bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of thePseudomonasQuinolone Signal on Denitrification inPseudomonas aeruginosa
Authors: Toyofuku Masanori , Nomura Nobuhiko , Kuno Eriko , Tashiro Yosuke , Nakajima Toshiaki , Uchiyama Hiroo 
Published: October 2008

ABSTRACTDenitrification is a well-studied respiratory system that is also important in the biogeochemical nitrogen cycle. Environmental signals such as oxygen and N-oxides have been demonstrated to regulate denitrification, though how denitrification is regulated in a bacterial community remains obscure.Pseudomonas aeruginosais a ubiquitous bacterium that controls numerous genes through cell-to-cell signals. The bacterium possesses at least twoN-acyl-l-homoserine lactone (AHL) signals. In our previous study, these quorum-sensing signals controlled denitrification inP. aeruginosa. In addition to the AHL signals, a third cell-to-cell communication signal, 2-heptyl-3-hydroxy-4-quinolone, referred to as thePseudomonasquinolone signal (PQS), has been characterized. In this study, we examined the effect of PQS on denitrification to obtain more insight into the respiratory regulation in a bacterial community. Denitrification inP. aeruginosawas repressed by PQS, which was partially mediated by PqsR and PqsE. Measuring the denitrifying enzyme activities indicated that nitrite reductase activity was increased by PQS, whereas PQS inhibited nitric oxide reductase and the nitrate-respiratory chain activities. This is the first report to demonstrate that PQS influences enzyme activities, suggesting this effect is not specific toP. aeruginosa. Furthermore, when iron was supplied to the PQS-added medium, denitrifying activity was almost restored, indicating that the iron chelating property of PQS affected denitrification. Thus, our data indicate that PQS regulates denitrification primarily through iron chelation. The PQS effect on denitrification was relevant in a condition where oxygen was limited and denitrification was induced, suggesting its role in controlling denitrification where oxygen is present.
Different Signaling Roles of Two Conserved Residues in the Cytoplasmic Hairpin Tip of Tsr, the
Escherichia coli
Serine Chemoreceptor
Authors: Mowery Patricia , Ostler Jeffery B. , Parkinson John S. 
Published: October 2008

ABSTRACT

Bacterial chemoreceptors form ternary signaling complexes with the histidine kinase CheA through the coupling protein CheW. Receptor complexes in turn cluster into cellular arrays that produce highly sensitive responses to chemical stimuli. In
Escherichia coli
, receptors of different types form mixed trimer-of-dimers signaling teams through the tips of their highly conserved cytoplasmic domains. To explore the possibility that the hairpin loop at the tip of the trimer contact region might promote interactions with CheA or CheW, we constructed and characterized mutant receptors with amino acid replacements at the two nearly invariant hairpin charged residues of Tsr: R388, the most tip-proximal trimer contact residue, and E391, the apex residue of the hairpin turn. Mutant receptors were subjected to in vivo tests for the assembly and function of trimers, ternary complexes, and clusters. All R388 replacements impaired or destroyed Tsr function, apparently through changes in trimer stability or geometry. Large-residue replacements locked R388 mutant ternary complexes in the kinase-off (F, H) or kinase-on (W, Y) signaling state, suggesting that R388 contributes to signaling-related conformational changes in the trimer. In contrast, most E391 mutants retained function and all formed ternary signaling complexes efficiently. Hydrophobic replacements of any size (G, A, P, V, I, L, F, W) caused a novel phenotype in which the mutant receptors produced rapid switching between kinase-on and -off states, indicating that hairpin tip flexibility plays an important role in signal state transitions. These findings demonstrate that the receptor determinants for CheA and CheW binding probably lie outside the hairpin tip of the receptor signaling domain.
Metabolic Network Model of a Human Oral Pathogen
Authors: Mazumdar Varun , Snitkin Evan S. , Amar Salomon , Segrè Daniel 
Published: October 2008

ABSTRACTThe microbial community present in the human mouth is engaged in a complex network of diverse metabolic activities. In addition to serving as energy and building-block sources, metabolites are key players in interspecies and host-pathogen interactions. Metabolites are also implicated in triggering the local inflammatory response, which can affect systemic conditions such as atherosclerosis, obesity, and diabetes. While the genome of several oral pathogens has been sequenced, quantitative understanding of the metabolic functions of any oral pathogen at the system level has not been explored yet. Here we pursue the computational construction and analysis of the genome-scale metabolic network ofPorphyromonas gingivalis, a gram-negative anaerobe that is endemic in the human population and largely responsible for adult periodontitis. Integrating information from the genome, online databases, and literature screening, we built a stoichiometric model that encompasses 679 metabolic reactions. By using flux balance approaches and automated network visualization, we analyze the growth capacity under amino-acid-rich medium and provide evidence that amino acid preference and cytotoxic by-product secretion rates are suitably reproduced by the model. To provide further insight into the basic metabolic functions ofP. gingivalisand suggest potential drug targets, we study systematically how the network responds to any reaction knockout. We focus specifically on the lipopolysaccharide biosynthesis pathway and identify eight putative targets, one of which has been recently verified experimentally. The current model, which is amenable to further experimental testing and refinements, could prove useful in evaluating the oral microbiome dynamics and in the development of novel biomedical applications.
Identification of Two Genes, sll0804 and slr1306, as Putative Components of the CO
2
-Concentrating Mechanism in the Cyanobacterium
Synechocystis
sp. Strain PCC 6803
Authors: Zhang Shulu , Spann Kevin W. , Frankel Laurie K. , Moroney James V. , Bricker Terry M. 
Published: October 2008

ABSTRACT

Insertional transposon mutations in the sll0804 and slr1306 genes were found to lead to a loss of optimal photoautotrophy in the cyanobacterium
Synechocystis
sp. strain PCC 6803 grown under ambient CO
2
concentrations (350 ppm). Mutants containing these insertions (4BA2 and 3ZA12, respectively) could grow photoheterotrophically on glucose or photoautotrophically at elevated CO
2
concentrations (50,000 ppm). Both of these mutants exhibited an impaired affinity for inorganic carbon. Consequently, the Sll0804 and Slr1306 proteins appear to be putative components of the carbon-concentrating mechanism in
Synechocystis
sp. strain PCC 6803.
Molecular detection of nematicidal crystalliferousBacillus thuringiensisstrains of Iran and evaluation of their toxicity on free-living and plant-parasitic nematodes
Authors: Salehi Jouzani Gholamreza , Seifinejad Ali , Saeedizadeh Abbas , Nazarian Amin , Yousefloo Majid , Soheilivand Saeed , Mousivand Maryam , Jahangiri Rosa , Yazdani Mehdi , Amiri Reza Maali , Akbari Sepideh 
Published: October 2008

The characterization of nematode-effective strains and cry genes in the Iranian Bacillus thuringiensis (Bt) collection (70 isolates) is presented. Characterization was based on PCR analysis using 12 specific primers for cry5, cry6, cry12, cry13, cry14, and cry21 genes encoding proteins active against nematodes, crystal morphology, and protein band patterns as well as their nematicidal activity on root-knot nematode ( Meloidogyne incognita ) and two free-living nematodes ( Chiloplacus tenuis and Acrobeloides enoplus ). PCR results with primers for these genes showed that 22 isolates (31.5%) contain a minimum of one nematode-active cry gene. Strains containing the cry6 gene were the most abundant and represent 22.8% of the isolates. Bt strains harboring cry14 genes were also abundant (14.2%). cry21 and cry5 genes were less abundant, found in 4.2% and 2.8% of the strains, respectively. In total, six different nematode-active cry gene profiles were detected in this collection. Four isolates did not show the expected PCR product size for cry5, cry6, and cry21 genes; they might contain potentially novel insecticidal crystal protein genes. Twenty-two Bt isolates containing nematode-active cry genes were selected for preliminary bioassays on M. incognita. Based on these bioassays, four isolates were selected for detailed bioassays. Isolates YD5 and KON4 at 2 × 108 CFU/mL concentrations showed 77% and 81% toxicity on M. incognita, respectively. The free-living nematodes C. tenuis and A. enoplus were more susceptible and the highest mortality was observed within 48 h of incubation at all of the concentrations tested. Maximum mortality was recorded for isolates SN1 and KON4 at 2 × 108 CFU/mL concentrations and resulted in 68% and 77% adults deaths of C. tenuis and 68% and 72% for A. enoplus, respectively. Our results showed that PCR is a useful technique for toxicity prediction of nematicidal Bt isolates.
Enhanced plant nutrient use efficiency with PGPR and AMF in an integrated nutrient management system
Authors: Adesemoye A.O. , Torbert H.A. , Kloepper J.W. 
Published: October 2008

A 3 year field study was conducted with field corn from 2005 to 2007 to test the hypothesis that microbial inoculants that increase plant growth and yield can enhance nutrient uptake, and thereby remove more nutrients, especially N, P, and K from the field as part of an integrated nutrient management system. The field trial evaluated microbial inoculants, which include a commercially available plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhiza fungi (AMF), and their combination across 2 tillage systems (no-till and conventional till) and 2 fertilization regimes (poultry litter and ammonium nitrate). Data were collected on plant height, yield (dry mass of ears and silage), and nutrient content of corn grain and silage. In addition, nutrient content of soil was determined, and bioavailability of soil nutrient was measured with plant root simulator probes. Results showed that inoculants promoted plant growth and yield. For example, grain yields (kg·ha–1) in 2007 for inoculants were 7717 for AMF, 7260 for PGPR+AMF, 7313 for PGPR, 5725 for the control group, and for fertilizer were 7470 for poultry litter and 6537 for NH4NO3. Nitrogen content per gram of grain tissues was significantly enhanced in 2006 by inoculant, fertilizer, and their interactions. Significantly higher amounts of N, P, and K were removed from the plots with inoculants, based on total nutrient content of grain per plot. These results supported the overall hypothesis and indicate that application of inoculants can lead to reduction in the build up of N, P, and K in agricultural soils. Further studies should be conducted to combine microbial inoculants with reduced rates of fertilizer.
Analysis of time-lapse data from the Alba Field 4C/4D seismic survey
Authors: Hanson R. , Condon P. , Behrens R. , Groves S. , MacLeod M. 
Published: October 2008

The 1998 Alba 3D Ocean Bottom Cable (OBC) survey was designed to accomplish multiple objectives. The primary goal was to image low impedance reservoir sands with converted wave (PS) reflections; one important secondary goal was to image fluid movement by comparing the OBC data with a 1989 streamer survey. Modelling shows that a strong original oil–water contact reflector should be visible throughout much of the field and that water saturation changes should be observable by analysing the time-lapse differences between the 1989 streamer data and 1998 OBC survey. Differences between the 1989 and 1998 seismic field data confirm that fluid changes are clearly visible near several producing and injector wells. However, extracting additional quantitative saturation information from the seismic data has proven difficult, possibly because of: (a) complex interaction between the fluids, sands and shales within the Alba reservoir; (b) moderate to poor repeatability of the seismic response to reservoir fluids.
The focus of this paper is the acquisition and analysis of Alba time-lapse data. We show that production- and injection-related effects are predicted by modelling and observed in the data and then we make an attempt to relate these effects quantitatively to oil production and water injection. Despite the challenges in using the Alba time-lapse data quantitatively, the data have been successfully used qualitatively for well planning risk assessment and for guiding reservoir simulation efforts. Lessons from this work will be used in any future time-lapse surveys at Alba.
Alwyn North Triassic Main gas-condensate: drilling deeper promotes production
Authors: Harker S. D. , Richardson G. , Sides L. E. , Cooper R. 
Published: October 2008

Production of oil and gas in the Alwyn North Field, UKCS, commenced in 1987 from Middle Jurassic Brent and Lower Jurassic Statfjord reservoirs. In 1988, a deepened Statfjord producer well (3/9a-N21) detected gas in the underlying Triassic, but testing was not possible at that time. The 3/10b-2 exploration well, drilled in 1992 to the east of the field, tested gas at low rates from a poor quality Triassic reservoir section. In 1995 well 3/9a-N33, a deviated well, was drilled from the Alwyn platform to evaluate the productivity of the deep Triassic. This well penetrated 770 m of Upper Lunde section, which was tested at 1.3×10
6
m
3
per day of gas plus 4400 STB per day of condensate.

The Alwyn trap comprises a westerly dipping fault panel structure. Erosion over the crest of the tilted panel and the eastern-facing scarp slope by the Base Cretaceous Unconformity (BCU) truncates the Jurassic section down to the Upper Triassic. Sealing of the Triassic Main accumulation is by uppermost Triassic shales of the overlying Statfjord Formation and by Cretaceous mudrocks onlapping onto the BCU. Hydrocarbon charging of the Triassic Upper Lunde sandstones is from mature Late Jurassic Kimmeridge Clay source rocks that are juxtaposed against the reservoir along parts of the eastern frontal fault of the Alwyn panel.
The Upper Lunde (of Carnian to Rhaetian age) is a low net:gross reservoir section up to 800 m thick. The sediments are of semi-arid fluvial, floodplain and lacustrine origins, with the best reservoirs occurring in fluvial channel sandstones. The Late Triassic comprises four informal zones from A (top seal), through B and C to D reservoirs, above the Middle Lunde shale. The Triassic reservoir fluids are gas-condensate in the B and C units with an intraformational seal at the C–D boundary, beneath which lies volatile oil in the D unit.
A total of eight further Triassic production wells were added to the AlwynNorth Field by the end of 2001, as the development plan for Triassic Main progressed. These wells contribute in the order of 60% to the Alwyn North daily production.
Estimation of oil and gas column heights in prospects using probabilistic basin modelling methods
Authors: Sylta Øyvind , Krokstad Wenche 
Published: October 2008

Source rock and reservoir rock properties are often poorly constrained in the exploration for oil and gas. Geological analogues may be used to create source rock and reservoir rock models in areas with only sparse well data coverage. Exploration risks are often influenced by uncertainties in the rock facies models. This paper outlines a methodology for assessing the consequences of using two or more source and reservoir models on hydrocarbon phase distributions in prospects.
Each source rock and reservoir rock scenario is represented by computerized maps (grids) of thickness, porosities and other properties. The uncertainties of each scenario are described using probabilistic properties. The reservoir thickness may be represented by a uniform distribution with the mean described using a map (grid) with a standard deviation of, for example, 50 m. A Monte Carlo simulation is carried out for this part of the petroleum system and the resulting probabilities of oil and gas in prospects are compiled by weighting each run to calibration wells. The results can be plotted as a map of most likely oil and gas column heights. An uncertainty map is also plotted. The results can be used to rank drilling locations with respect to large oil columns and low uncertainties. The oil and gas column probabilities can be estimated for each well location.
As (more) wells are drilled within a petroleum system the best match simulations can be used to further refine predictions as well as to create an updated map of the petroleum system.
Organic geochemical characteristics of the bituminous Eocene units in the Çorum–Suluova Basin, Central Anatolia, Turkey
Authors: Altunsoy M. , Özçelik O. , Yalçin Erik N. 
Published: October 2008

In the Çorum–Suluova Basin (central Anatolia) the Eocene Çeltek and Armutlu formations consist of conglomerate, sandstone, siltstone, marl, mudstone, shale, limestone, clayey limestone, bituminous shale and coal. Total organic carbon (TOC) values in the Çeltek Formation range between 0.1 and 8%. Rock-Eval analyses on core samples with the highest TOC values give hydrogen index (HI) values from 45–846 mgHC g
−1
TOC and oxygen index (OI) values from 9–64 mgCO
2
g
−1
TOC. The organic matter can be classified as Type I and Type II kerogen on the modified van Krevelen diagram.
T
max
values vary between 428° and 440°C, with an average of 436°C, indicating the catagenesis stage. Based on the microscopic studies, organic matter is composed of predominantly autochthonous algal and amorphous material, with a minor contribution of terrestrial material. The Çeltek Formation can be regarded as a source rock for hydrocarbons. The TOC content of the Armutlu Formation is poor. Samples consist of terrestrial and reworked organic matter. Vitrinite reflectance values are between 0.27% and 0.43%, with an average of 0.34%.
T
max
values are between 433°C and 436°C, with an average of 435°C. The HI value is between 29 mgHC g
−1
TOC and 39 mgHC g
−1
TOC. Considering the data, the Armutlu Formation cannot be the source rock.
From seismic to bed: surface–subsurface correlations within the turbiditic Cellino Formation (central Italy)
Authors: Carruba S. , Casnedi R. , Felletti F. 
Published: October 2008

The area east of the Gran Sasso Chain in central Italy has been explored in detail because it holds a hydrocarbon field (Cellino Field), located in the Lower Pliocene foredeep turbidites of the Cellino Formation. Correlation has been made between the hydrocarbon-bearing sedimentary bodies and the same stratigraphic intervals cropping out only few kilometres to the west. The area, thus, offers a rare example where comparison can be made between lithofacies – observed in the field, electrofacies – displayed by the electric logs of the wells, and seismofacies – revealed by seismic survey.
This surface–subsurface integrated study of the Cellino Formation has revealed the presence of different turbiditic facies associations, their related electrical expressions and the possibility of a seismostratigraphic subdivision of the unit. These correlations exemplify the different resolution of these three complementary methods of investigation.
Analysis of petroleum system criticals of the Matruh–Shushan Basin, Western Desert, Egypt
Authors: Metwalli Farouk I. , Pigott John D. 
Published: October 2008

A systematic analysis of petroleum system criticals can provide a robust review of a basin's hydrocarbon potential through time and space. The ten essential petroleum system criticals that express the extensive and intensive variables are: source generation volume (S
gv
), source-rock richness (S
gr
), source-rock quality (S
rq
), source-rock maturity (S
rm
), reservoir rock volume (R
rv
), reservoir rock quality (R
rq
), reservoir rock hydrocarbon type (R
rhct
), reservoir rock seal and closure (R
rsc
), flux migration path (F
mp
) and petroleum system timing (PS
t
). The Matruh–Shushan Basin of the Western Desert, Egypt, forms the basis for an example of the application of this technique.

Modelling and empirical data of source-rock criticals reveal that the Mesozoic source generation megasequence is restricted in the Matruh–Shushan Basin. Presently, these areas lie buried at their maximum experienced temperatures. Potential reservoirs in portions of the north and central Western Desert were dependent upon lateral migration path criticals for their charge. Progressive uplift and basin inversion since the middle Palaeozoic provided favourable conditions for lateral migration in the Mesozoic. The main potential source rocks in the present basins are the Lower Cretaceous Alam El Bueib (AEB) and the Jurassic Khatatba. Although both share mixed kerogen types (II/III), they attained their highest levels of thermal maturity at different times. Basin modelling suggests the Lower Cretaceous AEB entered the oil window in the Late Cretaceous, while the Jurassic Khatatba of the deeper part of the basin entered the oil window in the Turonian.
Charge risks increase in the deeper basin megasequences in which migration hydrocarbons must traverse the basin updip. The migration pathways were principally lateral ramps and faults which enabled migration into the shallower post-Late Cretaceous structured reservoirs.
Basin modelling incorporating an analysis of the petroleum system criticals has outlined the spatial and temporal extent of the different petroleum systems in the Matruh–Shushan Basin and can help guide the next exploration phase. While oil exploration is now focused appropriately along Late Cretaceous and Tertiary migration paths, these results suggest deeper sections may have reservoirs charged with significant unrealized gas potential.