes Antarctic sea ice. In contrast, the reduced convective overturn warms subsurface waters in the Southern Ocean, which, combined with the imposed freshening, results in a reduction in the meridional steric height gradient and hence a slowdown of the Antarctic Circumpolar Current (ACC). The reduction in ACC strength is, however, only modest at 1.5 Sv. These responses are thus of only weak magnitude, and the system recovers to its original state over time scales of decades. An extreme scenario experiment with essentially instantaneous addition of this meltwater load shows similar results, indicating the limited response of the climate system to the freshening implied by Antarctic sea ice melt. An additional experiment in which a much larger freshwater forcing of approximately 0.4 Sv is applied over 100 yr confirms the relatively weak response of the model’s climate state to such forcing, relative to the well-documented climatic effects of freshwater forcing added to the North Atlantic.
Mitral Valve Repair for Ischemic Mitral Regurgitation
Authors: Calafiore Antonio M. , Iacò Angela L. , Contini Marco , Bivona Antonio , Varone Egidio , Greco Patrizia , Scandura Salvatore 
Published: August 2008

Our aim was to evaluate midterm results in patients who underwent mitral valve repair (MVR) for ischermic mitral regurgitation (IMR) in our most recent experience. From March 2006 to March 2008, 105 patients underwent MVR for IMR. Mean IMR grade was 2.6 ± 1.1, with 46 patients having ≤2/4 and 59 ≥3/4. Five patients (4.8%) died within first month; Two-year freedom from death any cause was 85.5% ± 3.8, freedom from cardiac death was 88.7% ± 3.4. NYHA Class of the survivors was 1.3 ± 0.6, with 3 patients in NYHA Class III. Freedom from death any cause and NYHA Class III-IV was 78.6% ± 4.6. IMR grade decreased from 2.6 ± 1.1 to 0.1 ± 0.3 at the discharge and to 0.5 ± 0.3 after a mean of 7 ± 4 months, with no patient with IMR grade 3/4 or 4/4. MVR for IMR should be performed in patients with moderate-or-more IMR grade or when the MV is excessively dilated, to achieve good midterm results.
CO2 sequestration in basaltic rock at the Hellisheidi site in SW Iceland: stratigraphy and chemical composition of the rocks at the injection site
Authors: Alfredsson H. A. , Hardarson B. S. , Franzson H. , Gislason S. R. 
Published: August 2008

AbstractStorage of CO2 as solid Ca, Mg, and Fe carbonates in basaltic rocks may provide a long-lasting solution for reduction of industrial CO2 emissions. Here, we report on the underground stratigraphy of the chemical composition and crystallinity of rocks and their alteration state at a targeted field site for injection of CO2-charged waters, the Hellisheidi area in SW Iceland.
In situ monitoring of the biofilm formation of Pseudomonas putida on hematite using flow-cell ATR-FTIR spectroscopy to investigate the formation of inner-sphere bonds between the bacteria and the mineral
Authors: Ojeda J. J. , Romero-Gonzalez M. E. , Pouran H. M. , Banwart S. A. 
Published: August 2008

AbstractIn situ flow-cell ATR-FTIR using a hematite-coated germanium crystal was used to investigate the chemical interactions between Pseudomonas putida and hematite in real time, when compared with cells not attached to the mineral surface. ATR-FTIR spectra of bacteria growing on hematite showed a shift in the carboxylate signal when compared to the samples obtained from free cells, indicating a chemical interaction between the carboxylate groups and the Fe metal ions of the hematite surface. Small differences in the polysaccharide and phosphoryl regions of the IR spectra of bacteria attached to hematite were also observed. This work shows how the use of in-situ flow-cell experiments with a mineral-coated germanium crystal allows a better description of the bacterial interactions with minerals in real time, as an initial step to understand the fundamental mechanisms involved in the relationship between bacteria and mineral surfaces.
In situ investigation of the redox front above an underground rock cavern and estimation of its moving rate
Authors: Oyama T. , Inohara Y. , Nagaoka T. 
Published: August 2008

AbstractAn investigation and evaluation of the redox conditions around an underground rock cavern are important from the viewpoint of the safety assessment of the subsurface geological disposal of radioactive wastes. The in situ redox conditions around a cavern excavated in Neogene pyroclastic rocks were investigated. Rock samples were collected from a tunnel wall crossing the oxidation front, and the properties of pore water seeping into small holes drilled in the tunnel wall were determined. Chemical analysis of the rock samples revealed that pyrite-bearing rocks belowthe oxidation front were oxidized by the dissolved oxygen in the groundwater infiltrating from the surface. The water properties changed with increasing oxidation of the rocks. From the amount of oxygen-consuming components in the rocks, the migration rate of the oxidation front was estimated to be ~0.2 mm/y due to the flowrate of groundwater (0.1 m/y) containing oxygen.
Weathering of soil minerals by angiosperm and gymnosperm trees
Authors: Andrews M. Y. , Ague J. J. , Berner R. A. 
Published: August 2008

AbstractWeathering of terrestrial Ca- and Mg-bearing silicate minerals is an important control on atmospheric CO2 on geological time scales. It has been determined that vascular plants can accelerate mineral weathering as compared to non-vascular plants or non-vegetated surfaces. This indicates that the evolution of vascular plants, particularly the deep-rooted trees, may play a large role in the long-term carbon cycle and its regulation of the atmosphere. The weathering impact of the separate evolutionary appearances of the gymnosperms in the Palaeozoic and the angiosperms in the Mesozoic, and the shifting ecological dominance from the former to the latter, is currently poorly understood. This study aims to contribute to our understanding of the quantitative weathering rates of the angiosperms and gymnosperms by examining plant-mineral interactions of the two tree types in a temperate field setting underlain by granodiorite. Results include determinations of soil element fluxes and etching of minerals. The observed root-mineral interactions resulted in only slightly more weathering of Ca-bearing minerals by the angiosperms. However, we observed significantly more weathering of the Mg-bearing minerals by the gymnosperms. These results suggest that increasing dominance of the angiosperms in forests in the Mesozoic may have had a small or neutral impact on accelerating overall mineral weathering and regulating CO2, but that this impact may be lithology-dependent.
The effect of fluid composition on the mechanism of the aragonite to calcite transition
Authors: Perdikouri C. , Kasioptas A. , Putnis C. V. , Putnis A. 
Published: August 2008

AbstractExperiments were performed to investigate the transformation of natural aragonite crystals to calcite by reaction with aqueous solutions of calcium carbonate at hydrothermal conditions for different periods of time. X-ray powder diffraction (XRD), scanning electron microscopy (SEM), Raman spectroscopy and Laser ablation inductively coupled mass spectrometry (LA-ICP-MS) were used to characterize the reaction product. The results indicate that the replacement of aragonite by calcite follows an interface-coupled dissolution-precipitation mechanism.
High-resolution imaging of biotite dissolution and measurement of activation energy
Authors: McMaster T. J. , Smits M. M. , Haward S. J. , Leake J. R. , Banwart S. , Ragnarsdottir K. V. 
Published: August 2008

AbstractWe have used a direct imaging technique, in situ atomic force microscopy(AFM) to observe the earliest stages of the dissolution of a biotite surface byoxalic acid at temperatures close to ambient conditions, using a speciallydesigned AFM liquid cell and non-invasive intermittent contact mode of operation. From the nm-resolution data sets in x, yand z dimensions, we have measured dissolution rates and determined activation energies for the process as a function of temperature, via a mass-loss calculation. The value of Ea obtained, 49±2 kJ mol-1, appears to be too high to indicate a diffusion-controlled process and is more in line with expectations based on a process limited by the rate of ligand-induced metal cation detachment from the (001) surface. This is consistent with visual observations of the relative rates of etch-pit formation and growth, and accepted knowledge of the biotite crystal structure. Separate calculations based on planar area etch-pit growth, and measurements of etch-pit perimeters confirm this result, and also indicate substantiallyhigher activation energy, up to 80 kJ mol-1, when the edge pits are in an incipient stage.
Aquifer characterization with tracer test technique; permanent CO2 sequestration into basalt, SW Iceland
Authors: Rezvani Khalilabad M. , Axelsson G. , Gislason S. R. 
Published: August 2008

AbstractMineral sequestration is among several promising methods of CO2 reduction. It involves incorporation of CO2 into a solid phase via precipitation of carbonate minerals. A prerequisite to carbonate precipitation is the availability of aqueous metal cations and a network of porous media for fluid flow and water-rock interactions. The Hellisheidi-Threngsli lava field in SW Iceland comprises ideal conditions for studying the feasibility of permanent CO2 storage as minerals in basaltic rocks. In this paper we report on a tracer test conducted between two wells at the Hellisheidi-Threngsli site to characterize the physical properties of the main aquifers. The results suggest that most of the water flow between the wells is through an homogenous thick layer with high tortuosity along flow paths and a high reactive surface area for water-rock interactions.
Ectomycorrhizal fungi in mineral soil
Authors: Rosling A. , Rosenstock N. 
Published: August 2008

AbstractEctomycorrhizal fungi are mutualistic symbionts of many forest trees and play a major role in nutrient uptake. They form diverse communities in boreal forest soils but functional differences within this group of fungi remain largely unknown. We study ectomycorrhzal fungi in mineral soil to determine how abiotic preferences influence their spatial distribution in stratified soil profiles. This is achieved by correlative field studies of species distribution and soil characteristics at a spatial resolution relevant to soil heterogeneity and mycelial size. Field sampling strategies are being evaluated to establish a protocol for simultaneous small-sample analysis of ectomycorrhizal community and soil chemical variables. Species-specific substrate preferences are examined by studies of regulation of enzymatic and biogeochemical activity in response to relevant organic and inorganic sources of phosphorus. Studies of four species in the genus Piloderma have demonstrated that different strategies to obtain phosphorus are reflected by their spatial distribution in a podzol soil profile.
Dissolution of diopside and basaltic glass: the effect of carbonate coating
Authors: Stockmann G. , Wolff-Boenisch D. , Gíslason S. R. , Oelkers E. H. 
Published: August 2008

AbstractFar-from-equilibrium dissolution experiments with diopside and basaltic glass in mixed-flow reactors at 70°C and pH 8.2 show that solute concentrations do not reach steady state over the experimental duration of 45—60 days. Chemical modelling indicates that during the dissolution experiments, solutions have become supersaturated with respect to carbonates in the case of diopside, and carbonates, clay minerals and zeolites in the case of the basaltic glass. Decreasing dissolution is therefore interpreted as a result of secondary surface precipitates blocking the reactive surface area. Calcite formation was supported in both experiments by a significant increase in Ca (and Sr) concentrations as pH was abruptly lowered from 8.2 to 7 because this change increased carbonate solubility and caused all potential carbonate precipitates to re-dissolve. The reduction in pH also led to an increase in Si concentration for diopside and a decrease in Si concentration for basaltic glass. This observation is in accordance with previous experiments on the pH-dependent dissolution rates of pyroxenes and basaltic glass.
Solute profiles in soils, weathering gradients and exchange equilibrium/disequilibrium
Authors: White A. F. , Schulz M. S. , Stonestrom D. A. , Vivit D. V. , Fitzpatrick J. , Bullen T. 
Published: August 2008

AbstractThe spatial and temporal changes in hydrology and pore water elemental and 87/86Sr compositions were used to determine contemporary weathering rates in a 65 to 226 ky old soil chronosequence formed from granitic sediments deposited on marine terraces along coastal California. Cl-corrected Na, K and Si increased with depth denoting inputs from the weathering of plagioclase and K-feldspar. Solute 87/86Sr exhibited progressive mixing of sea water-dominated precipitation with inputs from less radiogenic plagioclase. Linear approximations to these weathering gradients were used to determine plagioclase weathering rates of between 0.38 and 8.9x10-15 moles m-2 s-1. The lack of corresponding weathering gradients for Ca and Sr indicated short-term equilibrium with the clay ion exchange pool which requires periodic resetting by natural perturbations to maintain continuity, in spite of soil composition changes reflecting the effects of long-term weathering.
Anaerobic pyrite oxidation rates determined via direct volume-loss measurements: a Vertical Scanning Interferometric approach
Authors: Avery E. R. , Benning L. G. 
Published: August 2008

AbstractPresented here are quantitative dissolution rate data (volume of pyrite lost/time) for the inorganic oxidation of pyrite in synthetic, anaerobic and acidic (pH 2) hydrothermal vent fluids (HVF) from experiments where the volume loss was measured directly via Vertical Scanning Interferometry (VSI). The VSI-derived reaction rate was 2.12x10-10±1.14x10-1 mol/m2/min, which is ∼2 to 4 orders of magnitude slower than pyrite oxidation rates previously determined using traditional batch experiments where rates are calculated based on changes in solution chemistry. This lower rate stems primarily from differences in experimental conditions (i.e. water to rock ratios, vigorous vs. gentle stir rates, grain-size effects, time), yet the rates derived here are believed to be more representative of pyrite oxidation in natural environments where more static and high solution to solid rate conditions prevail, such as seafloor conditions or acid-mine-drainage environments.
Dissolution rates of crystalline basalt at pH 4 and 10 and 25-75°C
Authors: Gudbrandsson S. , Wolff-Boenisch D. , Gíslason S. R. , Oelkers E. H. 
Published: August 2008

AbstractFar-from-equilibrium dissolution rates of crystalline basalt were measured in a mixed-flow reactor at pH 4 and 10, and at temperatures from 25 to 75ºC. The material used was obtained from a dyke on Stapafell Mountain on Reykjanes peninsula in Iceland because of its similarity with previous experiments on dissolution rates on basaltic glass by Oelkers and Gislason (2001) and Gislason and Oelkers (2003). Comparison of dissolution rates of basaltic glass and of crystalline basalt of similar chemical composition (from Gislason and Oelkers, 2003) indicates lower rates for crystalline material.