bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental controls on the Late Holocene carbonate sedimentation of a karstic lake in the Middle‐Atlas Mountains (Lake Afourgagh, Morocco)
Authors: Détriché Sébastien , Bréhéret Jean‐Gabriel , Karrat L'houcine , Hinschberger Florent , Macaire Jean‐Jacques 
Published: January 2013

AbstractThe Lake Afourgagh sediment record and facies successions provide an outstanding example of environmentally controlled carbonate sedimentation. Afourgagh is a small, shallow permanent lake located in the Middle‐Atlas Mountains in Morocco in a karstic context. It is fed by ground waters that are relatively enriched in Mg resulting from the leaching of the Jurassic dolomitic bedrock of the catchment. This eutrophic lake is episodically restricted and characterized by alkaline waters with a fluctuating high Mg/Ca ratio. The maximum extension of the Holocene shoreline coincides with evidence of a lake stabilization level corresponding to the outflow of the lake through a wadi. Lakeshore terrace sediments deposited on an alluvial fan siltstone during the past ca 2500 cal yr bp comprise four main facies: a littoral crust, palaeosols, palustrine silts and charophyte tufas, which reflect different environments from the shoreline toward the deeper water. In the more distal parts, the charophyte tufas display a well‐expressed lamination punctuated by the development of microstromatolites on algae thalli. The mineralogical composition of the carbonates is linked to the facies. While the charophyte tufas are characterized by a relatively high content in aragonite, in addition to low‐Mg calcite, the littoral crust is mainly composed of magnesite. This pattern is related to the evolving chemistry of water due to the influence of charophyte proliferation during dry summers. Calcium‐carbonate precipitation on algae thalli (both bioinduced and microbially mediated) progressively induces an increase in the Mg/Ca ratio of the lake water, while the capillary evaporation of shallow ground waters causes precipitation of a magnesite precursor on the shoreline, producing magnesite during early diagenesis. This effect is characteristic of two episodes: part of the Roman Warm Period and the beginning of the Dark Age Cold Period. The carbonate mineralogy of the different depositional sequences at Afourgagh indicates lake‐level and water‐chemistry fluctuations under a climatic influence. Therefore, among other regional records, the Lake Afourgagh sedimentary record provides useful evidence for reconstructing these environmental changes.
Deep hypothermia protects against acute hypoxia in vivo in rats: a mechanism related to the attenuation of oxidative stress
Authors: Alva Norma , Azuara Daniel , Palomeque Jesús , Carbonell Teresa 
Published: January 2013

New Findings
What is the central question of this study?Hypoxia generates extreme physiological stress. This stress leads to the formation of oxidants. The effects of hypothermia in oxidative stress are less well known, but hypothermia has recently been used to protect against ischaemic lesions. The mechanisms of such protection are, to date, unknown.
What is the main finding and its importance?We have used extreme conditions of hypoxia (10% oxygen) and hypothermia (22°C) to analyse the oxidant–antioxidant balance in rats. Our experimental findings suggest that hypothermia plays a protective role against lipid peroxidation in vivo through the preservation of reduced/oxidized glutathione, providing new insights into the use of hypothermia.
There is growing interest in using hypothermia to prevent hypoxic damage in clinical and experimental models, although the mechanisms regulated by hypothermia are still unclear. As reactive oxygen and nitrogen species are the main factors causing cellular damage, our objective was to study the scope of hypothermia in preventing hypoxia‐induced oxidative damage. We analysed systemic and hepatic indicators of oxidative stress after an acute hypoxic insult (10% oxygen in breathing air) in normothermic (37°C body temperature) and hypothermic conditions (22°C) in rats. Exposure to hypoxia resulted in tissue damage (aspartate aminotransferase increased from 54.6 ± 6.9 U l−1 in control animals to 116 ± 1.9 U l−1 in hypoxia, and alanine aminotransferase increased from 19 ± 0.8 to 34 ± 2.9 U l−1), oxidative stress (nitric oxide metabolites increased from 10.8 ± 0.4 μm in control rats to 23 ± 2.7 μm in hypoxia, and thiobarbituric reactive substances increased from 3.3 ± 0.2 to 5.9 ± 0.4 nm) and antioxidant consumption (reduced/oxidized glutathione ratio changed from 9.8 ± 0.3 to 6.8 ± 0.3). In contrast, when hypothermia was applied prior to hypoxia, the situation was reversed, with a reduction in aspartate aminotransferase (from 116 ± 1.9 in hypoxic animals to 63 ± 7.8 U l−1 in animals exposed to hypothermia followed by hypoxia), alanine aminotransferase (from 34 ± 2.9 to 19 ± 0.9 U l−1), oxidative stress (nitric oxide metabolites decreased from 23 ± 2.7 to 17.8 ± 1.9 μm and thiobarbituric acid‐reactive substances decreased from 5.9 ± 0.4 to 4.3 ± 0.2 nm) and antioxidant preservation (reduced/oxidized glutathione ratio changed from 6.8 ± 0.3 to 11.1 ± 0.1). Hypoxia induced a decrease in liver enzymatic antioxidant activities even during hypothermia. Both treatments, hypoxia and hypothermia, produced a similar increase in hepatic caspase‐3 activity. In conclusion, hypothermia prevented the tissue damage and oxidative stress elicited by hypoxia. Our results provide new evidence concerning the protective mechanism of hypothermia in vivo.
Genetic Tools To Enhance the Study of Gene Function and Regulation in Staphylococcus aureus
Authors: Bose Jeffrey L. , Fey Paul D. , Bayles Kenneth W. 
Published: January 2013

ABSTRACT

The
bursa aurealis
transposon has been used to create transposon insertion libraries of
Bacillus anthracis
and
Staphylococcus aureus
. To provide a set of genetic tools to enhance the utility of these libraries, we generated an allelic-exchange system that allows for the replacement of the transposon with useful genetic markers and fluorescent reporter genes. These tools were tested in the Nebraska Transposon Mutant Library (NTML), containing defined transposon insertions in 1,952 nonessential
S. aureus
genes. First, we generated a plasmid that allows researchers to replace the genes encoding green fluorescent protein (GFP) and erythromycin resistance in the transposon with a noncoding DNA fragment, leaving a markerless mutation within the chromosome. Second, we produced allelic-exchange plasmids to replace the transposon with alternate antibiotic resistance cassettes encoding tetracycline, kanamycin, and spectinomycin resistance, allowing for the simultaneous selection of multiple chromosomal mutations. Third, we generated a series of fluorescent reporter constructs that, after allelic exchange, generate transcriptional reporters encoding codon-optimized enhanced cyan fluorescent protein (ECFP), enhanced yellow fluorescent protein (EYFP), DsRed.T3(DNT), and eqFP650, as well as superfolder green fluorescent protein (sGFP). Overall, combining the NTML with this allelic-exchange system provides an unparalleled resource for the study of
S. aureus
.
Genetic Diversity of Cryptosporidium spp. within a Remote Population of Soay Sheep on St. Kilda Islands, Scotland
Authors: Connelly L. , Craig B. H. , Jones B. , Alexander C. L. 
Published: January 2013

ABSTRACT

This is the first report to characterize the genotypes and subtypes of
Cryptosporidium
species infecting a geographically isolated population of feral Soay sheep (
Ovis aries
) on Hirta, St. Kilda, Scotland, during two distinct periods: (i) prior to a population crash and (ii) as host numbers increased.
Cryptosporidium
DNA was extracted by freeze-thawing of immunomagnetically separated (IMS) bead-oocyst complexes, and species were identified following nested-PCR-restriction fragment length polymorphism (RFLP)/PCR sequencing at two
Cryptosporidium
18S rRNA loci. Two hundred fifty-five samples were analyzed, and the prevalent
Cryptosporidium
species in single infections were identified as
C. hominis
(11.4% of all samples tested),
C. parvum
(9%),
C. xiaoi
(12.5%), and
C. ubiquitum
(6.7%).
Cryptosporidium parvum
was also present with other
Cryptosporidium
species in 27.1% of all samples tested.
Cryptosporidium parvum
- and
C. hominis
-positive isolates were genotyped using two nested-PCR assays that amplify the
Cryptosporidium
glycoprotein 60 gene (
GP60
).
GP60
gene analysis showed the presence of two
Cryptosporidium
genotypes, namely,
C. parvum
IIaA19G1R1 and
C. hominis
IbA10G2. This study reveals a higher diversity of
Cryptosporidium
species/genotypes than was previously expected. We suggest reasons for the high diversity of
Cryptosporidium
parasites within this isolated population and discuss the implications for our understanding of cryptosporidiosis.
Symbiont-Mediated Protection against Fungal Pathogens in Pea Aphids: a Role for Pathogen Specificity?
Authors: Parker Benjamin J. , Spragg Chelsea J. , Altincicek Boran , Gerardo Nicole M. 
Published: January 2013

ABSTRACT

Here we show that a bacterial endosymbiont,
Regiella insecticola
, protects pea aphids (
Acyrthosiphon pisum
) from the aphid-specific fungal entomopathogen
Zoophthora occidentalis
but not from the generalist insect fungal pathogen
Beauveria bassiana
. This finding highlights the complex influence of fungi on the dynamics of this economically important agricultural pest.
Recent Evolutionary Radiation and Host Plant Specialization in the Xylella fastidiosa Subspecies Native to the United States
Authors: Nunney Leonard , Vickerman Danel B. , Bromley Robin E. , Russell Stephanie A. , Hartman John R. , Morano Lisa D. , Stouthamer Richard 
Published: January 2013

ABSTRACT

The bacterial pathogen,
Xylella fastidiosa
, infects many plant species in the Americas, making it a good model for investigating the genetics of host adaptation. We used multilocus sequence typing (MLST) to identify isolates of the native U.S. subsp.
multiplex
that were largely unaffected by intersubspecific homologous recombination (IHR) and to investigate how their evolutionary history influences plant host specialization. We identified 110 “non-IHR” isolates, 2 minimally recombinant “intermediate” ones (including the subspecific type), and 31 with extensive IHR. The non-IHR and intermediate isolates defined 23 sequence types (STs) which we used to identify 22 plant hosts (73% trees) characteristic of the subspecies. Except for almond, subsp.
multiplex
showed no host overlap with the introduced subspecies (subspecies
fastidiosa
and
sandyi
). MLST sequences revealed that subsp.
multiplex
underwent recent radiation (<25% of subspecies age) which included only limited intrasubspecific recombination (ρ/θ = 0.02); only one isolated lineage (ST50 from ash) was older. A total of 20 of the STs grouped into three loose phylogenetic clusters distinguished by nonoverlapping hosts (excepting purple leaf plum): “almond,” “peach,” and “oak” types. These host differences were not geographical, since all three types also occurred in California. ST designation was a good indicator of host specialization. ST09, widespread in the southeastern United States, only infected oak species, and all peach isolates were ST10 (from California, Florida, and Georgia). Only ST23 had a broad host range. Hosts of related genotypes were sometimes related, but often host groupings crossed plant family or even order, suggesting that phylogenetically plastic features of hosts affect bacterial pathogenicity.
Development of a Rapid, Sensitive, and Field-Deployable Razor Ex BioDetection System and Quantitative PCR Assay for Detection of Phymatotrichopsis omnivora Using Multiple Gene Targets
Authors: Arif M. , Fletcher J. , Marek S. M. , Melcher U. , Ochoa-Corona F. M. 
Published: January 2013

ABSTRACT

A validated, multigene-based method using real-time quantitative PCR (qPCR) and the Razor Ex BioDetection system was developed for detection of
Phymatotrichopsis omnivora.
This soilborne fungus causes Phymatotrichopsis root rot of cotton, alfalfa, and other dicot crops in the southwestern United States and northern Mexico, leading to significant crop losses and limiting the range of crops that can be grown in soils where the fungus is established. It is on multiple lists of regulated organisms. Because
P. omnivora
is difficult to isolate, accurate and sensitive culture-independent diagnostic tools are needed to confirm infections by this fungus. Specific PCR primers and probes were designed based on
P. omnivora
nucleotide sequences of the genes encoding rRNA internal transcribed spacers, beta-tubulin, and the second-largest subunit of RNA polymerase II (RPB2). PCR products were cloned and sequenced to confirm their identity. All primer sets allowed early detection of
P. omnivora
in infected but asymptomatic plants. A modified rapid DNA purification method, which facilitates a quick (∼30-min) on-site assay capability for
P. omnivora
detection, was developed. Combined use of three target genes increased the assay accuracy and broadened the range of detection. To our knowledge, this is the first report of a multigene-based, field-deployable, rapid, and reliable identification method for a fungal plant pathogen and should serve as a model for the development of field-deployable assays of other phytopathogens.
Quantitative Detection of Viable Bifidobacterium bifidum BF-1 Cells in Human Feces by Using Propidium Monoazide and Strain-Specific Primers
Authors: Fujimoto Junji , Watanabe Koichi 
Published: January 2013

ABSTRACT

We developed a PCR-based method to detect and quantify viable
Bifidobacterium bifidum
BF-1 cells in human feces. This method (PMA-qPCR) uses propidium monoazide (PMA) to distinguish viable from dead cells and quantitative PCR using a BF-1-specific primer set designed from the results of randomly amplified polymorphic DNA analysis. During long-term culture (10 days), the number of viable BF-1 cells detected by counting the number of CFU on modified MRS agar, by measuring the ATP contents converted to CFU, and by using PMA-qPCR decreased from about 10
10
to 10
6
cells/ml; in contrast, the total number of (viable and dead) BF-1 cells detected by counting 4′,6-diamidino-2-phenylindolee (DAPI)-stained cells and by using qPCR without PMA and reverse transcription-qPCR remained constant. The number of viable BF-1 cells in fecal samples detected by using PMA-qPCR was highly and significantly correlated with the number of viable BF-1 cells added to the fecal samples, within the range of 10
5.3
to 10
10.3
cells/g feces (wet weight) (
r
> 0.99,
P
< 0.001). After 12 healthy subjects ingested 10
10.3
to 10
11.0
CFU of BF-1 in a fermented milk product daily for 28 days, 10
4.5 ï¿½ 1.5
(mean ï¿½ standard deviation [SD]) BF-1 CFU/g was detected in fecal samples by using strain-specific selective agar; in contrast, 10
6.2 ï¿½ 0.4
viable BF-1 cells/g were detected by using PMA-qPCR, and a total of 10
7.6 ï¿½ 0.7
BF-1 cells/g were detected by using qPCR without PMA. Thus, the number of viable BF-1 cells detected by PMA-qPCR was about 50 times higher (
P
< 0.01) than that detected by the culture-dependent method. We conclude that strain-specific PMA-qPCR can be used to quickly and accurately evaluate viable BF-1 in feces.
Constitutive Expression of the Cytochrome P450 EthABCD Monooxygenase System Enables Degradation of Synthetic Dialkyl Ethers in Aquincola tertiaricarbonis L108
Authors: Schuster Judith , Purswani Jessica , Breuer Uta , Pozo Clementina , Harms Hauke , Mï¿½ller Roland H. , Rohwerder Thore 
Published: January 2013

ABSTRACT

In
Rhodococcus ruber
IFP 2001,
Rhodococcus zopfii
IFP 2005, and
Gordonia
sp. strain IFP 2009, the cytochrome P450 monooxygenase EthABCD catalyzes hydroxylation of methoxy and ethoxy residues in the fuel oxygenates methyl
tert
-butyl ether (MTBE), ethyl
tert
-butyl ether (ETBE), and
tert
-amyl methyl ether (TAME). The expression of the IS
3
-type transposase-flanked
eth
genes is ETBE dependent and controlled by the regulator EthR (C. Malandain et al., FEMS Microbiol. Ecol. 72:289–296, 2010). In contrast, we demonstrated by reverse transcription-quantitative PCR (RT-qPCR) that the betaproteobacterium
Aquincola tertiaricarbonis
L108, which possesses the
ethABCD
genes but lacks
ethR
, constitutively expresses the P450 system at high levels even when growing on nonether substrates, such as glucose. The mutant strain
A. tertiaricarbonis
L10, which is unable to degrade dialkyl ethers, resulted from a transposition event mediated by a rolling-circle IS
91
-type element flanking the
eth
gene cluster in the wild-type strain L108. The constitutive expression of Eth monooxygenase is likely initiated by the housekeeping sigma factor σ
70
, as indicated by the presence in strain L108 of characteristic −10 and −35 binding sites upstream of
ethA
which are lacking in strain IFP 2001. This enables efficient degradation of diethyl ether, diisopropyl ether, MTBE, ETBE, TAME, and
tert
-amyl ethyl ether (TAEE) without any lag phase in strain L108. However, ethers with larger residues,
n
-hexyl methyl ether, tetrahydrofuran, and alkyl aryl ethers, were not attacked by the Eth system at significant rates in resting-cell experiments, indicating that the residue in the ether molecule which is not hydroxylated also contributes to the determination of substrate specificity.
Cytochrome P450 Initiates Degradation ofcis-Dichloroethene by Polaromonas sp. Strain JS666
Authors: Nishino Shirley F. , Shin Kwanghee A. , Gossett James M. , Spain Jim C. 
Published: January 2013

ABSTRACTPolaromonassp. strain JS666 grows oncis-1,2-dichoroethene (cDCE) as the sole carbon and energy source under aerobic conditions, but the degradation mechanism and the enzymes involved are unknown. In this study, we established the complete pathway forcDCE degradation through heterologous gene expression, inhibition studies, enzyme assays, and analysis of intermediates. Several lines of evidence indicate that a cytochrome P450 monooxygenase catalyzes the initial step ofcDCE degradation. Both the transient accumulation of dichloroacetaldehyde incDCE-degrading cultures and dichloroacetaldehyde dehydrogenase activities in cell extracts of JS666 support a pathway for degradation ofcDCE through dichloroacetaldehyde. The mechanism minimizes the formation ofcDCE epoxide. The molecular phylogeny of the cytochrome P450 gene and the organization of neighboring genes suggest that thecDCE degradation pathway recently evolved in a progenitor capable of degrading 1,2-dichloroethane either by the recruitment of the cytochrome P450 monooxygenase gene from an alkane catabolic pathway or by selection for variants of the P450 in a preexisting 1,2-dichloroethane catabolic pathway. The results presented here add yet another role to the broad array of productive reactions catalyzed by cytochrome P450 enzymes.
Homeostasis and Catabolism of Choline and Glycine Betaine: Lessons from Pseudomonas aeruginosa
Authors: Wargo Matthew J. 
Published: January 2013

ABSTRACTMost sequenced bacteria possess mechanisms to import choline and glycine betaine (GB) into the cytoplasm. The primary role of choline in bacteria appears to be as the precursor to GB, and GB is thought to primarily act as a potent osmoprotectant. Choline and GB may play accessory roles in shaping microbial communities, based on their limited availability and ability to enhance survival under stress conditions. Choline and GB enrichment near eukaryotes suggests a role in the chemical relationships between these two kingdoms, and some of these interactions have been experimentally demonstrated. While many bacteria can convert choline to GB for osmoprotection, a variety of soil- and water-dwelling bacteria have catabolic pathways for the multistep conversion of choline, via GB, to glycine and can thereby use choline and GB as sole sources of carbon and nitrogen. In these choline catabolizers, the GB intermediate represents a metabolic decision point to determine whether GB is catabolized or stored as an osmo- and stress protectant. This minireview focuses on this decision point inPseudomonas aeruginosa, which aerobically catabolizes choline and can use GB as an osmoprotectant and a nutrient source.P. aeruginosais an experimentally tractable and ecologically relevant model to study the regulatory pathways controlling choline and GB homeostasis in choline-catabolizing bacteria. The study ofP. aeruginosaassociations with eukaryotes and other bacteria also makes this a powerful model to study the impact of choline and GB, and their associated regulatory and catabolic pathways, on host-microbe and microbe-microbe relationships.
Genome Instability in Lactobacillus rhamnosus GG
Authors: Sybesma Wilbert , Molenaar Douwe , van IJcken Wilfred , Venema Koen , Kort Remco 
Published: January 2013

ABSTRACT

We describe here a comparative genome analysis of three dairy product isolates of
Lactobacillus rhamnosus
GG (LGG) and the ATCC 53103 reference strain to the published genome sequence of
L. rhamnosus
GG. The analysis showed that in two of three isolates, major DNA segments were missing from the genomic islands LGGISL1,2. The deleted DNA segments consist of 34 genes in one isolate and 84 genes in the other and are flanked by identical insertion elements. Among the missing genes are the
spaCBA
genes, which encode pilin subunits involved in adhesion to mucus and persistence of the strains in the human intestinal tract. Subsequent quantitative PCR analyses of six commercial probiotic products confirmed that two more products contain a heterogeneous population of
L. rhamnosus
GG variants, including genotypes with or without
spaC
. These results underline the relevance for quality assurance and control measures targeting genome stability in probiotic strains and justify research assessing the effect of genetic rearrangements in probiotics on the outcome of
in vitro
and
in vivo
efficacy studies.
Influence of Therapeutic Ceftiofur Treatments of Feedlot Cattle on Fecal and Hide Prevalences of Commensal Escherichia coli Resistant to Expanded-Spectrum Cephalosporins, and Molecular Characterization of Resistant Isolates
Authors: Schmidt John W. , Griffin Dee , Kuehn Larry A. , Brichta-Harhay Dayna M. 
Published: January 2013

ABSTRACT

In the United States, the
bla
CMY-2
gene contained within incompatibility type A/C (IncA/C) plasmids is frequently identified in extended-spectrum-cephalosporin-resistant (ESC
r
)
Escherichia coli
strains from both human and cattle sources. Concerns have been raised that therapeutic use of ceftiofur in cattle may increase the prevalence of ESC
r
E. coli
. We report that herd ESC
r
E. coli
fecal and hide prevalences throughout the residency of cattle at a feedlot, including during the period of greatest ceftiofur use at the feedlot, were either not significantly different (
P
≥ 0.05) or significantly less (
P
< 0.05) than the respective prevalences at arrival. Longitudinal sampling of cattle treated with ceftiofur demonstrated that once the transient increase of ESC
r
E. coli
shedding that follows ceftiofur injection abated, ceftiofur-injected cattle were no more likely than untreated members of the same herd to shed ESC
r
E. coli
. Pulsed-field gel electrophoresis (PFGE) genotyping, antibiotic resistance phenotyping, screening for presence of the
bla
CMY-2
gene, and plasmid replicon typing were performed on 312 ESC
r
E. coli
isolates obtained during six sampling periods spanning the 10-month residence of cattle at the feedlot. The identification of only 26 unique PFGE genotypes, 12 of which were isolated during multiple sampling periods, suggests that clonal expansion of feedlot-adapted
bla
CMY-2
E. coli
strains contributed more to the persistence of
bla
CMY-2
than horizontal transfer of IncA/C plasmids between
E. coli
strains at this feedlot. We conclude that therapeutic use of ceftiofur at this cattle feedlot did not significantly increase the herd prevalence of ESC
r
E. coli
.