bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Chlamydia pneumoniae by colorimetric in situ hybridization
Authors: ALAKÄRPPÄ HANNU , SURCEL HELJÄ‐MARJA , LAITINEN KIRSI , JUVONEN TATU , SAIKKU PEKKA , LAURILA AINO 
Published: August 2009

Chlamydia pneumoniae causes chronic infections, which have been associated with cardiovascular diseases. The antigenic structures of the organism have been detected in atherosclerotic lesions by immunohistochemistry.We wanted to further evaluate the presence and localization of C. pneumoniae in different tissues by in situ hybridization. We established a new colorimetric in situ hybridization method using a digoxigenin‐labelled probe and studied the localization of C. pneumoniae in formalin‐fixed, paraffin‐embedded lungs of infected mice. We also used the method to study its presence in 12 abdominal aortic aneurysms. In C. pneumoniae‐infected mice, the organism was first detected in bronchial epithelial cells, and later in pneumocytes and endothelial cells. C. pneumoniae was also present in five of eight abdominal aortic aneurysms previously shown to be positive by immunohistochemistry. The findings are in accordance with the invasive nature of C. pneumoniae, and confirm its presence in abdominal aortic aneurysms.
Deviation from the cosmological constant or systematic errors?
Authors: Qi Shi , Lu Tan , Wang Fa-Yin 
Published: August 2009

Abstract
In the work of Qi, Wang & Lu, gamma-ray bursts (GRBs) are used together with an earlier Type Ia supernova (SN Ia) data set to constrain the dark energy equation of state (EOS) in a nearly model-independent way. The improvements made by including GRBs show a slight shift of the dark energy EOS toward w &gt; −1 at redshifts z≳ 0.5. It is interesting that, when we have more SNe Ia, SNe Ia themselves also show the same trend. Motivated by the fact that both SNe Ia and GRBs seem to prefer a dark energy EOS greater than −1 at redshifts z≳ 0.5, we perform a careful investigation of this situation, including more careful treatments of measurement errors of GRBs and cross-checking the results by using different ways of including GRBs. We find that the deviation of dark energy from the cosmological constant at redshifts z≳ 0.5 is large enough that we should pay close attention to it with future observational data. Such a deviation may arise from some biasing systematic errors in the handling of SNe Ia and/or GRBs, or more interestingly from the nature of the dark energy itself.
Spin-down rate and inferred dipole magnetic field of the soft gamma-ray repeater SGR 1627–41
Authors: Esposito P. , Burgay M. , Possenti A. , Turolla R. , Zane S. , De Luca A. , Tiengo A. , Israel G. L. , Mattana F. , Mereghetti S. , Bailes M. , Romano P. , Götz D. , Rea N. 
Published: August 2009

Abstract
Using Chandra data taken in 2008 June, we detected pulsations at 2.594 39(4) s in the soft gamma-ray repeater SGR 1627−41. This is the second measurement of the source spin period and allows us to derive for the first time a long-term spin-down rate of (1.9 ± 0.4) × 10−11 s s−1. From this value, we infer for SGR 1627−41 a characteristic age of ∼2.2 kyr, a spin-down luminosity of ∼4 × 1034 erg s−1 (one of the highest among sources of the same class), and a surface dipole magnetic field strength of ∼2 × 1014 G. These properties confirm the magnetar nature of SGR 1627−41; however, they should be considered with caution since they were derived on the basis of a period derivative measurement made using two epochs only, and magnetar spin-down rates are generally highly variable. The pulse profile, double-peaked and with a pulsed fraction of 13 ± 2 per cent in the 2–10 keV range, closely resembles that observed by XMM–Newton in 2008 September. Having for the first time a timing model for this soft gamma-ray repeater (SGR), we also searched for a pulsed signal in archival radio data collected with the Parkes radio telescope 9 months after the previous X-ray outburst. No evidence for radio pulsations was found, down to a luminosity level ∼10–20 times fainter (for a 10 per cent duty cycle and a distance of 11 kpc) than the peak luminosity shown by the known radio magnetars.
Synovial Inflammation in Patients with Osteonecrosis of the Femoral Head
Authors: Rabquer Bradley J. , Tan Giselle J. , Shaheen Philip J. , Haines III G. Kenneth , Urquhart Andrew G. , Koch Alisa E. 
Published: August 2009

AbstractMuch of the work aimed at elucidating the pathogenesis of osteonecrosis (ON) of the femoral head has focused on bone blood supply, with little attention to the surrounding synovial tissue (ST). We hypothesized that patients with ON exhibit synovial inflammation. Using immunohistological techniques, we found that a large population of patients with ON had synovial inflammation. Moreover, a population of ON patients had inflamed ST without having an inflammatory disease co‐morbidity. The inflammatory infiltrate in these patients comprised primarily CD4+ T cells and CD68+ macrophages, the latter of which expressed increased levels of cellular adhesion molecules. Our results suggest the presence of a previously unrecognized population of ON patients without a diagnosed inflammatory co‐morbidity and a highly inflammed synovium consisting primarily of a macrophage and CD4+ T‐cell infi ltrate.
Retinol‐Binding Protein in Serum and Urine of Hyperthyroid Cats before and after Treatment with Radioiodine
Authors: Van Hoek I. , Meyer E. , Duchateau L. , Peremans K. , Smets P. , Daminet S. 
Published: August 2009

Background:Retinol‐binding protein (RBP) is suggested as a clinically useful marker of renal function in cats.Hypothesis:Serum and urinary RBP concentrations in hyperthyroid (HT) cats differ from those in healthy (H) cats; radioiodine (131I) treatment influences serum and urinary RBP concentrations in HT cats.Animals:Ten HT and 8 H cats.Methods:RBP concentration was evaluated in feline serum and urine samples from a prospective study.Results:There was a significant (P= .003) difference in the urinary RBP/creatinine (uRBP/c) ratios of H (−) and untreated HT (1.4 ± 1.5 × 10−2 μg/mg) cats. Serum total thyroxine concentration (1.8 ± 1.9 μg/dL, 24 weeks) and uRBP/c (0.6 ± 1.0 × 10−2 μg/mg, 24 weeks) decreased significantly (P< .001) in HT cats at all time points after treatment with131I, and these variables were significantly correlated with one another (r= 0.42,P= .007). Serum RBP concentrations from HT cats (199 ± 86 μg/L) did not differ significantly (P= .98) from those of H cats (174 ± 60) and did not change after treatment with131I (182 ± 124 μg/L,P= .80).Conclusion and Clinical Importance:The presence of urinary RBP in HT cats is a potential marker of tubular dysfunction that is correlated to thyroid status, although it is independent of circulating RBP concentrations. The decreased uRBP/c combined with the absence of changes in serum RBP after treatment suggests that the suspected tubular dysfunction was partly reversible with treatment of131I.
Longitudinal Study of
Escherichia coli
O157:H7 in a Beef Cattle Feedlot and Role of High-Level Shedders in Hide Contamination
Authors: Arthur Terrance M. , Keen James E. , Bosilevac Joseph M. , Brichta-Harhay Dayna M. , Kalchayanand Norasak , Shackelford Steven D. , Wheeler Tommy L. , Nou Xiangwu , Koohmaraie Mohammad 
Published: August 2009

ABSTRACT

The objectives of the study described here were (i) to investigate the dynamics of
Escherichia coli
O157:H7 fecal and hide prevalence over a 9-month period in a feedlot setting and (ii) to determine how animals shedding
E. coli
O157:H7 at high levels affect the prevalence and levels of
E. coli
O157:H7 on the hides of other animals in the same pen. Cattle (
n
= 319) were distributed in 10 adjacent pens, and fecal and hide levels of
E. coli
O157:H7 were monitored. When the fecal pen prevalence exceeded 20%, the hide pen prevalence was usually (25 of 27 pens) greater than 80%. Sixteen of 19 (84.2%) supershedder (>10
4
CFU/g) pens had a fecal prevalence greater than 20%. Significant associations with hide and high-level hide (≥40 CFU/100 cm
2
) contamination were identified for (i) a fecal prevalence greater than 20%, (ii) the presence of one or more high-density shedders (≥200 CFU/g) in a pen, and (iii) the presence of one or more supershedders in a pen. The results presented here suggest that the
E. coli
O157:H7 fecal prevalence should be reduced below 20% and the levels of shedding should be kept below 200 CFU/g to minimize the contamination of cattle hides. Also, large and unpredictable fluctuations within and between pens in both fecal and hide prevalence of
E. coli
O157:H7 were detected and should be used as a guide when preharvest studies, particularly preharvest intervention studies, are designed.
Investigation of Associations of
Yarrowia lipolytica
,
Staphylococcus xylosus
, and
Lactococcus lactis
in Culture as a First Step in Microbial Interaction Analysis
Authors: Mansour S. , Bailly J. , Landaud S. , Monnet C. , Sarthou A. S. , Cocaign-Bousquet M. , Leroy S. , Irlinger F. , Bonnarme P. 
Published: August 2009

ABSTRACT

The interactions that may occur between microorganisms in different ecosystems have not been adequately studied yet. We investigated yeast-bacterium interactions in a synthetic medium using different culture associations involving the yeast
Yarrowia lipolytica
1E07 and two bacteria,
Staphylococcus xylosus
C2a and
Lactococcus lactis
LD61. The growth and biochemical characteristics of each microorganism in the different culture associations were studied. The expression of genes related to glucose, lactate, and amino acid catabolism was analyzed by reverse transcription followed by quantitative PCR. Our results show that the growth of
Y. lipolytica
1E07 is dramatically reduced by the presence of
S. xylosus
C2a. As a result of a low amino acid concentration in the medium, the expression of
Y. lipolytica
genes involved in amino acid catabolism was downregulated in the presence of
S. xylosus
C2a, even when
L. lactis
was present in the culture. Furthermore, the production of lactate by both bacteria had an impact on the lactate dehydrogenase gene expression of the yeast, which increased up to 30-fold in the three-species culture compared to the
Y. lipolytica
1E07 pure culture.
S. xylosus
C2a growth dramatically decreased in the presence of
Y. lipolytica
1E07. The growth of lactic acid bacteria was not affected by the presence of
S. xylosus
C2a or
Y. lipolytica
1E07, although the study of gene expression showed significant variations.
Multiplex PCR for Detection of Botulinum Neurotoxin-Producing Clostridia in Clinical, Food, and Environmental Samples
Authors: De Medici Dario , Anniballi Fabrizio , Wyatt Gary M. , Lindström Miia , Messelhäußer Ute , Aldus Clare F. , Delibato Elisabetta , Korkeala Hannu , Peck Michael W. , Fenicia Lucia 
Published: August 2009

ABSTRACTBotulinum neurotoxin (BoNT), the most toxic substance known, is produced by the spore-forming bacteriumClostridium botulinumand, in rare cases, also by some strains ofClostridium butyricumandClostridium baratii. The standard procedure for definitive detection of BoNT-producing clostridia is a culture method combined with neurotoxin detection using a standard mouse bioassay (SMB). The SMB is highly sensitive and specific, but it is expensive and time-consuming and there are ethical concerns due to use of laboratory animals. PCR provides a rapid alternative for initial screening for BoNT-producing clostridia. In this study, a previously described multiplex PCR assay was modified to detect all type A, B, E, and F neurotoxin genes in isolated strains and in clinical, food, environmental samples. This assay includes an internal amplification control. The effectiveness of the multiplex PCR method for detecting clostridia possessing type A, B, E, and F neurotoxin genes was evaluated by direct comparison with the SMB. This method showed 100% inclusivity and 100% exclusivity when 182 BoNT-producing clostridia and 21 other bacterial strains were used. The relative accuracy of the multiplex PCR and SMB was evaluated using 532 clinical, food, and environmental samples and was estimated to be 99.2%. The multiplex PCR was also used to investigate 110 freshly collected food and environmental samples, and 4 of the 110 samples (3.6%) were positive for BoNT-encoding genes.
Virulence Genes and Molecular Typing of Different Groups of
Escherichia coli
O157 Strains in Cattle
Authors: Tóth István , Schmidt Herbert , Kardos Gábor , Lancz Zsuzsanna , Creuzburg Kristina , Damjanova Ivelina , Pászti Judit , Beutin Lothar , Nagy Béla 
Published: August 2009

ABSTRACT

Characterization of an
Escherichia coli
O157 strain collection (
n
= 42) derived from healthy Hungarian cattle revealed the existence of diverse pathotypes. Enteropathogenic
E. coli
(EPEC;
eae
positive) appeared to be the most frequent pathotype (
n
= 22 strains), 11 O157 strains were typical enterohemorrhagic
E. coli
(EHEC;
stx
and
eae
positive), and 9 O157 strains were atypical, with none of the key
stx
and
eae
virulence genes detected. EHEC and EPEC O157 strains all carried
eae-
gamma,
tir-
gamma,
tccP
, and
paa
. Other virulence genes located on the pO157 virulence plasmid and different O islands (O island 43 [OI-43] and OI-122), as well as
espJ
and
espM
, also characterized the EPEC and EHEC O157 strains with similar frequencies. However, none of these virulence genes were detected by PCR in atypical O157 strains. Interestingly, five of nine atypical O157 strains produced cytolethal distending toxin V (CDT-V) and carried genes encoding long polar fimbriae. Macro-restriction fragment enzyme analysis (pulsed-field gel electrophoresis) revealed that these
E. coli
O157 strains belong to four main clusters. Multilocus sequence typing analysis revealed that five housekeeping genes were identical in EHEC and EPEC O157 strains but were different in the atypical O157 strains. These results suggest that the Hungarian bovine
E. coli
O157 strains represent at least two main clones: EHEC/EPEC O157:H7/NM (nonmotile) and atypical CDT-V-producing O157 strains with H antigens different from H7. The CDT-V-producing O157 strains represent a novel genogroup. The pathogenic potential of these strains remains to be elucidated.
Little Heterogeneity among Genes Encoding Heat-Labile and Heat-Stable Toxins of Enterotoxigenic
Escherichia coli
Strains Isolated from Diarrheal Pigs
Authors: Zhang Chengxian , Rausch Dana , Zhang Weiping 
Published: August 2009

ABSTRACT

To examine whether the heat-labile enterotoxin gene in porcine enterotoxigenic
Escherichia coli
(ETEC) strains is as divergent as in human ETEC strains, we sequenced the heat-labile and heat-stable toxin genes from 52 and 33 porcine ETEC strains, respectively. We found that the STa gene is identical, that the LT gene has only two mutations in 4 (of 52) strains, and that both mutations cause a reduction in GM1 binding and toxicity.
Zif, the Zoocin A Immunity Factor, Is a FemABX-Like Immunity Protein with a Novel Mode of Action
Authors: Gargis Shaw R. , Gargis Amy S. , Heath Harry E. , Heath Lucie S. , LeBlanc Paul A. , Senn Maria M. , Berger-Bächi Brigitte , Simmonds Robin S. , Sloan Gary L. 
Published: August 2009

ABSTRACT

Producer cell immunity to the streptococcolytic enzyme zoocin A, which is a
d
-alanyl-
l
-alanine endopeptidase, is due to Zif, the zoocin A immunity factor. Zif has high degrees of similarity to MurM and MurN (members of the FemABX family of proteins), which are responsible for the addition of amino acids to cross bridges during peptidoglycan synthesis in streptococci. In this study, purified peptidoglycans from strains with and without
zif
were compared to determine how Zif modifies the peptidoglycan layer to cause resistance to zoocin A. The peptidoglycan from each strain was hydrolyzed using the streptococcolytic phage lysin B30, and the resulting muropeptides were separated by reverse-phase high-pressure liquid chromatography, labeled with 4-sulfophenyl isothiocyanate, and analyzed by tandem mass spectrometry in the negative-ion mode. It was determined that Zif alters the peptidoglycan by increasing the proportion of cross bridges containing three
l
-alanines instead of two. This modification decreased binding of the recombinant target recognition domain of zoocin A to peptidoglycan. Zif-modified peptidoglycan also was less susceptible to hydrolysis by the recombinant catalytic domain of zoocin A. Thus, Zif is a novel FemABX-like immunity factor because it provides resistance to a bacteriolytic endopeptidase by lengthening the peptidoglycan cross bridge rather than by causing an amino acid substitution.
Microarray and Real-Time PCR Analyses of the Responses of High-Arctic Soil Bacteria to Hydrocarbon Pollution and Bioremediation Treatments
Authors: Yergeau Etienne , Arbour Mélanie , Brousseau Roland , Juck David , Lawrence John R. , Masson Luke , Whyte Lyle G. , Greer Charles W. 
Published: August 2009

ABSTRACT
High-Arctic soils have low nutrient availability, low moisture content, and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at the Canadian high-Arctic stations of Alert (ex situ approach) and Eureka (in situ approach). Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as quantitative reverse transcriptase PCR targeting key functional genes. The results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon-ring-hydroxylating dioxygenases were observed 1 month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e., ex situ versus in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation.
Development and Validation of a Species-Independent Functional Gene Microarray That Targets Lactic Acid Bacteria
Authors: Weckx Stefan , Allemeersch Joke , Van der Meulen Roel , Vrancken Gino , Huys Geert , Vandamme Peter , Van Hummelen Paul , De Vuyst Luc 
Published: August 2009

ABSTRACT
During the last few years, genome-related information has become available for many microorganisms, including important food-related bacteria. Lactic acid bacteria (LAB) are important industrially in the production of fermented foods such as dairy products, sausages, sourdoughs, and vegetables. Despite their limited metabolic capacity, LAB contribute considerably to important characteristics of fermented foods, such as flavor and texture. In the present study, a species-independent functional gene microarray was developed that targets 406 genes that play key roles in the production of sugar catabolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in the stress response. Also, genes linked to negative traits, such as antibiotic resistance and virulence, are represented. As LAB ecosystems contain a variety of species, there was a more global focus on these specific functional properties. Thus, an algorithm was used to design gene-specific oligonucleotides that preferably hybridize with multiple LAB species, thereby allowing controlled cross-hybridization. For proof of concept, the microarray composed of 2,269 30-mer oligonucleotides focused on LAB species that are prevalent in sourdough ecosystems. Validation hybridizations using DNA and RNA from 18 LAB strains, covering 86% of all the oligonucleotides, showed that there were wide ranges in intensity and high reproducibility between microarrays.
Identification of Particle Size Classes Inhibiting Protozoan Recovery from Surface Water Samples via U.S. Environmental Protection Agency Method 1623
Authors: Krometis Leigh-Anne H. , Characklis Gregory W. , Sobsey Mark D. 
Published: August 2009

ABSTRACT

Giardia
species recovery by U.S. Environmental Protection Agency method 1623 appears significantly impacted by a wide size range (2 to 30 μm) of particles in water and organic matter.
Cryptospori
dium
species recovery seems negatively correlated only with smaller (2 to 10 μm), presumably inorganic particles. Results suggest constituents and mechanisms interfering with method performance may differ by protozoan type.
Acetolactate Synthase from
Bacillus subtilis
Serves as a 2-Ketoisovalerate Decarboxylase for Isobutanol Biosynthesis in
Escherichia coli
Authors: Atsumi Shota , Li Zhen , Liao James C. 
Published: August 2009

ABSTRACT

A pathway toward isobutanol production previously constructed in
Escherichia coli
involves 2-ketoacid decarboxylase (Kdc) from
Lactococcus lactis
that decarboxylates 2-ketoisovalerate (KIV) to isobutyraldehyde. Here, we showed that a strain lacking Kdc is still capable of producing isobutanol. We found that acetolactate synthase from
Bacillus subtilis
(AlsS), which originally catalyzes the condensation of two molecules of pyruvate to form 2-acetolactate, is able to catalyze the decarboxylation of KIV like Kdc both in vivo and in vitro. Mutational studies revealed that the replacement of Q487 with amino acids with small side chains (Ala, Ser, and Gly) diminished only the decarboxylase activity but maintained the synthase activity.
Furfural Inhibits Growth by Limiting Sulfur Assimilation in EthanologenicEscherichia coliStrain LY180
Authors: Miller Elliot N. , Jarboe Laura R. , Turner Peter C. , Pharkya Priti , Yomano Lorraine P. , York Sean W. , Nunn David , Shanmugam K. T. , Ingram Lonnie O. 
Published: August 2009

ABSTRACTA wide variety of commercial products can be potentially made from monomeric sugars produced by the dilute acid hydrolysis of lignocellulosic biomass. However, this process is accompanied by side products such as furfural that hinder microbial growth and fermentation. To investigate the mechanism of furfural inhibition, mRNA microarrays of an ethanologenic strain ofEscherichia coli(LY180) were compared immediately prior to and 15 min after a moderate furfural challenge. Expression of genes and regulators associated with the biosynthesis of cysteine and methionine was increased by furfural, consistent with a limitation of these critical metabolites. This was in contrast to a general stringent response and decreased expression of many other biosynthetic genes. Of the 20 amino acids individually tested as supplements (100 μM each), cysteine and methionine were the most effective in increasing furfural tolerance with serine (precursor of cysteine), histidine, and arginine of lesser benefit. Supplementation with other reduced sulfur sources such asd-cysteine and thiosulfate also increased furfural tolerance. In contrast, supplementation with taurine, a sulfur source that requires 3 molecules of NADPH for sulfur assimilation, was of no benefit. Furfural tolerance was also increased by inserting a plasmid encodingpntAB, a cytoplasmic NADH/NADPH transhydrogenase. Based on these results, a model is proposed for the inhibition of growth in which the reduction of furfural by YqhD, an enzyme with a lowKmfor NADPH, depletes NADPH sufficiently to limit the assimilation of sulfur into amino acids (cysteine and methionine) by CysIJ (sulfite reductase).