bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of Tinto River Sediment Microbial Communities: Importance of Sulfate-Reducing Bacteria and Their Role in Attenuating Acid Mine Drainage
Authors: Sánchez-Andrea Irene , Knittel Katrin , Amann Rudolf , Amils Ricardo , Sanz José Luis 
Published: April 2012

ABSTRACT

Tinto River (Huelva, Spain) is a natural acidic rock drainage (ARD) environment produced by the bio-oxidation of metallic sulfides from the Iberian Pyritic Belt. This study quantified the abundance of diverse microbial populations inhabiting ARD-related sediments from two physicochemically contrasting sampling sites (SN and JL dams). Depth profiles of total cell numbers differed greatly between the two sites yet were consistent in decreasing sharply at greater depths. Although catalyzed reporter deposition fluorescence
in situ
hybridization with domain-specific probes showed that
Bacteria
(>98%) dominated over
Archaea
(<2%) at both sites, important differences were detected at the class and genus levels, reflecting differences in pH, redox potential, and heavy metal concentrations. At SN, where the pH and redox potential are similar to that of the water column (pH 2.5 and +400 mV), the most abundant organisms were identified as iron-reducing bacteria:
Acidithiobacillus
spp. and
Acidiphilium
spp., probably related to the higher iron solubility at low pH. At the JL dam, characterized by a banded sediment with higher pH (4.2 to 6.2), more reducing redox potential (−210 mV to 50 mV), and a lower solubility of iron, members of sulfate-reducing genera
Syntrophobacter
,
Desulfosporosinus
, and
Desulfurella
were dominant. The latter was quantified with a newly designed CARD-FISH probe. In layers where sulfate-reducing bacteria were abundant, pH was higher and redox potential and levels of dissolved metals and iron were lower. These results suggest that the attenuation of ARD characteristics is biologically driven by sulfate reducers and the consequent precipitation of metals and iron as sulfides.
Recombinogenic Properties of Pyrococcus furiosus Strain COM1 Enable Rapid Selection of Targeted Mutants
Authors: Farkas Joel , Stirrett Karen , Lipscomb Gina L. , Nixon William , Scott Robert A. , Adams Michael W. W. , Westpheling Janet 
Published: April 2012

ABSTRACT

We recently reported the isolation of a mutant of
Pyrococcus furiosus
, COM1, that is naturally and efficiently competent for DNA uptake. While we do not know the exact nature of this mutation, the combined transformation and recombination frequencies of this strain allow marker replacement by direct selection using linear DNA. In testing the limits of its recombination efficiency, we discovered that marker replacement was possible with as few as 40 nucleotides of flanking homology to the target region. We utilized this ability to design a strategy for selection of constructed deletions using PCR products with subsequent excision, or “pop-out,” of the selected marker. We used this method to construct a “markerless” deletion of the
trpAB
locus in the GLW101 (COM1 Δ
pyrF
) background to generate a strain (JFW02) that is a tight tryptophan auxotroph, providing a genetic background with two auxotrophic markers for further strain construction. The utility of
trpAB
as a selectable marker was demonstrated using prototrophic selection of plasmids and genomic DNA containing the wild-type
trpAB
alleles. A deletion of
radB
was also constructed that, surprisingly, had no obvious effect on either recombination or transformation, suggesting that its gene product is not involved in the COM1 phenotype. Attempts to construct a
radA
deletion mutation were unsuccessful, suggesting that this may be an essential gene. The ease and speed of this procedure will facilitate the construction of strains with multiple genetic changes and allow the construction of mutants with deletions of virtually any nonessential gene.
TatAc, the Third TatA Subunit of
Bacillus subtilis
, Can Form Active Twin-Arginine Translocases with the TatCd and TatCy Subunits
Authors: Monteferrante Carmine G. , Baglieri Jacopo , Robinson Colin , van Dijl Jan Maarten 
Published: April 2012

ABSTRACT

Two independent twin-arginine translocases (Tat) for protein secretion were previously identified in the Gram-positive bacterium
Bacillus subtilis
. These consist of the TatAd-TatCd and TatAy-TatCy subunits. The function of a third TatA subunit named TatAc was unknown. Here, we show that TatAc can form active protein translocases with TatCd and TatCy.
Detecting Genetic Introgression: High Levels of Intersubspecific Recombination Found in Xylella fastidiosa in Brazil
Authors: Nunney Leonard , Yuan Xiaoli , Bromley Robin E. , Stouthamer Richard 
Published: April 2012

ABSTRACT

Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in
Xylella fastidiosa
subsp.
pauca
from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (
leuA
,
petC
,
malF
,
cysG
, and
holC
). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another
X. fastidiosa
subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that
X. fastidiosa
subsp.
pauca
became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly
X. fastidiosa
subsp.
multiplex
). This hypothesis predicts that nonrecombinant native
X. fastidiosa
subsp.
pauca
(not yet isolated) does not cause disease in citrus or coffee.
Expression of the Arginine Deiminase Pathway Genes in Lactobacillus sakei Is Strain Dependent and Is Affected by the Environmental pH
Authors: Rimaux T. , Rivière A. , Illeghems K. , Weckx S. , De Vuyst L. , Leroy F. 
Published: April 2012

ABSTRACT

The adaptation of
Lactobacillus sakei
to a meat environment is reflected in its metabolic potential. For instance, the ability to utilize arginine through the arginine deiminase (ADI) pathway, resulting in additional ATP, represents a competitive benefit. In
L. sakei
CTC 494, the
arc
operon (
arcABCTDR
) shows the same gene order and organization as that in
L. sakei
23K, the genome sequence of which is known. However, differences in relative gene expression were found, and these seemed to be optimal in different growth phases, namely, the highest relative gene expression level was in the end exponential growth phase in the case of
L. sakei
CTC 494 and in the mid-exponential growth phase of
L. sakei
23K. Also, the environmental pH influenced the relative expression level of the
arc
operon, as shown for
L. sakei
CTC 494, with the highest relative expression level occurring at the optimal pH for growth (pH 6.0). Deviations from this optimal pH (pH 5.0 and pH 7.0) resulted in an overall decline of the relative expression level of all genes of the
arc
operon. Furthermore, a differential relative expression of the individual genes of the
arc
operon was found, with the highest relative gene expression occurring for the first two genes of the
arc
operon (
arcA
and
arcB
). Finally, it was shown that some
L. sakei
strains were able to convert agmatine into putrescine, suggesting an operational agmatine deiminase pathway in these strains, a metabolic trait that is undesirable in meat fermentations. This study shows that this metabolic trait is most probably encoded by a previously erroneously annotated second putative
arc
operon.
Involvement of a Natural Fusion of a Cytochrome P450 and a Hydrolase in Mycophenolic Acid Biosynthesis
Authors: Hansen Bjarne Gram , Mnich Ewelina , Nielsen Kristian Fog , Nielsen Jakob Blæsbjerg , Nielsen Morten Thrane , Mortensen Uffe Hasbro , Larsen Thomas Ostenfeld , Patil Kiran Raosaheb 
Published: April 2012

ABSTRACT

Mycophenolic acid (MPA) is a fungal secondary metabolite and the active component in several immunosuppressive pharmaceuticals. The gene cluster coding for the MPA biosynthetic pathway has recently been discovered in
Penicillium brevicompactum
, demonstrating that the first step is catalyzed by MpaC, a polyketide synthase producing 5-methylorsellinic acid (5-MOA). However, the biochemical role of the enzymes encoded by the remaining genes in the MPA gene cluster is still unknown. Based on bioinformatic analysis of the MPA gene cluster, we hypothesized that the step following 5-MOA production in the pathway is carried out by a natural fusion enzyme MpaDE, consisting of a cytochrome P450 (MpaD) in the N-terminal region and a hydrolase (MpaE) in the C-terminal region. We verified that the fusion gene is indeed expressed in
P. brevicompactum
by obtaining full-length sequence of the
mpaDE
cDNA prepared from the extracted RNA. Heterologous coexpression of
mpaC
and the fusion gene
mpaDE
in the MPA-nonproducer
Aspergillus nidulans
resulted in the production of 5,7-dihydroxy-4-methylphthalide (DHMP), the second intermediate in MPA biosynthesis. Analysis of the strain coexpressing
mpaC
and the
mpaD
part of
mpaDE
shows that the P450 catalyzes hydroxylation of 5-MOA to 4,6-dihydroxy-2-(hydroxymethyl)-3-methylbenzoic acid (DHMB). DHMB is then converted to DHMP, and our results suggest that the hydrolase domain aids this second step by acting as a lactone synthase that catalyzes the ring closure. Overall, the chimeric enzyme MpaDE provides insight into the genetic organization of the MPA biosynthesis pathway.
Interleukin-10 Induction Is an Important Virulence Function of the Yersinia pseudotuberculosis Type III Effector YopM
Authors: McPhee Joseph B. , Mena Patricio , Zhang Yue , Bliska James B. 
Published: May 2012

ABSTRACTPathogenicYersiniaspecies modulate host immune responses through the activity of a plasmid-encoded type III secretion system and its associated effector proteins. One effector, YopM, is a leucine-rich-repeat-containing protein that is important for virulence in murine models ofYersiniainfection. Although the mechanism by which YopM promotes virulence is unknown, we previously demonstrated that YopM was required for the induction of high levels of the immunosuppressive cytokine interleukin-10 (IL-10) in sera of C57BL/6J mice infected withYersinia pseudotuberculosis. To determine if IL-10 production is important for the virulence function of YopM, C57BL/6J or congenic IL-10−/−mice were infected intravenously with wild-type oryopMmutantY. pseudotuberculosisstrains. Analysis of cytokine levels in serum and bacterial colonization in the spleen and liver showed that YopM is required for IL-10 induction in C57BL/6J mice infected with either the IP32953 or the 32777 strain ofY. pseudotuberculosis, demonstrating that the phenotype is conserved in the species. In single-strain infections, the ability of the 32777ΔyopMmutant to colonize the liver was significantly increased by the delivery of exogenous IL-10 to C57BL/6J mice. In mixed infections, the competitive advantage of ayopM+32777 strain over an isogenicyopMmutant to colonize spleen and liver, as observed for C57BL/6J mice, was significantly reduced in IL-10−/−animals. Thus, by experimentally controlling IL-10 levels in a mouse infection model, we obtained evidence that the induction of this cytokine is an important mechanism by which YopM contributes toY. pseudotuberculosisvirulence.
Socio-demographic determinants of worsening in frailty among community-dwelling older people in 11 European countries
Authors: Etman Astrid , Burdorf Alex , Van der Cammen Tischa J M , Mackenbach Johan P , Van Lenthe Frank J 
Published: April 2012

BackgroundThe rapid increase of frail older people worldwide will have a substantial impact on healthcare systems. The frailty process may be delayed or even reversed, which makes it attractive for early interventions. However, little is known about the determinants of frailty state changes. The aim of this study is to compare socio-demographic determinants of worsening in frailty state in 11 European countries.MethodsData of 14 424 community-dwelling persons aged ≥55 years, enrolled in 2004 in the Survey of Health, Ageing and Retirement in Europe, were analysed. Three frailty states were identified (non-frail, pre-frail and frail) using Fried's criteria, and frailty state changes over a 2-year period were determined. Multinomial regression analyses adjusted for baseline frailty state were conducted to investigate whether sex, age, marital status and level of education determined a worsening in frailty state in the total and country-specific European population.ResultsOf all individuals, 22.1% worsened, 61.8% showed no change and 16.1% improved in frailty state. Women, those aged ≥65 years, and lower educated persons showed an increased risk of worsening in frailty state. In Southern European countries, there was an earlier and larger increase in risk of worsening in frailty state in life, which was more pronounced in women compared with men.ConclusionsIn Europe, persons aged ≥65 years, women and lower educated persons are at increased risk of worsening in frailty state. Differences between countries indicate that interventions aimed at delaying the frailty process in Southern European countries should start earlier with more attention towards women.
Seven-year hospital and nursing home care use according to age and proximity to death: variations by cause of death and socio-demographic position
Authors: Martikainen Pekka , Murphy Michael , Metsä-Simola Niina , Häkkinen Unto , Moustgaard Heta 
Published: April 2012

BackgroundProvision of hospital and long-term care services for the growing number of older people is a major policy concern. The authors estimate hospital and nursing home care use by age and proximity to death for selected causes and by gender, education and marital status.MethodsA 40% random sample of the Finnish population aged 65+ years alive at the end of 1997 was followed to death in 1998–2002. Use of hospital and nursing home care was assessed up to 7 years prior to death for those who died and prior to the end of 2002 for survivors.ResultsIn the 7-year period, before death total average care days were 294 (95% CI 286 to 301) for men and 430 (95% CI 423 to 438) for women. For surviving men and women, the corresponding figures were 89 (95% CI 86 to 92) and 136 (95% CI 130 to 141) days. Use of hospital and particularly nursing home care increased rapidly with age, while proximity to death was more important for hospital care. The married used less care than the non-married. Care use of those dying from dementia was approximately twice that for all causes combined and was substantial for an extended period before death.ConclusionsThe effects of age are more substantial for nursing home than for hospital care use, and both are larger the older the age at death. Care use will be considerably higher among the non-married. Increasing longevity coupled with a rising trend of dementia is likely to mean a major shift towards higher nursing home care use in the future.
Dose–response relationships between physical activity, walking and health-related quality of life in mid-age and older women
Authors: Heesch Kristiann C , van Uffelen Jannique G Z , van Gellecum Yolanda R , Brown Wendy J 
Published: April 2012

BackgroundAlthough physical activity is associated with health-related quality of life (HRQL), the nature of the dose–response relationship remains unclear.ObjectivesTo examine the concurrent and prospective dose–response relationships between total physical activity (TPA) and (only) walking with HRQL in two age cohorts of women.MethodsParticipants were 10 698 women born in 1946–1951 and 7646 born in 1921–1926, who completed three mailed surveys for the Australian Longitudinal Study on Women's Health. They reported weekly TPA minutes (sum of walking, moderate and vigorous minutes). HRQL was measured with the Medical Outcomes Study Short-Form 36 Health Status Survey (SF-36). Linear mixed models, adjusted for socio-demographic and health-related variables, were used to examine associations between TPA level (none, very low, low, intermediate, sufficient, high and very high) and SF-36 scores. For women who reported walking as their only physical activity, associations between walking and SF-36 scores were also examined.ResultsCurvilinear trends were observed between TPA and walking with SF-36 scores. Concurrently, HRQL scores increased significantly with increasing TPA and walking, in both cohorts, with increases less marked above sufficient activity levels. Prospectively, associations were attenuated although significant and meaningful improvements in physical functioning and vitality were observed across most TPA and walking categories above the low category.ConclusionFor women in their 50s–80s without clinical depression, greater amounts of TPA are associated with better current and future HRQL, particularly physical functioning and vitality. Even if walking is their only activity, women, particularly those in their 70s–80s, have better HRQL.
Evaluation of PIMA point-of-care CD4 testing in a large UK HIV service
Authors: Herbert Sophie , Edwards Simon , Carrick Gina , Copas Andrew , Sandford Christopher , Amphlett Marc , Benn Paul 
Published: April 2012

ObjectivesTo evaluate the performance and patient acceptability of the PIMA point-of-care (POCT) CD4 test.MethodsParallel POCT and laboratory CD4 testing were performed in newly diagnosed HIV patients and those with chronic infection attending routine or emergency clinics. Demographics, clinical status and time taken for CD4 results to be available were recorded. Patient acceptability was assessed using a five-point Likert scale. POCT and laboratory results were compared.Results283 patients underwent POCT and laboratory CD4 testing. Paired laboratory and POCT results were available in 269 patients. After excluding 15 patients tested during the lead-in period, the test comparison was based on 254 results. Most patients were asymptomatic, male and white British reflecting this patient cohort. 236 patients were chronically infected and 47 were newly diagnosed HIV positive. The POCT result was available within 30 min (86%). The laboratory and POCT results were strongly correlated, r=0.93 (p<0.001), but were generally lower for the POCT (201/254 (79%): p<0.001). As a percentage of the laboratory count, the median (95% range) POCT was 87% (57%–126%). The difference between the POCT and laboratory result was greater for those patients attending the emergency clinic. The sensitivity and specificity of the POCT, to identify patients with laboratory CD4 below 350, were 95% (95% CI 88% to 98%) and 88% (95% CI 82% to 93%), respectively. 235 (83%) patients completed the questionnaire and the POCT was highly acceptable.ConclusionsPOCT CD4 was highly correlated with laboratory CD4 testing in this cohort, provided immediate results and was highly acceptable to patients.
Comparison of berry composition of selectedVacciniumspecies (Ericaceae) withGaylussacia dumosa1This article is part of a Special Issue entitled “A tribute to Sam Vander Kloet FLS: Pure and applied research from blueberries to heathland ecology”.
Authors: Forney Charles F. , Kalt Wilhelmina , Vander Kloet Sam P. 
Published: May 2012

The genus Vaccinium contains a wide array of plants distributed throughout the world including several commercial species as well as epiphytic shrubs and lianas in the tropics. Vaccinium dumosum Andrews was reclassified as Gaylussacia dumosa (Andrews) Torr. & A. Gray in 1843 owing to its single seeded 10-locular ovary. Since then, evidence suggests G. dumosa be returned to Vaccinium. In this study, fruit composition of G. dumosa was compared with that of Vaccinium corymbosum L., Vaccinium angustifolium Aiton, Vaccinium gaulteriifolium (Griff.) Hook. f., Vaccinium acrobracteatum K. Sch., and Vaccinium hirsutum Buckley. Ripe fruit from each species were collected and analyzed. In each of the species, primary sugars were glucose and fructose, and acids were quinic, malic, and citric. Total phenolic content correlated with antioxidant capacity. Anthocyanin profiles showed that fruit from each of the species studied contained no pelargonidin glucosides, which are common in fruit of other genera. A total of 27 volatile compounds, dominated by terpenes and several esters, were detected. These volatiles were all found in four of the species including G. dumosa. No volatile compounds were detected in G. dumosa that were not found in the Vaccinium species. Gaylussacia dumosa showed no chemical composition that was significantly different than that of the Vaccinium species surveyed, suggesting that G. dumosa is aligned with Vaccinium.
Gold grain morphology and composition as an exploration tool: application to gold exploration in covered areas
Authors: Townley Brian K. , Hérail Gerard , Maksaev Victor , Palacios Carlos , Parseval Philippe de , Sepulveda Fabían , Orellana Rodrigo , Rivas Pablo , Ulloa Cesar 
Published: May 2012

The results of research in the use of Au grain morphological and compositional properties applied in primary Au ore exploration are presented here. Two different and independent topics are discussed: (1) morphological characteristics of Au grains from active stream sediments for use as a distance-to-source indicator; (2) compositional signature of Au grains from various deposit types for use as a discrimination tool for source type and present deposit erosion level determination. The purpose of this study is to improve and integrate these two approaches as an exploration tool for Andean covered areas.
Au grain morphology for over 1500 nuggets recovered from 60 active stream sediment samples in the Coastal Cordillera of Central Chile shows morphological variations (general shape, outline, surface, primary crystal imprints, associated minerals, flatness index) characteristic of three distance ranges (0–50 m; 50–300 m; >300 m) from source. Comparison with results from other similar studies of Au morphology characteristics in different climatic and/or sedimentological environments (arid, semi-arid, wet, lateritic, fluvial, fluvio-glacial and glacial) resulted in the determination of the recommended parameters (outline, surface, associated minerals, flatness index) to be used as distance-to-source indicator, independent of the climatic and/or sedimentological environment.
Au grain morphological characteristics may assist in location of target but are not indicators of source type. Study of Au composition via electron microprobe analysis of Au grain cores from epithermal, Au-rich porphyry and Au-rich porphyry Cu systems indicated Au–Ag–Cu contents to be the best discrimination tool for these different types of Au-bearing deposits. In addition, such analysis of grains recovered at different vertical levels from the Cerro Casale Au-rich porphyry provides evidence that the Au compositional signature for a single type of deposit can also aid in the determination of vertical position. This may provide an estimate of the current level of erosion and remaining potential of the source. Some limitations of the proposed techniques are: (1) Au liberated from rock fragments already distant from source would be common in cordilleran and glacial environments, although this would be a detectable feature; (2) these techniques are applicable only for coarse-Au sources; (3) estimate of erosion level of liberated Au is limited to the case here presented.