bluuebunny/crossref_metadata_2025_split huggingface dataset:
An analysis of uncertainty in non‐equilibrium and equilibrium geothermobarometry
Authors: ASHWORTH J. R. , SHEPLEV V. S. , KHLESTOV V. V. , ANANYEV V. A. 
Published: January 2005

AbstractIn statistically optimised P–T estimation, the contributions to overall uncertainty from different sources are represented by ellipses. One source, for a diffusion‐controlled reaction at non‐equilibrium, is diffusion modelling of the reaction texture. This modelling is used to estimate ratios, Q, between free‐energy differences, ΔG, of reactions among mineral end‐members, to replace the equilibrium condition ΔG = 0. The associated uncertainty is compared with those already inherent in the equilibrium case (from end‐member data, activity models and mineral compositions). A compact matrix formulation is introduced for activity coefficients, and their partial derivatives governing error propagation. The non‐equilibrium example studied is a corona reaction with the assemblage Grt–Opx–Cpx–Pl–Qtz. Two garnet compositions are used, from opposite sides of the corona. In one of them, affected by post‐reaction Fe, Mg exchange with pyroxene, the problem of reconstructing the original composition is overcome by direct use of ratios between chemical‐potential differences, given by the diffusion modelling. The number of geothermobarometers in the optimisation is limited by near‐degeneracies. Their weightings are affected by strong correlations among Q ratios. Uncertainty from diffusion modelling is not large in comparison with other sources. Overall precision is limited mainly by uncertainties in activity models. Hypothetical equilibrium P–T are also estimated for both garnet compositions. By this approach, departure from equilibrium can be measured, with statistical uncertainties. For the example, the result for difference from equilibrium pressure is 1.2 ± 0.7 kbar.
Identification and Partial Characterization of the Nonribosomal Peptide Synthetase Gene Responsible for Cereulide Production in Emetic
Bacillus cereus
Authors: Ehling-Schulz Monika , Vukov Natasa , Schulz Anja , Shaheen Ranad , Andersson Maria , Märtlbauer Erwin , Scherer Siegfried 
Published: January 2005

ABSTRACT

Cereulide, a depsipeptide structurally related to valinomycin, is responsible for the emetic type of gastrointestinal disease caused by
Bacillus cereus
. Due to its chemical structure, (
d
-
O
-Leu-
d
-Ala-
l
-
O
-Val-
l
-Val)
3
, cereulide might be synthesized nonribosomally. Therefore, degenerate PCR primers targeted to conserved sequence motifs of known nonribosomal peptide synthetase (NRPS) genes were used to amplify gene fragments from a cereulide-producing
B. cereus
strain. Sequence analysis of one of the amplicons revealed a DNA fragment whose putative gene product showed significant homology to valine activation NRPS modules. The sequences of the flanking regions of this DNA fragment revealed a complete module that is predicted to activate valine, as well as a putative carboxyl-terminal thioesterase domain of the NRPS gene. Disruption of the peptide synthetase gene by insertion of a kanamycin cassette through homologous recombination produced cereulide-deficient mutants. The valine-activating module was highly conserved when sequences from nine emetic
B. cereus
strains isolated from diverse geographical locations were compared. Primers were designed based on the NRPS sequence, and the resulting PCR assay, targeting the
ces
gene, was tested by using a panel of 143
B. cereus
group strains and 40 strains of other bacterial species showing PCR bands specific for only the cereulide-producing
B. cereus
strains.
Activity and Diversity of Methanogens in a Petroleum Hydrocarbon-Contaminated Aquifer
Authors: Kleikemper Jutta , Pombo Silvina A. , Schroth Martin H. , Sigler William V. , Pesaro Manuel , Zeyer Josef 
Published: January 2005

ABSTRACT

Methanogenic activity was investigated in a petroleum hydrocarbon-contaminated aquifer by using a series of four push-pull tests with acetate, formate, H
2
plus CO
2
, or methanol to target different groups of methanogenic
Archaea
. Furthermore, the community composition of methanogens in water and aquifer material was explored by molecular analyses, i.e., fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes amplified with the
Archaea
-specific primer set ARCH915 and UNI-b-rev, and sequencing of DNA from dominant DGGE bands. Molecular analyses were subsequently compared with push-pull test data. Methane was produced in all tests except for a separate test where 2-bromoethanesulfonate, a specific inhibitor of methanogens, was added. Substrate consumption rates were 0.11 mM day
−1
for methanol, 0.38 mM day
−1
for acetate, 0.90 mM day
−1
for H
2
, and 1.85 mM day
−1
for formate. Substrate consumption and CH
4
production during all tests suggested that at least three different physiologic types of methanogens were present: H
2
plus CO
2
or formate, acetate, and methanol utilizers. The presence of 15 to 20 bands in DGGE profiles indicated a diverse archaeal population. High H
2
and formate consumption rates agreed with a high diversity of methanogenic
Archaea
consuming these substrates (16S rRNA gene sequences related to several members of the
Methanomicrobiaceae
) and the detection of
Methanomicrobiaceae
by using FISH (1.4% of total DAPI [4′,6-diamidino-2-phenylindole]-stained microorganisms in one water sample; probe MG1200). Considerable acetate consumption agreed with the presence of sequences related to the obligate acetate degrader
Methanosaeata concilii
and the detection of this species by FISH (5 to 22% of total microorganisms; probe Rotcl1). The results suggest that both aceticlastic and CO
2
-type substrate-consuming methanogens are likely involved in the terminal step of hydrocarbon degradation, while methanogenesis from methanol plays a minor role. DGGE profiles further indicate similar archaeal community compositions in water and aquifer material. The combination of hydrogeological and molecular methods employed in this study provide improved information on the community and the potential activity of methanogens in a petroleum hydrocarbon-contaminated aquifer.
Cyt1A of
Bacillus thuringiensis
Delays Evolution of Resistance to Cry11A in the Mosquito
Culex quinquefasciatus
Authors: Wirth Margaret C. , Park Hyun-Woo , Walton William E. , Federici Brian A. 
Published: January 2005

ABSTRACT

Insecticides based on
Bacillus thuringiensis
subsp.
israelensis
have been used for mosquito and blackfly control for more than 20 years, yet no resistance to this bacterium has been reported. Moreover, in contrast to
B. thuringiensis
subspecies toxic to coleopteran or lepidopteran larvae, only low levels of resistance to
B. thuringiensis
subsp.
israelensis
have been obtained in laboratory experiments where mosquito larvae were placed under heavy selection pressure for more than 30 generations. Selection of
Culex quinquefasciatus
with mutants of
B. thuringiensis
subsp.
israelensis
that contained different combinations of its Cry proteins and Cyt1Aa suggested that the latter protein delayed resistance. This hypothesis, however, has not been tested experimentally. Here we report experiments in which separate
C. quinquefasciatus
populations were selected for 20 generations to recombinant strains of
B. thuringiensis
that produced either Cyt1Aa, Cry11Aa, or a 1:3 mixture of these strains. At the end of selection, the resistance ratio was 1,237 in the Cry11Aa-selected population and 242 in the Cyt1Aa-selected population. The resistance ratio, however, was only 8 in the population selected with the 1:3 ratio of Cyt1Aa and Cry11Aa strains. When the resistant mosquito strain developed by selection to the Cyt1Aa-Cry11Aa combination was assayed against Cry11Aa after 48 generations, resistance to this protein was 9.3-fold. This indicates that in the presence of Cyt1Aa, resistance to Cry11Aa evolved, but at a much lower rate than when Cyt1Aa was absent. These results indicate that Cyt1Aa is the principal factor responsible for delaying the evolution and expression of resistance to mosquitocidal Cry proteins.
Enantioselective Synthesis ofS-Equol from Dihydrodaidzein by a Newly Isolated Anaerobic Human Intestinal Bacterium
Authors: Wang Xiu-Ling , Hur Hor-Gil , Lee Je Hyeon , Kim Ki Tae , Kim Su-Il 
Published: January 2005

ABSTRACTA newly isolated rod-shaped, gram-negative anaerobic bacterium from human feces, named Julong 732, was found to be capable of metabolizing the isoflavone dihydrodaidzein toS-equol under anaerobic conditions. The metabolite, equol, was identified by using electron impact ionization mass spectrometry,1H and13C nuclear magnetic resonance spectroscopy, and UV spectral analyses. However, strain Julong 732 was not able to produce equol from daidzein, and tetrahydrodaidzein and dehydroequol, which are most likely intermediates in the anaerobic metabolism of dihydrodaidzein, were not detected in bacterial culture medium containing dihydrodaidzein. Chiral stationary-phase high-performance liquid chromatography eluted only one metabolite,S-equol, which was produced from a bacterial culture containing a racemic mixture of dihydrodaidzein. Strain Julong 732 did not show racemase activity to transformR-equol toS-equol and vice versa. Its full 16S rRNA gene sequence (1,429 bp) had 92.8% similarity to that ofEggerthella hongkongenisHKU10. This is the first report of a single bacterium capable of converting a racemic mixture of dihydrodaidzein to enantiomeric pureS-equol.
Mercury Adaptation among Bacteria from a Deep-Sea Hydrothermal Vent
Authors: Vetriani Costantino , Chew Yein S. , Miller Susan M. , Yagi Jane , Coombs Jonna , Lutz Richard A. , Barkay Tamar 
Published: January 2005

ABSTRACT

Since deep-sea hydrothermal vent fluids are enriched with toxic metals, it was hypothesized that (i) the biota in the vicinity of a vent is adapted to life in the presence of toxic metals and (ii) metal toxicity is modulated by the steep physical-chemical gradients that occur when anoxic, hot fluids are mixed with cold oxygenated seawater. We collected bacterial biomass at different distances from a diffuse flow vent at 9°N on the East Pacific Rise and tested these hypotheses by examining the effect of mercuric mercury [Hg(II)] on vent bacteria. Four of six moderate thermophiles, most of which were vent isolates belonging to the genus
Alcanivorax
, and six of eight mesophiles from the vent plume were resistant to >10 μM Hg(II) and reduced it to elemental mercury [Hg(0)]. However, four psychrophiles that were isolated from a nearby inactive sulfide structure were Hg(II) sensitive. A neighbor-joining tree constructed from the deduced amino acids of a PCR-amplified fragment of
merA
, the gene encoding the mercuric reductase (MR), showed that sequences obtained from the vent moderate thermophiles formed a unique cluster (bootstrap value, 100) in the MR phylogenetic tree, which expanded the known diversity of this locus. The temperature optimum for Hg(II) reduction by resting cells and MR activity in crude cell extracts of a vent moderate thermophile corresponded to its optimal growth temperature, 45°C. However, the optimal temperature for activity of the MR encoded by transposon Tn
501
was found to be 55 to 65°C, suggesting that, in spite of its original isolation from a mesophile, this MR is a thermophilic enzyme that may represent a relic of early evolution in high-temperature environments. Results showing that there is enrichment of Hg(II) resistance among vent bacteria suggest that these bacteria have an ecological role in mercury detoxification in the vent environment and, together with the thermophilicity of MR, point to geothermal environments as a likely niche for the evolution of bacterial mercury resistance.
Redox Interactions betweenSaccharomyces cerevisiaeandSaccharomyces uvarumin Mixed Culture under Enological Conditions
Authors: Cheraiti Naoufel , Guezenec Stéphane , Salmon Jean-Michel 
Published: January 2005

ABSTRACTWine yeast starters that contain a mixture of different industrial yeasts with various properties may soon be introduced to the market. The mechanisms underlying the interactions between the different strains in the starter during alcoholic fermentation have never been investigated. We identified and investigated some of these interactions in a mixed culture containing two yeast strains grown under enological conditions. The inoculum contained the same amount (each) of a strain ofSaccharomyces cerevisiaeand a natural hybrid strain ofS. cerevisiaeandSaccharomyces uvarum. We identified interactions that affected biomass, by-product formation, and fermentation kinetics, and compared the redox ratios of monocultures of each strain with that of the mixed culture. The redox status of the mixed culture differed from that of the two monocultures, showing that the interactions between the yeast strains involved the diffusion of metabolite(s) within the mixed culture. Since acetaldehyde is a potential effector of fermentation, we investigated the kinetics of acetaldehyde production by the different cultures. TheS. cerevisiae-S. uvarumhybrid strain produced large amounts of acetaldehyde for which theS. cerevisiaestrain acted as a receiving strain in the mixed culture. Since yeast response to acetaldehyde involves the same mechanisms that participate in the response to other forms of stress, the acetaldehyde exchange between the two strains could play an important role in inhibiting some yeast strains and allowing the growth of others. Such interactions could be of particular importance in understanding the ecology of the colonization of complex fermentation media byS. cerevisiae.
Clinical and Environmental Isolates of
Legionella pneumophila
Serogroup 1 Cannot Be Distinguished by Sequence Analysis of Two Surface Protein Genes and Three Housekeeping Genes
Authors: Aurell Helena , Farge Pierre , Meugnier Hélène , Gouy Manolo , Forey Françoise , Lina Gérard , Vandenesch François , Etienne Jerome , Jarraud Sophie 
Published: January 2005

ABSTRACT

We used gene sequencing to determine whether clinical (sporadic, epidemic, and endemic) and environmental isolates of
Legionella pneumophila
serogroup (sg) 1 belong to specific lineages. A total of 178 clinical and environmental
L. pneumophila
sg 1 isolates, defined by pulsed-field gel electrophoresis and epidemiological data as sporadic, epidemic, or endemic, were analyzed for polymorphisms in five gene fragments. The fragments belonged to three housekeeping genes (coding for aconitase [
acn
], aspartate-β-semialdehyde dehydrogenase [
asd
], and RNA polymerase β subunit [
rpoB
]) and two surface protein genes (coding for the macrophage infectivity potentiator [
mip
] and the major outer membrane protein [
mompS
]). The phylogenetic tree inferred from sequence polymorphisms of the five genes identified two large clusters, one consisting of 133 poorly differentiated strains and containing two smaller clusters (10 and 2 strains) unrelated to each other and the other consisting of 42 strains. Clinical and environmental isolates could not be distinguished on this basis, and no link between genetic background and epidemiological type was found, suggesting that other factors are responsible for differences in pathogenicity.
Genetic Diversity and Horizontal Transfer of Genes Involved in Oxidation of Reduced Phosphorus Compounds by
Alcaligenes faecalis
WM2072
Authors: Wilson Marlena M. , Metcalf William W. 
Published: January 2005

ABSTRACT

Enrichment was performed to isolate organisms that could utilize reduced phosphorus compounds as their sole phosphorus sources. One isolate that grew well with either hypophosphite or phosphite was identified by 16S rRNA gene analysis as a strain of
Alcaligenes faecalis
. The genes required for oxidation of hypophosphite and phosphite by this organism were identified by using transposon mutagenesis and include homologs of the
ptxD
and
htxA
genes of
Pseudomonas stutzeri
WM88, which encode an NAD-dependent phosphite dehydrogenase (PtxD) and 2-oxoglutarate-dependent hypophosphite dioxygenase (HtxA). This organism also has the
htxB
,
htxC
, and
htxD
genes that comprise an ABC-type transporter, presumably for hypophosphite and phosphite transport. The role of these genes in reduced phosphorus metabolism was confirmed by analyzing the growth of mutants in which these genes were deleted. Sequencing data showed that
htxA
,
htxB
,
htxC
, and
htxD
are virtually identical to their homologs in
P. stutzeri
at the DNA level, indicating that horizontal gene transfer occurred. However,
A. faecalis ptxD
is very different from its
P. stutzeri
homolog and represents a new
ptxD
lineage. Therefore, this gene has ancient evolutionary roots in bacteria. These data suggest that there is strong evolutionary selection for the ability of microorganisms to oxidize hypophosphite and phosphite.
Effect of Sand and Sawdust Bedding Materials on the Fecal Prevalence of
Escherichia coli
O157:H7 in Dairy Cows
Authors: LeJeune Jeffrey T. , Kauffman Michael D. 
Published: January 2005

ABSTRACT

Farm management practices that reduce the prevalence of food-borne pathogens in live animals are predicted to enhance food safety. To ascertain the potential role of livestock bedding in the ecology and epidemiology of
Escherichia coli
O157:H7 on farms, the survival of this pathogen in used-sand and used-sawdust dairy cow bedding was determined. Additionally, a longitudinal study of mature dairy cattle housed on 20 commercial dairy farms was conducted to compare the prevalence of
E. coli
O157:H7 in cattle bedded on sand to that in cattle bedded on sawdust.
E. coli
O157:H7 persisted at higher concentrations in used-sawdust bedding than in used-sand bedding. The overall average herd level prevalence (3.1 versus 1.4%) and the number of sample days yielding any tests of feces positive for
E. coli
O157:H7 (22 of 60 days versus 13 of 60 days) were higher in sawdust-bedded herds. The choice of bedding material used to house mature dairy cows may impact the prevalence of
E. coli
O157:H7 on dairy farms.
Roseobacter
-Like Bacteria in Red and Mediterranean Sea Aerobic Anoxygenic Photosynthetic Populations
Authors: Oz Aia , Sabehi Gazalah , Koblízek Michal , Massana Ramon , Béjà Oded 
Published: January 2005

ABSTRACT

Bacteriochlorophyll
a
-containing aerobic anoxygenic phototrophs (AAnP) have been proposed to account for up to 11% of the total surface water microbial community and to potentially have great ecological importance in the world's oceans. Recently, environmental and genomic data based on analysis of the
pufM
gene identified the existence of α-proteobacteria as well as possible γ-like proteobacteria among AAnP in the Pacific Ocean. Here we report on analyses of environmental samples from the Red and Mediterranean Seas by using
pufM
as well as the
bchX
and
bchL
genes as molecular markers. The majority of photosynthesis genes retrieved from these seas were related to
Roseobacter
-like AAnP sequences. Furthermore, the sequence of a novel photosynthetic operon organization from an uncultured
Roseobacter
-like bacterial artificial chromosome retrieved from the Red Sea is described. The data show the presence of
Roseobacter
-like bacteria in Red and Mediterranean Sea AAnP populations in the seasons analyzed.
Cloning of
Beauveria bassiana
Chitinase Gene
Bbchit1
and Its Application To Improve Fungal Strain Virulence
Authors: Fang Weiguo , Leng Bo , Xiao Yuehua , Jin Kai , Ma Jincheng , Fan Yanhua , Feng Jing , Yang Xingyong , Zhang Yongjun , Pei Yan 
Published: January 2005

ABSTRACT

Entomopathogenic fungi can produce a series of chitinases, some of which act synergistically with proteases to degrade insect cuticle. However, chitinase involvement in insect fungus pathogenesis has not been fully characterized. In this paper, an endochitinase, Bbchit1, was purified to homogeneity from liquid cultures of
Beauveria bassiana
grown in a medium containing colloidal chitin. Bbchit1 had a molecular mass of about 33 kDa and pI of 5.4. Based on the N-terminal amino acid sequence, the chitinase gene,
Bbchit1
, and its upstream regulatory sequence were cloned.
Bbchit1
was intronless, and there was a single copy in
B. bassiana
. Its regulatory sequence contained putative CreA/Crel carbon catabolic repressor binding domains, which was consistent with glucose suppression of
Bbchit1
. At the amino acid level, Bbchit1 showed significant similarity to a
Streptomyces avermitilis
putative endochitinase, a
Streptomyces coelicolor
putative chitinase, and
Trichoderma harzianum
endochitinase Chit36Y. However,
Bbchit1
had very low levels of identity to other chitinase genes previously isolated from entomopathogenic fungi, indicating that
Bbchit1
was a novel chitinase gene from an insect-pathogenic fungus. A
gpd-Bbchit1
construct, in which
Bbchit1
was driven by the
Aspergiullus nidulans
constitutive promoter, was transformed into the genome of
B. bassiana
, and three transformants that overproduced Bbchit1 were obtained. Insect bioassays revealed that overproduction of Bbchit1 enhanced the virulence of
B. bassiana
for aphids, as indicated by significantly lower 50% lethal concentrations and 50% lethal times of the transformants compared to the values for the wild-type strain.
Role of Oxalic Acid Overexcretion in Transformations of Toxic Metal Minerals by
Beauveria caledonica
Authors: Fomina M. , Hillier S. , Charnock J. M. , Melville K. , Alexander I. J. , Gadd G. M. 
Published: January 2005

ABSTRACT

The fungus
Beauveria caledonica
was highly tolerant to toxic metals and solubilized cadmium, copper, lead, and zinc minerals, converting them into oxalates. This fungus was found to overexcrete organic acids with strong metal-chelating properties (oxalic and citric acids), suggesting that a ligand-promoted mechanism was the main mechanism of mineral dissolution. Our data also suggested that oxalic acid was the main mineral-transforming agent. Cadmium, copper, and zinc oxalates were precipitated by the fungus in the local environment and also in association with the mycelium. The presence of toxic metal minerals often led to the formation of mycelial cords, and in the presence of copper-containing minerals, these cords exhibited enhanced excretion of oxalic acid, which resulted in considerable encrustation of the cords by copper oxalate hydrate (moolooite). It was found that
B. caledonica
hyphae and cords were covered by a thick hydrated mucilaginous sheath which provided a microenvironment for chemical reactions, crystal deposition, and growth. Cryo-scanning electron microscopy revealed that mycogenic metal oxalates overgrew parental fungal hyphae, leaving a labyrinth of fungal tunnels within the newly formed mineral matter. X-ray absorption spectroscopy revealed that oxygen ligands played a major role in metal coordination within the fungal biomass during the accumulation of mobilized toxic metals by
B. caledonica
mycelium; these ligands were carboxylic groups in copper phosphate-containing medium and phosphate groups in pyromorphite-containing medium.