bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differentiating between intra‐ and extracellular chemiluminescence in diluted whole‐blood samples
Authors: RÁJECKÝ M. , LOJEK A. , ČÍŽ M. 
Published: August 2011

SummaryIntroduction:  The differentiation between extra‐ and intracellular production of reactive oxygen species (ROS) in whole blood was measured by luminol‐ and isoluminol‐enhanced chemiluminescence (CL).Methods:  Azide (total CL inhibition), azide + horseradish peroxidase (HRP, restoring extracellular CL), superoxide dismutase + catalase (depleting extracellular ROS) and HRP (enhancing extracellular CL) were used to modulate luminol‐ and isoluminol‐enhanced CL (10−6–10−3 m luminophores) of 125× diluted whole blood which was activated by both calcium ionophore A23187 (Ca‐I) and opsonized zymosan particles (OZP) separately.Results:  Both activators stimulated intra‐ and extracellular production of ROS. Luminol‐enhanced CL of Ca‐I‐activated samples detected the intracellular ROS, and with the addition of HRP detected the extracellular CL as well. CL enhanced with isoluminol in concentrations of 10−4 m or less was mostly extracellular. There was a mixture of intra‐ and extracellular CL in OZP‐activated samples, probably because of the ingestion of luminophore molecules.Conclusion:  Measurement of Ca‐I‐activated CL enhanced with 10−4 m luminol is recommended for the detection of intracellular ROS. The addition of HRP leads to the detection of overall ROS production while the OZP‐activated system with its addition of HRP can only be used to detect overall ROS production. Ca‐I‐activated CL enhanced with 10−4 m isoluminol and with addition of HRP is recommended for the detection of extracellular CL.
Kinds of Learning and the Likelihood of Future True Beliefs: Reply to Jäger on Reliabilism and the Value Problem
Authors: OLSSON ERIK J. , JÖNSSON MARTIN L. 
Published: August 2011

AbstractWe reply to Christoph Jäger's criticism of the conditional probability solution (CPS) to the value problem for reliabilism due to Goldman and Olsson (2009). We argue that while Jäger raises some legitimate concerns about the compatibility of CPS with externalist epistemology, his objections do not in the end reduce the plausibility of that solution.
Brazilian Clinical Trials Registry and the challenges for clinical research governance
Authors: Laguardia Josué , Piolli Alessandro Luís , Prevot Margareth , Ramalho Luciano , Gamarski Ricardo , Nishizawa Claudio 
Published: August 2011

AbstractOver the past five years, efforts to set up a Brazilian clinical trials registry have progressed from early discussions in academic forums through to the establishment of the registry as a web‐based computer platform. This article describes the process of developing and introducing the Brazilian Clinical Trials Registry (ReBEC), and its relationship with the authorities that regulate clinical research in Brazil. The Brazilian Clinical Trials Registry and the multilingual, free and open source, internet‐based software developed to manage it are outcomes of partnerships among Brazilian federal and international health agencies. Information for describing the technical and operational dimensions of Rebec was drawn from technical documents and the records of the OpenTrials software development team and the ReBEC executive and advisory committees, which are available in free‐access repositories. The Brazilian Clinical Trials Registry was launched in December 2010, and approved as a primary registry of the WHO ICTRP network in April 2011. ReBEC's arrival on‐line and its acceptance as an ICTRP primary registry is a significant step in consolidating a policy of free access to information on clinical research in Brazil.
Clinical accuracy of ExacTrac intracranial frameless stereotactic system
Authors: Ackerly T. , Lancaster C. M. , Geso M. , Roxby K. J. 
Published: August 2011

Purpose:In this paper, the authors assess the accuracy of the Brainlab ExacTrac system for frameless intracranial stereotactic treatments in clinical practice.Methods:They recorded couch angle and image fusion results (comprising lateral, longitudinal, and vertical shifts, and rotation corrections about these axes) for 109 stereotactic radiosurgery and 166 stereotactic radiotherapy patient treatments. Frameless stereotactic treatments involve iterative 6D image fusion corrections applied until the results conform to customizable pass criteria, theirs being 0.7 mm and 0.5° for each axis. The planning CT slice thickness was 1.25 mm. It has been reported in the literature that the CT slices' thickness impacts the accuracy of localization to bony anatomy. The principle of invariance with respect to patient orientation was used to determine spatial accuracy.Results:The data for radiosurgery comprised 927 image pairs, of which 532 passed (pass ratio of 57.4%). The data for radiotherapy comprised 15983 image pairs, of which 10 050 passed (pass ratio of 62.9%). For stereotactic radiotherapy, the combined uncertainty of ExacTrac calibration, image fusion, and intrafraction motion was (95% confidence interval) 0.290–0.302 and 0.306–0.319 mm in the longitudinal and lateral axes, respectively. The combined uncertainty of image fusion and intrafraction motion in the anterior‐posterior coordinates was 0.174–0.182 mm. For stereotactic radiosurgery, the equivalent ranges are 0.323–0.393, 0.337–0.409, and 0.231–0.281 mm. The overall spatial accuracy was 1.24 mm for stereotactic radiotherapy (SRT) and 1.35 mm for stereotactic radiosurgery (SRS).Conclusions:The ExacTrac intracranial frameless stereotactic system spatial accuracy is adequate for clinical practice, and with the same pass criteria, SRT is more accurate than SRS. They now use frameless stereotaxy exclusively at their center.
Effect of Light Intensity on the Relative Dominance of Toxigenic and Nontoxigenic Strains of Microcystis aeruginosa
Authors: LeBlanc Renaud Susan , Pick Frances R. , Fortin Nathalie 
Published: August 2011

ABSTRACT

In aquatic ecosystems, the factors that regulate the dominance of toxin-producing cyanobacteria over non-toxin-producing strains of the same species are largely unknown. One possible hypothesis is that limiting resources lead to the dominance of the latter because of the metabolic costs associated with toxin production. In this study, we tested the effect of light intensity on the performance of a microcystin-producing strain of
Microcystis aeruginosa
(UTCC 300) when grown in mixed cultures with non-microcystin-producing strains with similar intrinsic growth rates (UTCC 632 and UTCC 633). The endpoints measured included culture growth rates, microcystin concentrations and composition, and
mcyD
gene copy numbers determined using quantitative PCR (Q-PCR). In contrast to the predicted results, under conditions of low light intensity (20 μmol·m
−2
·s
−1
), the toxigenic strain became dominant in both of the mixed cultures based on gene copy numbers and microcystin concentrations. When grown under conditions of high light intensity (80 μmol·m
−2
·s
−1
), the toxigenic strain still appeared to dominate over nontoxigenic strain UTCC 632 but less so over strain UTCC 633. Microcystins may not be so costly to produce that toxigenic cyanobacteria are at a disadvantage in competition for limiting resources.
flaB
Gene as a Molecular Marker for Distinct Identification of Borrelia Species in Environmental Samples by the PCR-Restriction Fragment Length Polymorphism Method
Authors: Wodecka Beata 
Published: August 2011

ABSTRACT

A new protocol employing nested PCR-restriction fragment length polymorphism (RFLP) based on the
flaB
gene and two restriction enzymes was worked out. This protocol allows the identification of all
Borrelia
species transmitted by
Ixodes ricinus
in Europe, including
Borrelia miyamotoi
and 3 genetic variants of
B. garinii
. A dendrogram of
flaB
sequence similarity was in accordance with RFLP variants.
Biodiversity of Active and Inactive Bacteria in the Gut Flora of Wood-Feeding Huhu Beetle Larvae (Prionoplus reticularis)
Authors: Reid Nicola M. , Addison Sarah L. , Macdonald Lucy J. , Lloyd-Jones Gareth 
Published: August 2011

ABSTRACTHuhu grubs (Prionoplus reticularis) are wood-feeding beetle larvae endemic to New Zealand and belonging to the family Cerambycidae. Compared to the wood-feeding lower termites, very little is known about the diversity and activity of microorganisms associated with xylophagous cerambycid larvae. To address this, we used pyrosequencing to evaluate the diversity of metabolically active and inactive bacteria in the huhu larval gut. Our estimate, that the gut harbors at least 1,800 phylotypes, is based on 33,420 sequences amplified from genomic DNA and reverse-transcribed RNA. Analysis of genomic DNA- and RNA-derived data sets revealed that 71% of all phylotypes (representing 95% of all sequences) were metabolically active. Rare phylotypes contributed considerably to the richness of the community and were also largely metabolically active, indicating their participation in digestive processes in the gut. The dominant families in the active community (RNA data set) includedAcidobacteriaceae(24.3%),Xanthomonadaceae(16.7%),Acetobacteraceae(15.8%),Burkholderiaceae(8.7%), andEnterobacteriaceae(4.1%). The most abundant phylotype comprised 14% of the active community and affiliated withDyella ginsengisoli(Gammaproteobacteria), suggesting that aDyella-related organism is a likely symbiont. This study provides new information on the diversity and activity of gut-associated microorganisms that are essential for the digestion of the nutritionally poor diet consumed by wood-feeding larvae. Many huhu gut phylotypes affiliated with insect symbionts or with bacteria present in acidic environments or associated with fungi.
Molecular Enumeration of an Ecologically Important Cyanophage in a Laurentian Great Lake
Authors: Matteson Audrey R. , Loar Star N. , Bourbonniere Richard A. , Wilhelm Steven W. 
Published: August 2011

ABSTRACT

Considerable research has shown that cyanobacteria and the viruses that infect them (cyanophage) are pervasive and diverse in global lake populations. Few studies have seasonally analyzed freshwater systems, and little is known about the bacterial and viral communities that coexist during the harsh winters of the Laurentian Great Lakes. Here, we employed quantitative PCR to estimate the abundance of cyanomyoviruses in this system, using the portal vertex
g20
gene as a proxy for cyanophage abundance and to determine the potential ecological relevance of these viruses. Cyanomyoviruses were abundant in both the summer and the winter observations, with up to 3.1 × 10
6
copies of
g20
genes ml
−1
found at several stations and depths in both seasons, representing up to 4.6% of the total virus community. Lake Erie was productive during both our observations, with high chlorophyll
a
concentrations in the summer (up to 10.3 μg liter
−1
) and winter (up to 5.2 μg liter
−1
). Both bacterial and viral abundances were significantly higher during the summer than during the winter (
P
< 0.05). Summer bacterial abundances ranged from 3.3 × 10
6
to 1.6 × 10
7
ml
−1
while winter abundances ranged between ∼3.4 × 10
5
and 1.2 × 10
6
ml
−1
. Total virus abundances were high during both months, with summer abundances significantly higher at most stations, ranging from 6.5 × 10
7
to 8.8 × 10
7
ml
−1
, and with winter abundances ranging from 3.4 × 10
7
to 6.6 × 10
7
ml
−1
. This work confirms that putative cyanomyoviruses are ubiquitous in both summer and winter months in this large freshwater lake system and that they are an abundant component of the virioplankton group.
Toward Improvement of Erythromycin A Production in an IndustrialSaccharopolyspora erythraea Strain via Facilitation of Genetic Manipulation with an Artificial
attB
Site for Specific Recombination
Authors: Wu Jiequn , Zhang Qinglin , Deng Wei , Qian Jiangchao , Zhang Siliang , Liu Wen 
Published: August 2011

ABSTRACT

Large-scale production of erythromycin A (Er-A) relies on the organism
Saccharopolyspora erythraea
, in which lack of a typical
attB
site largely impedes the application of phage ΦC31 integrase-mediated recombination into site-specific engineering. We herein report construction of an artificial
attB
site in an industrial
S. erythraea
strain, HL3168 E3, in an effort to break the bottleneck previously encountered during genetic manipulation mainly from homologous or unpredictable nonspecific integration. Replacement of a cryptic gene,
nrps1-1
, with a cassette containing eight
attB
DNA sequences did not affect the high Er-producing ability, setting the stage for precisely engineering the industrial Er-producing strain for foreign DNA introduction with a reliable conjugation frequency. Transfer of either exogenous or endogenous genes of importance to Er-A biosynthesis, including the
S
-adenosylmethionine synthetase gene for positive regulation,
vhb
for increasing the oxygen supply, and two tailoring genes,
eryK
and
eryG
, for optimizing the biotransformation at the late stage, was achieved by taking advantage of this facility, allowing systematic improvement of Er-A production as well as elimination of the by-products Er-B and Er-C in fermentation. The strategy developed here can generally be applicable to other strains that lack the
attB
site.
Unexpected Role for a Serine/Threonine-Rich Domain in the Candida albicans Iff Protein Family
Authors: Boisramé Anita , Cornu Amandine , Da Costa Grégory , Richard Mathias L. 
Published: August 2011

ABSTRACT

Glycosylphosphatidylinositol (GPI)-anchored proteins are an important class of cell wall proteins in
Candida albicans
because of their localization and their function, even if more than half of them have no characterized homolog in the databases. In this study, we focused on the IFF protein family, investigating their exposure on the cell surface and the sequences that determine their subcellular localization. Protein localization and surface exposure were monitored by the addition of a V5 tag on all members of the family. The data obtained using the complete proteins showed for Iff3 (or -9), Iff5, Iff6, and Iff8 a covalent linkage to the β-1,6-glucan network but, remarkably, showed that Iff2/Hyr3 was linked through disulfide bridges or NaOH-labile bonds. However, since some proteins of the Iff family were undetectable, we designed chimeric constructions using the last 60 amino acids of these proteins to test the localization signal. These constructions showed a β-1,6-glucan linkage for Iff1/Rbr3, Iff2/Hyr3, Iff4 and Iff7/Hyr4 C-terminal–Iff5 fusion proteins, and a membrane localization for the Iff10/Flo9 C terminus-Iff5 fusion protein. Immunofluorescence analyses coupled to these cell fraction data confirmed the importance of the length of the central serine/threonine-rich region for cell surface exposure. Further analysis of the Iff2/Hyr3 linkage to the cell surface showed for the first time that a serine/threonine central region of a GPI-anchored protein may be responsible for the disulfide and the NaOH bonds to the glucan and glycoproteins network and may also override the signal of the proximal ω site region.
Mitochondrial Genomic Dysfunction Causes Dephosphorylation of Sch9 in the Yeast Saccharomyces cerevisiae
Authors: Kawai Shigeyuki , Urban Jörg , Piccolis Manuele , Panchaud Nicolas , De Virgilio Claudio , Loewith Robbie 
Published: August 2011

ABSTRACT

TORC1-dependent phosphorylation of
Saccharomyces cerevisiae
Sch9 was dramatically reduced upon exposure to a protonophore or in respiration-incompetent ρ
0
cells but not in respiration-incompetent
pet
mutants, providing important insight into the molecular mechanisms governing interorganellar signaling in general and retrograde signaling in particular.
Candida albicans
SRR1
, a Putative Two-Component Response Regulator Gene, Is Required for Stress Adaptation, Morphogenesis, and Virulence
Authors: Desai Chirayu , Mavrianos John , Chauhan Neeraj 
Published: August 2011

ABSTRACT

We report here the identification and characterization of a previously uncharacterized, two-component response regulator gene (orf19.5843) from
Candida albicans
. Because of its apparent functions in stress adaptation, we have named this gene
SRR1
(
s
tress
r
esponse
r
egulator 1). Disruption of
SRR1
causes defects in hyphal development, reduced resistance to stress, and severe virulence attenuation in the mouse model of disseminated candidiasis.
Gulosibacter molinativorax ON4
T
Molinate Hydrolase, a Novel Cobalt-Dependent Amidohydrolase
Authors: Duarte Márcia , Ferreira-da-Silva Frederico , Lünsdorf Heinrich , Junca Howard , Gales Luís , Pieper Dietmar H. , Nunes Olga C. 
Published: August 2011

ABSTRACT

A new pathway of molinate mineralization has recently been described. Among the five members of the mixed culture able to promote such a process,
Gulosibacter molinativorax
ON4
T
has been observed to promote the initial breakdown of the herbicide into ethanethiol and azepane-1-carboxylate. In the current study, the gene encoding the enzyme responsible for molinate hydrolysis was identified and heterologously expressed, and the resultant active protein was purified and characterized. Nucleotide sequence analysis revealed that the gene encodes a 465-amino-acid protein of the metal-dependent hydrolase A subfamily of the amidohydrolase superfamily with a predicted molecular mass of 50.9 kDa. Molinate hydrolase shares the highest amino acid sequence identity (48 to 50%) with phenylurea hydrolases of
Arthrobacter globiformis
and
Mycobacterium brisbanense
. However, in contrast to previously described members of the metal-dependent hydrolase A subfamily, molinate hydrolase contains cobalt as the only active-site metal.
Lipoarabinomannan Localization and Abundance during Growth of Mycobacterium smegmatis
Authors: Dhiman Rakesh K. , Dinadayala Premkumar , Ryan Gavin J. , Lenaerts Anne J. , Schenkel Alan R. , Crick Dean C. 
Published: August 2011

ABSTRACTLipoarabinomannan (LAM) is a structurally heterogeneous amphipathic lipoglycan present inMycobacteriumspp. and other actinomycetes, which constitutes a major component of the cell wall and exhibits a wide spectrum of immunomodulatory effects. Analysis ofMycobacterium smegmatissubcellular fractions and spheroplasts showed that LAM and lipomannan (LM) were primarily found in a cell wall-enriched subcellular fraction and correlated with the presence (or absence) of the mycolic acids in spheroplast preparations, suggesting that LAM and LM are primarily associated with the putative outer membrane of mycobacteria. During the course of these studies significant changes in the LAM/LM content of the cell wall were noted relative to the age of the culture. The LAM content of theM. smegmatiscell wall was dramatically reduced as the bacilli approached stationary phase, whereas LM, mycolic acid, and arabinogalactan content appeared to be unchanged. In addition, cell morphology and acid-fast staining characteristics showed variations with growth phase of the bacteria. In the logarithmic phase, the bacteria were found to be classic rod-shaped acid-fast bacilli, while in the stationary phaseM. smegmatislost the characteristic rod shape and developed a punctate acid-fast staining pattern with carbolfuchsin. The number of viable bacteria was independent of LAM content and phenotype. Taken together, the results presented here suggest that LAM is primarily localized with the mycolic acids in the cell wall and that the cellular concentration of LAM inM. smegmatisis selectively modulated with the growth phase.
Negative Effect of Glucose onompAmRNA Stability: a Potential Role of Cyclic AMP in the Repression ofhfqin Escherichia coli
Authors: Lin Hsiao-Hsien , Hsu Chi-Cheng , Yang Chi-Dung , Ju Yih-Wei , Chen Yi-Pei , Tseng Ching-Ping 
Published: August 2011

ABSTRACTGlucose is a carbon source that is capable of modulating the level of cyclic AMP (cAMP)-regulated genes. In the present study, we found that the stability ofompAmRNA was reduced inEscherichia coliwhen glucose (40 mM) was present in Luria-Bertani (LB) medium. This effect was associated with a low level of cAMP induced by the glucose. The results were confirmed with an adenylyl cyclase mutant with low levels of cAMP that are not modulated by glucose. Northern blot and Western blot analyses revealed that the host factor I (Hfq) (both mRNA and protein) levels were downregulated in the presence of cAMP. Furthermore, we showed that a complex of cAMP receptor protein (CRP) and cAMP binds to a specific P3hfqpromoter region ofhfqand regulateshfqexpression. The regulation of thehfqgene was confirmedin vivousing anhfq-deficient mutant transformed with an exogenoushfqgene containing the promoter. These results demonstrated that expression ofhfqwas repressed by the CRP-cAMP complex. The presence of glucose resulted in increased Hfq protein levels, which decreasedompAmRNA stability. An additional experiment showed that cAMP also increased the stability offurmRNA. Taken together, these results suggested that the repression of Hfq by cAMP may contribute to the stability of other mRNA inE. coli.
The Biofilm Inhibitor Carolacton Disturbs Membrane Integrity and Cell Division of Streptococcus mutans through the Serine/Threonine Protein Kinase PknB
Authors: Reck Michael , Rutz Katrin , Kunze Brigitte , Tomasch Jürgen , Surapaneni Subhash Kumar , Schulz Stefan , Wagner-Döbler Irene 
Published: August 2011

ABSTRACT

Carolacton, a secondary metabolite isolated from the myxobacterium
Sorangium cellulosum
, disturbs
Streptococcus mutans
biofilm viability at nanomolar concentrations. Here we show that carolacton causes leakage of cytoplasmic content (DNA and proteins) in growing cells at low pH and provide quantitative data on the membrane damage. Furthermore, we demonstrate that the biofilm-specific activity of carolacton is due to the strong acidification occurring during biofilm growth. The chemical conversion of the ketocarbonic function of the molecule to a carolacton methylester did not impact its activity, indicating that carolacton is not functionally activated at low pH by a change of its net charge. A comparative time series microarray analysis identified the VicKRX and ComDE two-component signal transduction systems and genes involved in cell wall metabolism as playing essential roles in the response to carolacton treatment. A sensitivity testing of mutants with deletions of all 13 viable histidine kinases and the serine/threonine protein kinase PknB of
S. mutans
identified only the Δ
pknB
deletion mutant as being insensitive to carolacton treatment. A strong overlap between the regulon of PknB in
S. mutans
and the genes affected by carolacton treatment was found. The data suggest that carolacton acts by interfering with PknB-mediated signaling in growing cells. The resulting altered cell wall morphology causes membrane damage and cell death at low pH.