bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Barley Succession and Take-All Disease as Environmental Factors Shaping the Rhizobacterial Community during Take-All Decline
Authors: Schreiner Karin , Hagn Alexandra , Kyselková Martina , Moënne-Loccoz Yvan , Welzl Gerhard , Munch Jean Charles , Schloter Michael 
Published: June 2010

ABSTRACTThe root disease take-all, caused byGaeumannomyces graminisvar.tritici, can be managed by monoculture-induced take-all decline (TAD). This natural biocontrol mechanism typically occurs after a take-all outbreak and is believed to arise from an enrichment of antagonistic populations in the rhizosphere. However, it is not known whether these changes are induced by the monoculture or by ecological rhizosphere conditions due to a disease outbreak and subsequent attenuation. This question was addressed by comparing the rhizosphere microflora of barley, either inoculated with the pathogen or noninoculated, in a microcosm experiment in five consecutive vegetation cycles. TAD occurred in soil inoculated with the pathogen but not in noninoculated soil. Bacterial community analysis using terminal restriction fragment length polymorphism of 16S rRNA showed pronounced population shifts in the successive vegetation cycles, but pathogen inoculation had little effect. To elucidate rhizobacterial dynamics during TAD development, a 16S rRNA-based taxonomic microarray was used.Actinobacteriawere the prevailing indicators in the first vegetation cycle, whereas the third cycle—affected most severely by take-all—was characterized byProteobacteria,Bacteroidetes,Chloroflexi,Planctomycetes, andAcidobacteria. Indicator taxa for the last cycle (TAD) belonged exclusively toProteobacteria, including several genera with known biocontrol traits. Our results suggest that TAD involves monoculture-induced enrichment of plant-beneficial taxa.
Evaluation of the
Limulus
Amebocyte Lysate and Recombinant Factor C Assays for Assessment of Airborne Endotoxin
Authors: Thorne Peter S. , Perry Sarah S. , Saito Rena , O'Shaughnessy Patrick T. , Mehaffy John , Metwali Nervana , Keefe Thomas , Donham Kelley J. , Reynolds Stephen J. 
Published: June 2010

ABSTRACT

As a potent inflammatory agent, endotoxin is a key analyte of interest for studies of lung ailments in domestic environments and occupational settings with organic dust. A relatively unexplored advance in endotoxin exposure assessment is the use of recombinant factor C (rFC) from the
Limulus
pathway in a fluorometric assay. In this study, we compared airborne endotoxin concentrations in laboratory- and field-collected parallel air samples using the kinetic
Limulus
amebocyte lysate (LAL) assay and the rFC assay. Air sampling was performed using paired Institute of Occupational Medicine (IOM) samplers, Button samplers, closed-face cassettes, and cyclone samplers. Field sampling was performed in 10 livestock production facilities, including those housing swine, chicken, turkey, dairy cows, cattle, and horses. Laboratory sampling was performed in exposure chambers using resuspended airborne dust collected in five livestock facilities. Paired samples were extracted in pyrogen-free water with 0.05% Tween 20 and analyzed using LAL and rFC assays. In 402 field sample pairs there was excellent agreement between endotoxin concentrations determined by LAL and rFC (
r
= 0.93;
P
< 0.0001). In 510 laboratory sample pairs there was also excellent agreement between the two assays (
r
= 0.86;
P
< 0.0001). Correlations for subgroups of facility or dust type ranged from 0.65 to 0.96. Mixed-model analysis of variance (ANOVA) for the field studies showed significant interactions of facility-sampler and facility-assay. rFC/LAL ratios of the geometric means were 0.9 to 1.14 for the samplers (not significantly different from 1.0). The data from this study demonstrate that the LAL assay and the rFC assay return similar estimates of exposure in livestock facilities. Both methods provided suitable lower limits of detection such that all but 19 of 1,824 samples were quantifiable.
Weathering-Associated Bacteria from the Damma Glacier Forefield: Physiological Capabilities and Impact on Granite Dissolution
Authors: Frey Beat , Rieder Stefan R. , Brunner Ivano , Plötze Michael , Koetzsch Stefan , Lapanje Ales , Brandl Helmut , Furrer Gerhard 
Published: June 2010

ABSTRACT

Several bacterial strains isolated from granitic rock material in front of the Damma glacier (Central Swiss Alps) were shown (i) to grow in the presence of granite powder and a glucose-NH
4
Cl minimal medium without additional macro- or micronutrients and (ii) to produce weathering-associated agents. In particular, four bacterial isolates (one isolate each of
Arthrobacter
sp.,
Janthinobacterium
sp.,
Leifsonia
sp., and
Polaromonas
sp.) were weathering associated. In comparison to what was observed in abiotic experiments, the presence of these strains caused a significant increase of granite dissolution (as measured by the release of Fe, Ca, K, Mg, and Mn). These most promising weathering-associated bacterial species exhibited four main features rendering them more efficient in mineral dissolution than the other investigated isolates: (i) a major part of their bacterial cells was attached to the granite surfaces and not suspended in solution, (ii) they secreted the largest amounts of oxalic acid, (iii) they lowered the pH of the solution, and (iv) they formed significant amounts of HCN. As far as we know, this is the first report showing that the combined action of oxalic acid and HCN appears to be associated with enhanced elemental release from granite, in particular of Fe. This suggests that extensive microbial colonization of the granite surfaces could play a crucial role in the initial soil formation in previously glaciated mountain areas.
Biosynthesis of Cylindrospermopsin and 7-Epicylindrospermopsin in
Oscillatoria
sp. Strain PCC 6506: Identification of the
cyr
Gene Cluster and Toxin Analysis
Authors: Mazmouz Rabia , Chapuis-Hugon Florence , Mann Stéphane , Pichon Valérie , Méjean Annick , Ploux Olivier 
Published: June 2010

ABSTRACT

Cylindrospermopsin is a cytotoxin produced by
Cylindrospermopsis raciborskii
and other cyanobacteria that has been implicated in human intoxications. We report here the complete sequence of the gene cluster responsible for the biosynthesis of this toxin in
Oscillatoria
sp. strain PCC 6506. This cluster of genes was found to be homologous with that of
C. raciborskii
but with a different gene organization. Using an enzyme-linked immunosorbent assay and an optimized liquid chromatography analytical method coupled to tandem mass spectrometry, we detected 7-epicylindrospermopsin, cylindrospermopsin, and 7-deoxycylindrospermopsin in the culture medium of axenic
Oscillatoria
PCC 6506 at the following relative concentrations: 68.6%, 30.2%, and 1.2%, respectively. We measured the intracellular and extracellular concentrations, per mg of dried cells of
Oscillatoria
PCC 6506, of 7-epicylindrospermopsin (0.18 μg/mg and 0.29 μg/mg, respectively) and cylindrospermopsin (0.10 μg/mg and 0.11 μg/mg, respectively). We showed that these two toxins accumulated in the culture medium of
Oscillatoria
PCC 6506 but that the ratio (2.5 ± 0.3) was constant with 7-epicylindrospermopsin being the major metabolite. We also determined the concentrations of these toxins in culture media of other
Oscillatoria
strains, PCC 6407, PCC 6602, PCC 7926, and PCC 10702, and found that, except for PCC 6602, they all produced 7-epicylindrospermopsin and cylindrospermopsin, with the former being the major toxin, except for PCC 7926, which produced very little 7-epicylindrospermopsin. All the cylindrospermopsin producers studied gave a PCR product using specific primers for the amplification of the
cyrJ
gene from genomic DNA.
Enumeration and Characterization of Antimicrobial-Resistant
Escherichia coli
Bacteria in Effluent from Municipal, Hospital, and Secondary Treatment Facility Sources
Authors: Galvin Sandra , Boyle Fiona , Hickey Paul , Vellinga Akke , Morris Dearbháile , Cormican Martin 
Published: June 2010

ABSTRACT

We describe a modification of the most probable number (MPN) method for rapid enumeration of antimicrobial-resistant
Escherichia
coli
bacteria in aqueous environmental samples.
E. coli
(total and antimicrobial-resistant) bacteria were enumerated in effluent samples from a hospital (
n
= 17) and municipal sewers upstream (
n
= 5) and downstream (
n
= 5) from the hospital, effluent samples from throughout the treatment process (
n
= 4), and treated effluent samples (
n
= 13). Effluent downstream from the hospital contained a higher proportion of antimicrobial-resistant
E. coli
than that upstream from the hospital. Wastewater treatment reduced the numbers of
E. coli
bacteria (total and antimicrobial resistant); however, antimicrobial-resistant
E. coli
was not eliminated, and
E. coli
resistant to cefotaxime (including extended-spectrum beta-lactamase [ESBL] producers), ciprofloxacin, and cefoxitin was present in treated effluent samples.
Predator-Prey Chemical Warfare Determines the Expression of Biocontrol Genes by Rhizosphere-Associated
Pseudomonas fluorescens
Authors: Jousset Alexandre , Rochat Laurène , Scheu Stefan , Bonkowski Michael , Keel Christoph 
Published: June 2010

ABSTRACT

Soil bacteria are heavily consumed by protozoan predators, and many bacteria have evolved defense strategies such as the production of toxic exometabolites. However, the production of toxins is energetically costly and therefore is likely to be adjusted according to the predation risk to balance the costs and benefits of predator defense. We investigated the response of the biocontrol bacterium
Pseudomonas fluorescens
CHA0 to a common predator, the free-living amoeba
Acanthamoeba castellanii
. We monitored the effect of the exposure to predator cues or direct contact with the predators on the expression of the
phlA
,
prnA
,
hcnA
, and
pltA
genes, which are involved in the synthesis of the toxins, 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin, hydrogen cyanide, and pyoluteorin, respectively. Predator chemical cues led to 2.2-, 2.0-, and 1.2-fold increases in
prnA
,
phlA
, and
hcnA
expression, respectively, and to a 25% increase in bacterial toxicity. The upregulation of the tested genes was related to the antiprotozoan toxicity of the corresponding toxins. Pyrrolnitrin and DAPG had the highest toxicity, suggesting that bacteria secrete a predator-specific toxin cocktail. The response of the bacteria was elicited by supernatants of amoeba cultures, indicating that water-soluble chemical compounds were responsible for induction of the bacterial defense response. In contrast, direct contact of bacteria with living amoebae reduced the expression of the four bacterial toxin genes by up to 50%, suggesting that protozoa can repress bacterial toxicity. The results indicate that predator-prey interactions are a determinant of toxin production by rhizosphere
P. fluorescens
and may have an impact on its biocontrol potential.
Complete Genome Sequence of the Electricity-Producing “
Thermincola potens
” Strain JR
Authors: Byrne-Bailey Kathryne G. , Wrighton Kelly C. , Melnyk Ryan A. , Agbo Peter , Hazen Terry C. , Coates John D. 
Published: June 2010

ABSTRACT

“
Thermincola potens
” strain JR is one of the first Gram-positive dissimilatory metal-reducing bacteria (DMRB) for which there is a complete genome sequence. Consistent with the physiology of this organism, preliminary annotation revealed an abundance of multiheme
c
-type cytochromes that are putatively associated with the periplasm and cell surface in a Gram-positive bacterium. Here we report the complete genome sequence of strain JR.
CcpA Mediates Proline Auxotrophy and Is Required forStaphylococcus aureusPathogenesis
Authors: Li Chunling , Sun Fei , Cho Hoonsik , Yelavarthi Vamshi , Sohn Changmo , He Chuan , Schneewind Olaf , Bae Taeok 
Published: June 2010

ABSTRACTHuman clinical isolates ofStaphylococcus aureus, for example, strains Newman and N315, cannot grow in the absence of proline, albeit their sequenced genomes harbor genes for two redundant proline synthesis pathways. We show here that under selective pressure,S. aureusNewman generates proline-prototrophic variants at a frequency of 3 × 10−6, introducing frameshift and missense mutations inccpAor IS1811insertions inptsH, two regulatory genes that carry out carbon catabolite repression (CCR) in staphylococci and other Gram-positive bacteria.S. aureusNewman variants with mutations inrocF(arginase),rocD(ornithine aminotransferase), andproC(Δ1-pyrroline 5-carboxylate [P5C] reductase) are unable to generate proline-prototrophic variants, whereas a variant with a mutation inocd(ornithine cyclodeaminase) is unaffected. Transposon insertion inccpAalso restored proline prototrophy. CcpA was shown to repress transcription ofrocFandrocD, encoding the first two enzymes, but not ofproC, encoding the third and final enzyme in the P5C reductase pathway. CcpA bound to the upstream regions ofrocFandrocDbut not to that ofproC. CcpA's binding to the upstream regions was greatly enhanced by phosphorylated HPr. The CCR-mediated proline auxotrophy was lifted when nonpreferred carbohydrates were used as the sole carbon source. TheccpAmutant displayed reduced staphylococcal load and replication in a murine model of staphylococcal abscess formation, indicating that carbon catabolite repression presents an important pathogenesis strategy ofS. aureusinfections.
Allelic Diversity amongHelicobacter pyloriOuter Membrane Protein GeneshomBandhomAGenerated by Recombination
Authors: Oleastro Mónica , Cordeiro Rita , Ménard Armelle , Gomes João Paulo 
Published: June 2010

ABSTRACTRecombination is one of the main mechanisms contributing toHelicobacter pylorigenomic variability.homBandhomAare paralogous genes coding forH. pyloriouter membrane proteins (OMPs). Both genes display allelic variation yielded by polymorphisms of the genes' middle regions, with six different alleles. This study used bioinformatic and statistical analyses to evaluate whether the allelic diversity ofhomBandhomAis generated by recombination. A detailed molecular analysis of the most prevalenthomBallelic variant was also performed to establish its molecular profile. The two most prevalenthomBandhomAallelic variants resulted from interallelic homologous recombination between the rarest allelic variants of each gene, with a crossover point localized in the middle of the genes, containing the allelic region. Molecular analysis of the most prevalenthomBallele revealed a geographic partition among Western and East Asian strains, more noticeable for the 5′ and 3′homBregions than for the middle allelic regions. In conclusion, the diversity of the 5′ and 3′homBregions reflect the strains' geographical origin, and variants likely occur via the accumulation of single nucleotide polymorphisms. On the other hand, homologous recombination seems to play an important role in the diversification of the highly polymorphichomBandhomAallele-defining regions, where the most prevalent alleles worldwide result from genomic exchange between the rarest variants of each gene, suggesting that the resulting combinations confer biological advantages toH. pylori. This phenomenon illustrates an evolutionary scenario in which recombination appears to be associated with ecological success.
Complete Genome Sequence of
Bifidobacterium longum
JDM301
Authors: Wei Yan-Xia , Zhang Zhuo-Yang , Liu Chang , Zhu Yong-Zhang , Zhu Yong-Qiang , Zheng Huajun , Zhao Guo-Ping , Wang Shengyue , Guo Xiao-Kui 
Published: June 2010

ABSTRACT

Bifidobacteria, known as probiotic bacteria, are high-G+C Gram-positive bacteria which naturally inhabit the human gastrointestinal tract and vagina. Recently, we completely sequenced
Bifidobacterium longum
JDM301, which is a widely used Chinese commercial strain with several probiotic properties.
Initial experience with angioplasty of symptomatic M2 MCA atheromatous lesions
Authors: Hussain Muhammad Shazam , Cheng-Ching Esteban , Bain Mark , Spiotta Alejandro M , Sivapatham Thinesh , Hui Ferdinand , Moskowitz Shaye I , Gupta Rishi 
Published: June 2010

Background and purposeSymptomatic intracranial atherosclerosis has been associated with a high rate of recurrent stroke. The safety of treatment of more distal atheromatous lesions with angioplasty has not been systematically reported.MethodsWe retrospectively reviewed our institutional database for all patients treated with intracranial angioplasty and stenting from January 2008 to July 2009. A total of 108 patients were treated and five patients were treated with angioplasty for a symptomatic M2 middle cerebral artery stenosis with fluctuating neurological examinations. We report our experience with these patients.ResultsAll five patients underwent technically successful treatment with a reduction of the stenosis to <50%. There were no periprocedural complications and all patients had cessation of their clinical fluctuations. Two patients were found to have symptomatic restenosis with one patient suffering a disabling stroke at 5 months and the second patient a transient ischemic attack at 4 months who was subsequently successfully re-treated with angioplasty and stent placement.ConclusionsAngioplasty of M2 MCA lesions is technically feasible in our cohort of neurologically unstable patients, but the durability of this treatment will require more extensive study.
Dynamic Single-Cell Network Profiles in Acute Myelogenous Leukemia Are Associated with Patient Response to Standard Induction Therapy
Authors: Kornblau Steven M. , Minden Mark D. , Rosen David B. , Putta Santosh , Cohen Aileen , Covey Todd , Spellmeyer David C. , Fantl Wendy J. , Gayko Urte , Cesano Alessandra 
Published: June 2010

Abstract
Purpose: Complete response to induction chemotherapy is observed in ∼60% of patients with newly diagnosed non-M3 acute myelogenous leukemia (AML). However, no methods exist to predict with high accuracy at the individual patient level the response to standard AML induction therapy.
Experimental Design: We applied single-cell network profiling (SCNP) using flow cytometry, a tool that allows a comprehensive functional assessment of intracellular signaling pathways in heterogeneous tissues, to two training cohorts of AML samples (n = 34 and 88) to predict the likelihood of response to induction chemotherapy.
Results: In the first study, univariate analysis identified multiple signaling “nodes” (readouts of modulated intracellular signaling proteins) that correlated with response (i.e., AUCROC ≥ 0.66; P ≤ 0.05) at a level greater than age. After accounting for age, similar findings were observed in the second study. For patients &lt;60 years old, complete response was associated with the presence of intact apoptotic pathways. In patients ≥60 years old, nonresponse was associated with FLT3 ligand–mediated increase in phosphorylated Akt and phosphorylated extracellular signal-regulated kinase. Results were independent of cytogenetics, FLT3 mutational status, and diagnosis of secondary AML.
Conclusions: These data emphasize the value of performing quantitative SCNP under modulated conditions as a basis for the development of tests highly predictive for response to induction chemotherapy. SCNP provides information distinct from other known prognostic factors such as age, secondary AML, cytogenetics, and molecular alterations and is potentially combinable with the latter to improve clinical decision making. Independent validation studies are warranted. Clin Cancer Res; 16(14); 3721–33. ©2010 AACR.
Intercohort Gene Expression Co-Analysis Reveals Chemokine Receptors as Prognostic Indicators in Ewing's Sarcoma
Authors: Bennani-Baiti Idriss M. , Cooper Aaron , Lawlor Elizabeth R. , Kauer Maximilian , Ban Jozef , Aryee Dave N.T. , Kovar Heinrich 
Published: June 2010

Abstract
Purpose: We report a novel analytic method, named intercohort co-analysis or Ican, which aids in the discovery of genes with predictive value for the progression or outcome of diseases from small-size cohorts. We tested this premise in Ewing's sarcoma (ES), a highly metastatic cancer of bone and soft tissues that lacks validated molecular metastasis and prognostic indicators.
Experimental Design: To uncover genes significantly expressed in ES patient subsets, we first determined a nonarbitrary gene expression significance cutoff based on expression levels in validated expressing and nonexpressing tissues. We next searched for genes that were consistently significantly expressed in several ES cohort and cell line datasets. Significantly expressed genes were independently validated by quantitative reverse transcription-PCR in an additional ES cohort.
Results: Analysis of ES cohorts revealed marked intercohort gene expression variability. After filtering out the intercohort variability, CXCR4 and CXCR7 were found to be consistently associated with specific ES subsets. Pairwise analyses showed CXCR4 to correlate with ES metastases, and CXCR4 and CXCR7 to patient survival, but not with several other clinicopathological variables.
Conclusion: Ican is a powerful novel method to identifying genes consistently associated with particular disease states in cancers for which large cohorts are not available, currently the case of most cancers. We report for the first time that high CXCR4 expression preferentially associates with metastatic ES, and that of CXCR7 with poor patient survival. Clin Cancer Res; 16(14); 3769–78. ©2010 AACR.
The Importance of Genetic Counseling, DNA Diagnostics, and Cardiologic Family Screening in Left Ventricular Noncompaction Cardiomyopathy
Authors: Hoedemaekers Yvonne M. , Caliskan Kadir , Michels Michelle , Frohn-Mulder Ingrid , van der Smagt Jasper J. , Phefferkorn Judith E. , Wessels Marja W. , ten Cate Folkert J. , Sijbrands Eric J.G. , Dooijes Dennis , Majoor-Krakauer Danielle F. 
Published: June 2010

Background—
Left ventricular (LV) noncompaction (LVNC) is a distinct cardiomyopathy featuring a thickened bilayered LV wall consisting of a thick endocardial layer with prominent intertrabecular recesses with a thin, compact epicardial layer. Similar to hypertrophic and dilated cardiomyopathy, LVNC is genetically heterogeneous and was recently associated with mutations in sarcomere genes. To contribute to the genetic classification for LVNC, a systematic cardiological family study was performed in a cohort of 58 consecutively diagnosed and molecularly screened patients with isolated LVNC (49 adults and 9 children).

Methods and Results—
Combined molecular testing and cardiological family screening revealed that 67%of LVNC is genetic. Cardiological screening with electrocardiography and echocardiography of 194 relatives from 50 unrelated LVNC probands revealed familial cardiomyopathy in 32 families (64%), including LVNC, hypertrophic cardiomyopathy, and dilated cardiomyopathy. Sixty-three percent of the relatives newly diagnosed with cardiomyopathy were asymptomatic. Of 17 asymptomatic relatives with a mutation, 9 had noncompaction cardiomyopathy. In 8 carriers, nonpenetrance was observed. This may explain that 44% (14 of 32) of familial disease remained undetected by ascertainment of family history before cardiological family screening. The molecular screening of 17 genes identified mutations in 11 genes in 41% (23 of 56) tested probands, 35% (17 of 48) adults and 6 of 8 children. In 18 families, single mutations were transmitted in an autosomal dominant mode. Two adults and 2 children were compound or double heterozygous for 2 different mutations. One adult proband had 3 mutations. In 50% (16 of 32) of familial LVNC, the genetic defect remained inconclusive.

Conclusion—
LVNC is predominantly a genetic cardiomyopathy with variable presentation ranging from asymptomatic to severe. Accordingly, the diagnosis of LVNC requires genetic counseling, DNA diagnostics, and cardiological family screening.