bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Affinity Immunochromatography Column-Based Tests for Sensitive Detection of
Clostridium botulinum
Neurotoxins and
Escherichia coli
O157
Authors: Brunt Jason , Webb Martin D. , Peck Michael W. 
Published: May 2010

ABSTRACT

Existing methods for detection of food-borne pathogens and their toxins are frequently time-consuming, require specialized equipment, and involve lengthy culture procedures and/or animal testing and are thus unsuitable for a rapid response to an emergency public health situation. A series of simple and rapid affinity immunochromatography column (AICC) assays were developed to detect
Clostridium botulinum
neurotoxin types A, B, E, and F and
Escherichia coli
O157 in food matrices. Specifically, for milk, grape juice with peach juice, and bottled water, the detection limit for the botulinum neurotoxin type A complex was 0.5 ng. Use of this method with a 10-ml sample would therefore result in a detection limit of 50 pg ml
−l
. Thus, this assay is approximately 2 orders of magnitude more sensitive than a comparable lateral-flow assay. For botulinum neurotoxin complex types B, E, and F, the minimum detection limit was 5 ng to 50 ng. Sensitive detection of
E. coli
O157 was achieved, and the detection limit was 500 cells. The AICC test was also shown to be specific, rapid, and user friendly. This test takes only 15 to 30 min to complete without any specialized equipment and thus is suitable for use in the field. It has the potential to replace existing methods for presumptive detection of botulinum neurotoxin types A, B, E, and F and
E. coli
O157 in contaminated matrices without a requirement for preenrichment.
Commonalities and Differences in Regulation of
N
-Acyl Homoserine Lactone Quorum Sensing in the Beneficial Plant-Associated
Burkholderia
Species Cluster
Authors: Suárez-Moreno Zulma Rocío , Devescovi Giulia , Myers Mike , Hallack Letícia , Mendonça-Previato Lucia , Caballero-Mellado Jesús , Venturi Vittorio 
Published: May 2010

ABSTRACT

The genus
Burkholderia
includes over 60 species isolated from a wide range of environmental niches and can be tentatively divided into two major species clusters. The first cluster includes pathogens such as
Burkholderia glumae
,
B. pseudomallei
, and
B. mallei
and 17 well-studied species of the
Burkholderia cepacia
complex. The other recently established cluster comprises at least 29 nonpathogenic species, which in most cases have been found to be associated with plants. It was previously established that
Burkholderia kururiensis
, a member of the latter cluster, possesses an
N
-acyl homoserine lactone (AHL) quorum-sensing (QS) system designated “BraI/R,” which is found in all species of the plant-associated cluster. In the present study, two other BraI/R-like systems were characterized in
B. xenovorans
and
B. unamae
and were designated the BraI/R
XEN
and BraI/R
UNA
systems, respectively. Several phenotypes were analyzed, and it was determined that exopolysaccharide was positively regulated by the BraIR-like system in the species
B. kururiensis
,
B. unamae
, and
B. xenovorans
, highlighting commonality in targets. However, the three BraIR-like systems also revealed differences in targets since biofilm formation and plant colonization were differentially regulated. In addition, a second AHL QS system designated XenI2/R2 and an unpaired LuxR solo protein designated BxeR solo were also identified and characterized in
B. xenovorans
LB400
T
. The two AHL QS systems of
B. xenovorans
are not transcriptionally regulating each other, whereas BxeR solo negatively regulated
xenI2
. The XenI2/R2 and BxeR solo proteins are not widespread in the
Burkholderia
species cluster. In conclusion, the present study represents an extensive analysis of AHL QS in the
Burkholderia
plant-associated cluster demonstrating both commonalities and differences, probably reflecting environmental adaptations of the various species.
Functional Characterization of
MAT1
-
1
-Specific Mating-Type Genes in the Homothallic Ascomycete Sordaria macrospora Provides New Insights into Essential and Nonessential Sexual Regulators
Authors: Klix V. , Nowrousian M. , Ringelberg C. , Loros J. J. , Dunlap J. C. , Pöggeler S. 
Published: May 2010

ABSTRACT

Mating-type genes in fungi encode regulators of mating and sexual development. Heterothallic ascomycete species require different sets of mating-type genes to control nonself-recognition and mating of compatible partners of different mating types. Homothallic (self-fertile) species also carry mating-type genes in their genome that are essential for sexual development. To analyze the molecular basis of homothallism and the role of mating-type genes during fruiting-body development, we deleted each of the three genes,
SmtA
-
1
(
MAT1
-
1
-
1
),
SmtA
-
2
(
MAT1
-
1
-
2
), and
SmtA
-
3
(
MAT1
-
1
-
3
), contained in the
MAT1
-
1
part of the mating-type locus of the homothallic ascomycete species
Sordaria macrospora
. Phenotypic analysis of deletion mutants revealed that the PPF domain protein-encoding gene
SmtA
-
2
is essential for sexual reproduction, whereas the α domain protein-encoding genes
SmtA
-
1
and
SmtA
-
3
play no role in fruiting-body development. By means of cross-species microarray analysis using
Neurospora crassa
oligonucleotide microarrays hybridized with
S. macrospora
targets and quantitative real-time PCR, we identified genes expressed under the control of
SmtA
-
1
and
SmtA
-
2
. Both genes are involved in the regulation of gene expression, including that of pheromone genes.
Adaptations of Candida albicans for Growth in the Mammalian Intestinal Tract
Authors: Rosenbach Ari , Dignard Daniel , Pierce Jessica V. , Whiteway Malcolm , Kumamoto Carol A. 
Published: May 2010

ABSTRACT

Although the fungus
Candida albicans
is a commensal colonizer of humans, the organism is also an important opportunistic pathogen. Most infections caused by
C. albicans
arise from organisms that were previously colonizing the host as commensals, and therefore successful establishment of colonization is a prerequisite for pathogenicity. To elucidate fungal activities that promote colonization, an analysis of the transcription profile of
C. albicans
cells recovered from the intestinal tracts of mice was performed. The results showed that within the
C. albicans
colonizing population, cells expressed genes characteristic of the laboratory-grown exponential phase and genes characteristic of post-exponential-phase cells. Thus, gene expression both promoted the ability to grow rapidly (a characteristic of exponential-phase cells) and enhanced the ability to resist stresses (a characteristic of post-exponential-phase cells). Similarities in gene expression in commensal colonizing cells and cells invading host tissue during disease were found, showing that
C. albicans
cells adopt a particular cell surface when growing within a host in both situations. In addition, transcription factors Cph2p and Tec1p were shown to regulate
C. albicans
gene expression during intestinal colonization.
Host Cell Invasion by Toxoplasma gondii Is Temporally Regulated by the Host Microtubule Cytoskeleton
Authors: Sweeney Kristin R. , Morrissette Naomi S. , LaChapelle Stephanie , Blader Ira J. 
Published: May 2010

ABSTRACTToxoplasma gondiiis an obligate intracellular protozoan parasite that invades and replicates within most nucleated cells of warm-blooded animals. The basis for this wide host cell tropism is unknown but could be because parasites invade host cells using distinct pathways and/or repertoires of host factors. Using synchronized parasite invasion assays, we found that host microtubule disruption significantly reduces parasite invasion into host cells early after stimulating parasite invasion but not at later time points. Host microtubules are specifically associated with the moving junction, which is the site of contact between the host cell and the invading parasite. Host microtubules are specifically associated with the moving junction of those parasites invading early after stimulating invasion but not with those invading later. Disruption of host microtubules has no effect on parasite contact, attachment, motility, or rate of penetration. Rather, host microtubules hasten the time before parasites commence invasion. This effect on parasite invasion is distinct from the role that host microtubules play in bacterial and viral infections, where they function to traffic the pathogen or pathogen-derived material from the host cell's periphery to its interior. These data indicate that the host microtubule cytoskeleton is a structure used byToxoplasmato rapidly infect its host cell and highlight a novel function for host microtubules in microbial pathogenesis.
The Frequency of Persisters in
Escherichia coli
Reflects the Kinetics of Awakening from Dormancy
Authors: Jõers Arvi , Kaldalu Niilo , Tenson Tanel 
Published: May 2010

ABSTRACT

A genetically homogenous bacterial population may contain physiologically distinct subpopulations. In one such case, a minor part of an otherwise antibiotic-sensitive bacterial population maintains a nondividing state even in a growth-supporting environment and is therefore not killed by bactericidal antibiotics. This phenomenon, called persistence, can lead to failure of antibiotic treatment. We followed the development of sensitivity to killing by ampicillin and norfloxacin when
Escherichia coli
cells were transferred from a stationary-phase culture into fresh growth medium. In parallel, we monitored growth resumption by individual bacteria. We found that bacteria in a population resumed growth and became sensitive to antibiotics at different times after transfer to fresh medium. Moreover, both growing and dormant bacteria coexisted in the same culture for many hours. The kinetics of awakening was strongly influenced by growth conditions: inocula taken from the same stationary-phase culture led to very different persister frequencies when they were transferred into different fresh media. Bactericidal antibiotics kill cells that have woken up, but the later-awakening subpopulation is tolerant to them and can be identified as persisters when the antibiotic is removed. Our observations demonstrate that persister count is a dynamic measure and that the persister frequency of a particular culture is not a fixed value.
Analysis of the Mechanism of Action of the Antisense RNA That Controls the Replication of the
repABC
Plasmid p42d
Authors: Cervantes-Rivera Ramón , Romero-López Cristina , Berzal-Herranz Alfredo , Cevallos Miguel A. 
Published: May 2010

ABSTRACT

Replication and segregation of the
Rhizobium etli
symbiotic plasmid (pRetCFN42d) depend on the presence of a
repABC
operon, which carries all the plasmid-encoded elements required for these functions. All
repABC
operons share three protein-encoding genes (
repA
,
repB
, and
repC
), an antisense RNA (ctRNA) coding gene, and at least one centromere-like region (
parS
). The products of
repA
and
repB
, in conjunction with the
parS
region, make up the segregation system, and they negatively regulate operon transcription. The last gene of the operon,
repC
, encodes the initiator protein. The ctRNA is a negative posttranscriptional regulator of
repC
. In this work, we analyzed the secondary structures of the ctRNA and its target and mapped the motifs involved in the complex formed between them. Essential residues for the effective interaction localize at the unpaired 5′ end of the antisense molecule and the loop of the target mRNA. In light of our results, we propose a model explaining the mechanism of action of this ctRNA in the regulation of plasmid replication in
R. etli
.
Functional Characterization of a Phospholipase A
2
Homolog from
Rickettsia typhi
Authors: Rahman M. Sayeedur , Ammerman Nicole C. , Sears Khandra T. , Ceraul Shane M. , Azad Abdu F. 
Published: May 2010

ABSTRACT

Phospholipase A
2
(PLA
2
) has long been proposed to be involved in rickettsial entry into host cells, escape from the phagosome to evade destruction by lysosomal exposure, and lysis of the host cells. However, the corresponding rickettsial gene(s) encoding a protein with PLA
2
activity has not been identified or functionally characterized. Here, we report that the
Rickettsia typhi
genome possesses two genes encoding patatin-like PLA
2
proteins, RT0590 and RT0522. Sequence analysis of RT0522 and RT0590 reveals the presence of the conserved motifs essential for PLA
2
activity. Transcriptional analysis indicates that RT0522, but not RT0590, is transcribed at all stages of intracellular growth of
R. typhi
in Vero cells. The differential gene expression pattern of RT0522 at various stages of growth suggests its potential role during
R. typhi
infection of host cells.
In silico
, RT0522 is predicted to be noncytoplasmic and its gene does not encode a recognizable signal peptide sequence. However, our data indicate that RT0522 is secreted into the host cytoplasm. In addition, we observe that RT0522 protein expression is cytotoxic to both yeast and Vero cells. Importantly, we demonstrate that recombinant RT0522 possesses phospholipase A activity that requires a eukaryotic host cofactor for activation. Both cytotoxicity and phospholipase A activity associated with RT0522 were reduced by PLA
2
inhibitors. Site-directed mutagenesis of predicted catalytic Ser/Asp residues of RT0522 also eliminates cytotoxicity and phospholipase A activity. To our knowledge, RT0522 is the first protein identified from
Rickettsia typhi
with functional phospholipase A activity.
Studies of the Commitment Step in the Germination of Spores of
Bacillus
Species
Authors: Yi Xuan , Setlow Peter 
Published: May 2010

ABSTRACT

Spores of
Bacillus
species are said to be committed when they continue through nutrient germination even when germinants are removed or their binding to spores' nutrient germinant receptors (GRs) is both reversed and inhibited. Measurement of commitment and the subsequent release of dipicolinic acid (DPA) during nutrient germination of spores of
Bacillus cereus
and
Bacillus subtilis
showed that heat activation, increased nutrient germinant concentrations, and higher average levels of GRs/spore significantly decreased the times needed for commitment, as well as lag times between commitment and DPA release. These lag times were also decreased dramatically by the action of one of the spores' two redundant cortex lytic enzymes (CLEs), CwlJ, but not by the other CLE, SleB, and CwlJ action did not affect the timing of commitment. The timing of commitment and the lag time between commitment and DPA release were also dependent on the specific GR activated to cause spore germination. For spore populations, the lag times between commitment and DPA release were increased significantly in spores that germinated late compared to those that germinated early, and individual spores that germinated late may have had lower appropriate GR levels/spore than spores that germinated early. These findings together provide new insight into the commitment step in spore germination and suggest several factors that may contribute to the large heterogeneity among the timings of various events in the germination of individual spores in spore populations.
Transcription-Associated Mutation in
Bacillus subtilis
Cells under Stress
Authors: Pybus Christine , Pedraza-Reyes Mario , Ross Christian A. , Martin Holly , Ona Katherine , Yasbin Ronald E. , Robleto Eduardo 
Published: May 2010

ABSTRACT

Adaptive (stationary phase) mutagenesis is a phenomenon by which nondividing cells acquire beneficial mutations as a response to stress. Although the generation of adaptive mutations is essentially stochastic, genetic factors are involved in this phenomenon. We examined how defects in a transcriptional factor, previously reported to alter the acquisition of adaptive mutations, affected mutation levels in a gene under selection. The acquisition of mutations was directly correlated to the level of transcription of a defective
leuC
allele placed under selection. To further examine the correlation between transcription and adaptive mutation, we placed a point-mutated allele,
leuC427
, under the control of an inducible promoter and assayed the level of reversion to leucine prototrophy under conditions of leucine starvation. Our results demonstrate that the level of Leu
+
reversions increased significantly in parallel with the induced increase in transcription levels. This mutagenic response was not observed under conditions of exponential growth. Since transcription is a ubiquitous biological process, transcription-associated mutagenesis may influence evolutionary processes in all organisms.
Single-Beat Versus Multibeat Real-Time 3D Echocardiography for Assessing Left Ventricular Volumes and Ejection Fraction
Authors: Macron Laurent , Lim Pascal , Bensaid Alexandre , Nahum Julien , Dussault Caroline , Mitchell-Heggs Laurens , Dubois-Randé Jean-Luc , Deux Jean-François , Gueret Pascal 
Published: May 2010

Background—
Real-time 3-dimensional echocardiography (RT3DE) is superior to 2D echocardiography in assessing left ventricular (LV) volumes and ejection fraction (EF), but its feasibility is limited by multibeat acquisition, which requires an optimal breath-hold and a regular heart rhythm. We sought to evaluate the accuracy and feasibility of single- and 2-beat RT3DE for LV volume and EF assessment.

Methods and Results—

Sixty-six consecutive patients referred for cardiac magnetic resonance (CMR) underwent RT3DE and CMR on the same day. Of the 50 patients (age, 59±18 years; 68%men; 42% coronary artery disease; LVEF=49±14%; limits, 14% to 76%) with an adequate RT3DE image quality, accuracy for LV volumes and EF measurements of single- and 2-beat modalities were compared with the conventional 4-beat acquisition and CMR. Correlations with CMR for LV end-diastolic volume (161±59 mL,
r
=0.93 to 0.94) and end-systolic volume (86±56 mL,
r
=0.93 to 0.96) were excellent regardless of the number of cardiac cycles used. However, because of the low temporal resolution (7±2 volumes per second), single-beat underestimated LVEF (bias, −5±8%) with greater bias than 2-beat (bias, 1±6%,
P
<0.001) and 4-beat (bias, 3±7%,
P
<0.001) modalities. Interestingly, 2-beat provided accuracy similar to 4-beat for end-diastolic volume (bias, −17±21 mL versus −15±23 mL), end-systolic volume (bias, −9±16 mL versus −12±17 mL), and LVEF (bias, 1±6% versus 3±7%) measurements, but fewer stitching artifacts were observed with 2- than 4-beat modalities (3% versus 30%).

Conclusions—
Compared with conventional multibeat acquisitions, 2-beat modality provides similar accuracy in LV volume and EF measurements and should be preferred due to fewer stitching artifacts. In contrast, the temporal resolution of single-beat modality appears insufficient to provide an accurate estimation of LVEF.
Russia and Europe: The Koenraad van Klenk Embassy to Moscow (1675-76)
Authors: Boterbloem Kees 
Published: May 2010

AbstractIn this article based on Russian, Dutch, German, English, and Latin sources, Kees Boterbloem shows how the Dutch Embassy led by Koenraad van Klenk that visited Muscovy in 1675 and 1676 unfolded to the satisfaction of both the Russian hosts and their Dutch guests. This was in large measure the result of van Klenk’s expert knowledge about Muscovy and his sober assessment of the foreign policy priorities of Tsars Aleksei and Fyodor as well as his own country’s government. Meanwhile, the evidence regarding the embassy and its historical context are testimony to of a sudden intensified Muscovite interest in Europe and European interest in Muscovy. It suggests that Muscovy was no longer an “Orientalized” or “barbaric” outsider and had entered the Concert of Europe a generation before historians propose that Peter the Great “opened Russia’s window to the West.”
Provocative Wealth: Non-Muslim Elites in Eighteenth-Century Aleppo
Authors: Boogert Maurits van den 
Published: May 2010

AbstractIn the Western sources, the Ottoman legal system is often portrayed as unreliable and incidents of Europeans or Ottoman protégés of Western embassies and consulates who claimed to have been maltreated abound. These reports strengthened the common notion in Europe that Ottoman government officials were rapacious and corrupt. The article challenges these views by analyzing two incidents from 18th-century Aleppo, which shed light not only on the dynamics of Ottoman-European relations on the ground, but also on the status of non-Muslim elites in the Ottoman Empire.
The Ottoman Ruling Group and the Religions of its Subjects in the Early Modern Age: a Survey of Current Research
Authors: Faroqhi Suraiya 
Published: May 2010

AbstractThroughout the early modern period, the Ottoman ruling group perpetuated a social order based on clear-cut hierarchies; this emphasis on hierarchy governed relationships between Muslim and non-Muslim subjects, and between the ruling group and the tax-paying population, regardless of religion. Within this system—where everybody was supposed to know his or her place and, ideally, remain in it—there was room for ad hoc agreements. While flexible arrangements were often made by lower-level office-holders and but tacitly condoned by the central administration, a widespread sense of hierarchy ensured that improvisation remained within the limits set by a framework fixed by Islamic law and sultanic commands. This paper reviews the work dealing with the manner in which the Ottoman ruling group regarded the religions of its subjects, mainly Islam and Orthodox Christianity, focusing on the manner in which the Ottoman establishment conceptualized its own relationship to Islamic traditions of rule.
Al-Fārābī on the Method of Astronomy
Authors: Janos Damien 
Published: May 2010

AbstractThis article analyzes al-Fārābī's (d. 950) conception of the astronomical method by examining rarely studied texts such as the K. al-mūsīqā and K. al-burhān and by addressing key issues such as the subject matter of astronomy, the techniques used to derive the first principles of this science, the relation between astrology, astronomy, physics, and metaphysics, and the place of al-Fārābī in the Arabic astronomical tradition. The analysis indicates that al-Fārābī's theories combine material from the Greek astronomical tradition, especially Geminus, as well as from the logical works of Aristotle, particularly the Posterior Analytics. Moreover, it enables us to view al-Fārābī as a link between the Greek astronomers on the one hand and Ibn Sīnā and Naşīr al-Dīn al-Tūsī on the other.
Julius Caesar Scaliger on Plant Generation and the Question of Species Constancy
Authors: Blank Andreas 
Published: May 2010

AbstractThe sixteenth-century physician and philosopher Julius Caesar Scaliger combines the view that living beings are individuated by a single substantial form with the view that the constituents of the organic body retain their identity due to the continued existence and operation of their own substantial forms. This essay investigates the implications of Scaliger's account of subordinate and dominant substantial forms for the question of the constancy of biological species. According to Scaliger, biological mutability involves not only change on the ontological level of accidents but, in some cases, also change on the level of substantial forms. While he shares the received view that substantial forms themselves cannot undergo change, he maintains that relations of domination and subordination between substantial forms can undergo change. He uses his theory of how such changes can occur to explain cases of revertible plant degeneration. Moreover, in his view plants that belong to previously unknown biological species can emerge from changes in the relations between the many forms contained in plant seeds.