bluuebunny/crossref_metadata_2025 huggingface dataset:
Host and Environmental Factors Modulate the Exposure of Free-Ranging and Farmed Red Deer (Cervus elaphus) to Coxiella burnetii
Authors: González-Barrio David , Velasco Ávila Ana Luisa , Boadella Mariana , Beltrán-Beck Beatriz , Barasona José Ángel , Santos João P. V. , Queirós João , García-Pérez Ana L. , Barral Marta , Ruiz-Fons Francisco
Published: July 2015

The control of multihost pathogens, such as
Coxiella burnetii
, should rely on accurate information about the roles played by the main hosts. We aimed to determine the involvement of the red deer (
Cervus elaphus
) in the ecology of
C. burnetii
. We predicted that red deer populations from broad geographic areas within a European context would be exposed to
C. burnetii
, and therefore, we hypothesized that a series of factors would modulate the exposure of red deer to
C. burnetii
. To test this hypothesis, we designed a retrospective survey of 47 Iberian red deer populations from which 1,751 serum samples and 489 spleen samples were collected. Sera were analyzed by enzyme-linked immunosorbent assays (ELISA) in order to estimate exposure to
C. burnetii
, and spleen samples were analyzed by PCR in order to estimate the prevalence of systemic infections. Thereafter, we gathered 23 variables—within environmental, host, and management factors—potentially modulating the risk of exposure of deer to
C. burnetii
, and we performed multivariate statistical analyses to identify the main risk factors. Twenty-three populations were seropositive (48.9%), and
C. burnetii
DNA in the spleen was detected in 50% of the populations analyzed. The statistical analyses reflect the complexity of
C. burnetii
ecology and suggest that although red deer may maintain the circulation of
C. burnetii
without third species, the most frequent scenario probably includes other wild and domestic host species. These findings, taken together with previous evidence of
C. burnetii
shedding by naturally infected red deer, point at this wild ungulate as a true reservoir for
C. burnetii
and an important node in the life cycle of
C. burnetii
, at least in the Iberian Peninsula.
The Host as the Driver of the Microbiota in the Gut and External Environment of Drosophila melanogaster
Authors: Wong Adam C.-N. , Luo Yuan , Jing Xiangfeng , Franzenburg Soeren , Bost Alyssa , Douglas Angela E.
Published: July 2015

Most associations between animals and their gut microbiota are dynamic, involving sustained transfer of food-associated microbial cells into the gut and shedding of microorganisms into the external environment with feces, but the interacting effects of host and microbial factors on the composition of the internal and external microbial communities are poorly understood. This study on laboratory cultures of the fruit fly
Drosophila melanogaster
reared in continuous contact with their food revealed time-dependent changes of the microbial communities in the food that were strongly influenced by the presence and abundance of
Drosophila
. When germfree
Drosophila
eggs were aseptically added to nonsterile food, the microbiota in the food and flies converged to a composition dramatically different from that in fly-free food, showing that
Drosophila
has microbiota-independent effects on the food microbiota. The microbiota in both the flies that developed from unmanipulated eggs (bearing microorganisms) and the associated food was dominated by the bacteria most abundant on the eggs, demonstrating effective vertical transmission via surface contamination of eggs. Food coinoculated with a four-species defined bacterial community of
Acetobacter
and
Lactobacillus
species revealed the progressive elimination of
Lactobacillus
from the food bearing few or no
Drosophila
, indicating the presence of antagonistic interactions between
Acetobacter
and
Lactobacillus. Drosophila
at high densities ameliorated the
Acetobacter/Lactobacillus
antagonism, enabling
Lactobacillus
to persist. This study with
Drosophila
demonstrates how animals can have major, coordinated effects on the composition of microbial communities in the gut and immediate environment.
Influence of
prgH
on the Persistence of Ingested Salmonella enterica in the Leafhopper Macrosteles quadrilineatus
Authors: Dundore-Arias José Pablo , Groves Russell L. , Barak Jeri D.
Published: July 2015

Phytophagous insects can encounter
Salmonella enterica
on contaminated plant surfaces and transmit externally adhered and internalized bacteria on and among leaves. Excretion of ingested
S. enterica
by the leafhopper
Macrosteles quadrilineatus
has been previously reported; however, the sites of persistence of ingested bacteria remain undetermined. Fluorescence microscopy revealed the presence and persistence of
S. enterica
in various organs of
M. quadrilineatus
fed an inoculated diet for 12 h and then moved to two consecutive noninoculated diets for a total of 48 h. Ingested
S. enterica
was predominantly observed in the filter chamber, midgut, and Malpighian tubules of
M. quadrilineatus
dissected immediately after acquisition and at 24- and 48-h post-acquisition access periods (post-AAPs). Additionally, we examined the potential roles of the
Salmonella
pathogenicity island 1 (SPI-1) and SPI-2 type III secretion systems (T3SSs) in the persistence and excretion of ingested
S. enterica
. In competition assays, a
prgH
mutant lacking a functional SPI-1 T3SS was recovered at significantly lower levels than the WT in insect homogenates at 24 h post-AAP, and complementation with
prgH
restored
S. enterica
persistence in
M. quadrilineatus
. Moreover, expression of
prgH
inside
M. quadrilineatus
was observed up to 48 post-AAP. No differences were observed between the WT and an
ssaK
mutant lacking a functional SPI-2 T3SS in insect homogenates or between the WT and either mutant in insect excretions. This study provides novel insight into the presence and persistence of
S. enterica
inside
M. quadrilineatus
and demonstrates that the SPI-1 T3SS influences the persistence of the pathogen in the gut of a potential vector.
Novel Strategies for Genomic Manipulation of Trichoderma reesei with the Purpose of Strain Engineering
Authors: Derntl Christian , Kiesenhofer Daniel P. , Mach Robert L. , Mach-Aigner Astrid R.
Published: July 2015

The state-of-the-art procedure for gene insertions into
Trichoderma reesei
is a cotransformation of two plasmids, one bearing the gene of interest and the other a marker gene. This procedure yields up to 80% transformation efficiency, but both the number of integrated copies and the loci of insertion are unpredictable. This can lead to tremendous pleiotropic effects. This study describes the development of a novel transformation system for site-directed gene insertion based on auxotrophic markers. For this purpose, we tested the applicability of the genes
asl1
(encoding an enzyme of the
l
-arginine biosynthesis pathway), the
hah1
(encoding an enzyme of the
l
-lysine biosynthesis pathway), and the
pyr4
(encoding an enzyme of the uridine biosynthesis pathway). The developed transformation system yields strains with an additional gene at a defined locus that are prototrophic and ostensibly isogenic compared to their parental strain. A positive transformation rate of 100% was achieved due to the developed split-marker system. Additionally, a double-auxotrophic strain that allows multiple genomic manipulations was constructed, which facilitates metabolic engineering purposes in
T. reesei
. By employing
goxA
of
Aspergillus niger
as a reporter system, the influence on the expression of an inserted gene caused by the orientation of the insertion and the transformation strategy used could be demonstrated. Both are important aspects to be considered during strain engineering.
Differences in Physical and Biochemical Properties of Thermus scotoductus SA-01 Cultured with Dielectric or Convection Heating
Authors: Cockrell Allison L. , Fitzgerald Lisa A. , Cusick Kathleen D. , Barlow Daniel E. , Tsoi Stanislav D. , Soto Carissa M. , Baldwin Jeffrey W. , Dale Jason R. , Morris Robert E. , Little Brenda J. , Biffinger Justin C.
Published: July 2015

A thermophile,Thermus scotoductusSA-01, was cultured within a constant-temperature (65°C) microwave (MW) digester to determine if MW-specific effects influenced the growth and physiology of the organism. As a control,T. scotoductuscells were also cultured using convection heating at the same temperature as the MW studies. Cell growth was analyzed by optical density (OD) measurements, and cell morphologies were characterized using electron microscopy imaging (scanning electron microscopy [SEM] and transmission electron microscopy [TEM]), dynamic light scattering (DLS), and atomic force microscopy (AFM). Biophysical properties (i.e., turgor pressure) were also calculated with AFM, and biochemical compositions (i.e., proteins, nucleic acids, fatty acids) were analyzed by attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. Gas chromatography-mass spectrometry (GC-MS) was used to analyze the fatty acid methyl esters extracted from cell membranes. Here we report successful cultivation of a thermophile with only dielectric heating. Under the MW conditions for growth, cell walls remained intact and there were no indications of membrane damage or cell leakage. Results from these studies also demonstrated thatT. scotoductuscells grown with MW heating exhibited accelerated growth rates in addition to altered cell morphologies and biochemical compositions compared with oven-grown cells.
Novel pH-Stable Glycoside Hydrolase Family 3 β-Xylosidase from Talaromyces amestolkiae: an Enzyme Displaying Regioselective Transxylosylation
Authors: Nieto-Domínguez Manuel , de Eugenio Laura I. , Barriuso Jorge , Prieto Alicia , Fernández de Toro Beatriz , Canales-Mayordomo Ángeles , Martínez María Jesús
Published: July 2015

This paper reports on a novel β-xylosidase from the hemicellulolytic fungus
Talaromyces amestolkiae
. The expression of this enzyme, called BxTW1, could be induced by beechwood xylan and was purified as a glycoprotein from culture supernatants. We characterized the gene encoding this enzyme as an intronless gene belonging to the glycoside hydrolase gene family 3 (GH3). BxTW1 exhibited transxylosylation activity in a regioselective way. This feature would allow the synthesis of oligosaccharides or other compounds not available from natural sources, such as alkyl glycosides displaying antimicrobial or surfactant properties. Regioselective transxylosylation, an uncommon combination, makes the synthesis reproducible, which is desirable for its potential industrial application. BxTW1 showed high pH stability and Cu
2+
tolerance. The enzyme displayed a pI of 7.6, a molecular mass around 200 kDa in its active dimeric form, and

K
m

and
V
max
values of 0.17 mM and 52.0 U/mg, respectively, using commercial
p
-nitrophenyl-β-
d
-xylopyranoside as the substrate. The catalytic efficiencies for the hydrolysis of xylooligosaccharides were remarkably high, making it suitable for different applications in food and bioenergy industries.
NADP
+
-Preferring
d
-Lactate Dehydrogenase from Sporolactobacillus inulinus
Authors: Zhu Lingfeng , Xu Xiaoling , Wang Limin , Dong Hui , Yu Bo , Ma Yanhe
Published: July 2015

Hydroxy acid dehydrogenases, including
l
- and
d
-lactate dehydrogenases (L-LDH and D-LDH), are responsible for the stereospecific conversion of 2-keto acids to 2-hydroxyacids and extensively used in a wide range of biotechnological applications. A common feature of LDHs is their high specificity for NAD
+
as a cofactor. An LDH that could effectively use NADPH as a coenzyme could be an alternative enzymatic system for regeneration of the oxidized, phosphorylated cofactor. In this study, a
d
-lactate dehydrogenase from a
Sporolactobacillus inulinus
strain was found to use both NADH and NADPH with high efficiencies and with a preference for NADPH as its coenzyme, which is different from the coenzyme utilization of all previously reported LDHs. The biochemical properties of the D-LDH enzyme were determined by X-ray crystal structural characterization and
in vivo
and
in vitro
enzymatic activity analyses. The residue Asn
174
was demonstrated to be critical for NADPH utilization. Characterization of the biochemical properties of this enzyme will contribute to understanding of the catalytic mechanism and provide referential information for shifting the coenzyme utilization specificity of 2-hydroxyacid dehydrogenases.
Interplay between Gliotoxin Resistance, Secretion, and the Methyl/Methionine Cycle in Aspergillus fumigatus
Authors: Owens Rebecca A. , O'Keeffe Grainne , Smith Elizabeth B. , Dolan Stephen K. , Hammel Stephen , Sheridan Kevin J. , Fitzpatrick David A. , Keane Thomas M. , Jones Gary W. , Doyle Sean
Published: July 2015

Mechanistic studies on gliotoxin biosynthesis and self-protection in
Aspergillus fumigatus
, both of which require the gliotoxin oxidoreductase GliT, have revealed a rich landscape of highly novel biochemistries, yet key aspects of this complex molecular architecture remain obscure. Here we show that an
A. fumigatus
Δ
gliA
strain is completely deficient in gliotoxin secretion but still retains the ability to efflux bisdethiobis(methylthio)gliotoxin (BmGT). This correlates with a significant increase in sensitivity to exogenous gliotoxin because gliotoxin trapped inside the cell leads to (i) activation of the
gli
cluster, as disabling
gli
cluster activation, via
gliZ
deletion, attenuates the sensitivity of an
A. fumigatus
Δ
gliT
strain to gliotoxin, thus implicating cluster activation as a factor in gliotoxin sensitivity, and (ii) increased methylation activity due to excess substrate (dithiol gliotoxin) for the gliotoxin
bis
-thiomethyltransferase GtmA. Intracellular dithiol gliotoxin is oxidized by GliT and subsequently effluxed by GliA. In the absence of GliA, gliotoxin persists in the cell and is converted to BmGT, with levels significantly higher than those in the wild type. Similarly, in the Δ
gliT
strain, gliotoxin oxidation is impeded, and methylation occurs unchecked, leading to significant
S
-adenosylmethionine (SAM) depletion and
S
-adenosylhomocysteine (SAH) overproduction. This in turn significantly contributes to the observed hypersensitivity of
gliT
-deficient
A. fumigatus
to gliotoxin. Our observations reveal a key role for GliT in preventing dysregulation of the methyl/methionine cycle to control intracellular SAM and SAH homeostasis during gliotoxin biosynthesis and exposure. Moreover, we reveal attenuated GliT abundance in the
A. fumigatus
Δ
gliK
strain, but not the Δ
gliG
strain, following exposure to gliotoxin, correlating with relative sensitivities. Overall, we illuminate new systems interactions that have evolved in gliotoxin-producing, compared to gliotoxin-naive, fungi to facilitate their cellular presence.
Characterization of Virulence-Related Phenotypes in Candida Species of the CUG Clade
Authors: Priest Shelby J. , Lorenz Michael C.
Published: July 2015

Candida
species cause a variety of mucosal and invasive infections and are, collectively, the most important human fungal pathogens in the developed world. The majority of these infections result from a few related species within the “CUG clade,” so named because they use a nonstandard translation for that codon. Some members of the CUG clade, such as
Candida albicans
, present significant clinical problems, whereas others, such as
Candida
(
Meyerozyma
)
guilliermondii
, are uncommon in patients. The differences in incidence rates are imperfectly correlated with virulence in animal models of infection, but comparative analyses that might provide an explanation for why some species are effective pathogens and others are not have been rare or incomplete. To better understand the phenotypic basis for these differences, we characterized eight CUG clade species—
C. albicans
,
C. dubliniensis
,
C. tropicalis
,
C. parapsilosis
,
Clavispora lusitaniae
,
M. guilliermondii
,
Debaryomyces hansenii
, and
Lodderomyces elongisporus
—for host-relevant phenotypes, including nutrient utilization, stress tolerance, morphogenesis, interactions with phagocytes, and biofilm formation. Two species deviated from expectations based on animal studies and human incidence.
C. dubliniensis
was quite robust, grouping in nearly all assays with the most virulent species,
C. albicans
and
C. tropicalis
, whereas
C. parapsilosis
was substantially less fit than might be expected from its clinical importance. These findings confirm the utility of
in vitro
measures of virulence and provide insight into the evolution of virulence in the CUG clade.
Heparan Sulfate Modulates Neutrophil and Endothelial Function in Antibacterial Innate Immunity
Authors: Xu Ding , Olson Joshua , Cole Jason N. , van Wijk Xander M. , Brinkmann Volker , Zychlinsky Arturo , Nizet Victor , Esko Jeffrey D. , Chang Yung-Chi
Published: July 2015

Recently, we showed that endothelial heparan sulfate facilitates entry of a bacterial pathogen into the central nervous system. Here, we show that normal bactericidal activity of neutrophils is influenced by the sulfation pattern of heparan sulfate. Inactivation of heparan sulfate uronyl 2-
O
-sulfotransferase (Hs2st) in neutrophils substantially reduced their bactericidal activity, and Hs2st deficiency rendered mice more susceptible to systemic infection with the pathogenic bacterium group B
Streptococcus
. Specifically, altered sulfation of heparan sulfate in mutant neutrophils affected formation of neutrophil extracellular traps while not influencing phagocytosis, production of reactive oxygen species, or secretion of granular proteases. Heparan sulfate proteoglycan(s) is present in neutrophil extracellular traps, modulates histone affinity, and modulates their microbial activity. Hs2st-deficient brain endothelial cells show enhanced binding to group B
Streptococcus
and are more susceptible to apoptosis, likely contributing to the observed increase in dissemination of group B
Streptococcus
into the brain of Hs2st-deficient mice following intravenous challenge. Taken together, our data provide strong evidence that heparan sulfate from both neutrophils and the endothelium plays important roles in modulating innate immunity.
BB0744 Affects Tissue Tropism and Spatial Distribution of Borrelia burgdorferi
Authors: Wager Beau , Shaw Dana K. , Groshong Ashley M. , Blevins Jon S. , Skare Jon T.
Published: July 2015

Borrelia burgdorferi
, the etiologic agent of Lyme disease, produces a variety of proteins that promote survival and colonization in both the
Ixodes
species vector and various mammalian hosts. We initially identified BB0744 (also known as p83/100) by screening for
B. burgdorferi
strain B31 proteins that bind to α
1
β
1
integrin and hypothesized that, given the presence of a signal peptide, BB0744 may be a surface-exposed protein. In contrast to this expectation, localization studies suggested that BB0744 resides in the periplasm. Despite its subsurface location, we were interested in testing whether BB0744 is required for borrelial pathogenesis. To this end, a
bb0744
deletion was isolated in a
B. burgdorferi
strain B31 infectious background, complemented, and queried for the role of BB0744 following experimental infection. A combination of bioluminescent imaging, cultivation of infected tissues, and quantitative PCR (qPCR) demonstrated that Δ
bb0744
mutant
B. burgdorferi
bacteria were attenuated in the ability to colonize heart tissue, as well as skin locations distal to the site of infection. Furthermore, qPCR indicated a significantly reduced spirochetal load in distal skin and joint tissue infected with Δ
bb0744
mutant
B. burgdorferi
. Complementation with
bb0744
restored infectivity, indicating that the defect seen in Δ
bb0744
mutant
B. burgdorferi
was due to the loss of BB0744. Taken together, these results suggest that BB0744 is necessary for tissue tropism, particularly in heart tissue, alters the ability of
B. burgdorferi
to disseminate efficiently, or both. Additional studies are warranted to address the mechanism employed by BB0744 that alters the pathogenic potential of
B. burgdorferi
.
A Candida albicans Strain Expressing Mammalian Interleukin-17A Results in Early Control of Fungal Growth during Disseminated Infection
Authors: Huppler Anna R. , Whibley Natasha , Woolford Carol A. , Childs Erin E. , He Jie , Biswas Partha S. , McGeachy Mandy J. , Mitchell Aaron P. , Gaffen Sarah L.
Published: July 2015

Candida albicans
is normally a commensal fungus of the human mucosae and skin, but it causes life-threatening systemic infections in hospital settings in the face of predisposing conditions, such as indwelling catheters, abdominal surgery, or antibiotic use. Immunity to
C. albicans
involves various immune parameters, but the cytokine interleukin-17A (IL-17A) (also known as IL-17) has emerged as a centrally important mediator of immune defense against both mucosal and systemic candidiasis. Conversely, IL-17A has been suggested to enhance the virulence of
C. albicans
, indicating that it may exert detrimental effects on pathogenesis. In this study, we hypothesized that a
C. albicans
strain expressing IL-17A would exhibit reduced virulence
in vivo
. To that end, we created a
Candida
-optimized expression cassette encoding murine IL-17A, which was transformed into the DAY286 strain of
C. albicans
.
Candida
-derived IL-17A was indistinguishable from murine IL-17A in terms of biological activity and detection in standard enzyme-linked immunosorbent assays (ELISAs). Expression of IL-17A did not negatively impact the growth of these strains
in vitro
. Moreover, the IL-17A-expressing
C. albicans
strains showed significantly reduced pathogenicity in a systemic model of
Candida
infection, mainly evident during the early stages of disease. Collectively, these findings suggest that IL-17A mitigates the virulence of
C. albicans
.
Phenotypic Suppression of Streptomycin Resistance by Mutations in Multiple Components of the Translation Apparatus
Authors: Carr Jennifer F. , Lee Hannah J. , Jaspers Joshua B. , Dahlberg Albert E. , Jogl Gerwald , Gregory Steven T.
Published: July 2015

The bacterial ribosome and its associated translation factors are frequent targets of antibiotics, and antibiotic resistance mutations have been found in a number of these components. Such mutations can potentially interact with one another in unpredictable ways, including the phenotypic suppression of one mutation by another. These phenotypic interactions can provide evidence of long-range functional interactions throughout the ribosome and its functional complexes and potentially give insights into antibiotic resistance mechanisms. In this study, we used genetics and experimental evolution of the thermophilic bacterium
Thermus thermophilus
to examine the ability of mutations in various components of the protein synthesis apparatus to suppress the streptomycin resistance phenotypes of mutations in ribosomal protein S12, specifically those located distant from the streptomycin binding site. With genetic selections and strain constructions, we identified suppressor mutations in EF-Tu or in ribosomal protein L11. Using experimental evolution, we identified amino acid substitutions in EF-Tu or in ribosomal proteins S4, S5, L14, or L19, some of which were found to also relieve streptomycin resistance. The wide dispersal of these mutations is consistent with long-range functional interactions among components of the translational machinery and indicates that streptomycin resistance can result from the modulation of long-range conformational signals.

IMPORTANCE
The thermophilic bacterium
Thermus thermophilus
has become a model system for high-resolution structural studies of macromolecular complexes, such as the ribosome, while its natural competence for transformation facilitates genetic approaches. Genetic studies of
T. thermophilus
ribosomes can take advantage of existing high-resolution crystallographic information to allow a structural interpretation of phenotypic interactions among mutations. Using a combination of genetic selections, strain constructions, and experimental evolution, we find that certain mutations in the translation apparatus can suppress the phenotype of certain antibiotic resistance mutations. Suppression of resistance can occur by mutations located distant in the ribosome or in a translation factor. These observations suggest the existence of long-range conformational signals in the translating ribosome, particularly during the decoding of mRNA.
Gliding Motility of Mycoplasma mobile on Uniform Oligosaccharides
Authors: Kasai Taishi , Hamaguchi Tasuku , Miyata Makoto
Published: July 2015

The binding and gliding of
Mycoplasma mobile
on a plastic plate covered by 53 uniform oligosaccharides were analyzed. Mycoplasmas bound to and glided on only 21 of the fixed sialylated oligosaccharides (SOs), showing that sialic acid is essential as the binding target. The affinities were mostly consistent with our previous results on the inhibitory effects of free SOs and suggested that
M. mobile
recognizes SOs from the nonreducing end with four continuous sites as follows. (i and ii) A sialic acid at the nonreducing end is tightly recognized by tandemly connected two sites. (iii) The third site is recognized by a loose groove that may be affected by branches. (iv) The fourth site is recognized by a large groove that may be enhanced by branches, especially those with a negative charge. The cells glided on uniform SOs in manners apparently similar to those of the gliding on mixed SOs. The gliding speed was related inversely to the mycoplasma's affinity for SO, suggesting that the detaching step may be one of the speed determinants. The cells glided faster and with smaller fluctuations on the uniform SOs than on the mixtures, suggesting that the drag caused by the variation in SOs influences gliding behaviors.

IMPORTANCE
Mycoplasma is a group of bacteria generally parasitic to animals and plants. Some
Mycoplasma
species form a protrusion at a pole, bind to solid surfaces, and glide in the direction of the protrusion. These procedures are essential for parasitism. Usually, mycoplasmas glide on mixed sialylated oligosaccharides (SOs) derived from glycoprotein and glycolipid. Since gliding motility on uniform oligosaccharides has never been observed, this study gives critical information about recognition and interaction between receptors and SOs.
DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales
Authors: van Wolferen Marleen , Ma Xiaoqing , Albers Sonja-Verena
Published: July 2015

The
ups
operon of
Sulfolobus
species is highly induced upon UV stress. Previous studies showed that the pili encoded by this operon are involved in cellular aggregation, which is essential for subsequent DNA exchange between cells, resulting in homologous recombination. The presence of this pilus system increases the fitness of
Sulfolobus
cells under UV light-induced stress conditions, as the transfer of DNA takes place in order to repair UV-induced DNA lesions via homologous recombination. Four conserved genes (
saci_1497
to
saci_1500
) which encode proteins with putative DNA processing functions are present downstream of the
ups
operon. In this study, we show that after UV treatment the cellular aggregation of strains with
saci_1497
,
saci_1498
, and
saci_1500
deletions is similar to that of wild-type strains; their survival rates, however, were reduced and similar to or lower than those of the pilus deletion strains, which could not aggregate anymore. DNA recombination assays indicated that
saci_1498
, encoding a ParB-like protein, plays an important role in DNA transfer. Moreover, biochemical analysis showed that the endonuclease III encoded by
saci_1497
nicks UV-damaged DNA. In addition, RecQ-like helicase Saci_1500 is able to unwind homologous recombination intermediates, such as Holliday junctions. Interestingly, a
saci_1500
deletion mutant was more sensitive to UV light but not to the replication-stalling agents hydroxyurea and methyl methanesulfonate, suggesting that Saci_1500 functions specifically in the UV damage pathway. Together these results suggest a role of Saci_1497 to Saci_1500 in the repair or transfer of DNA that takes place after UV-induced damage to the genomic DNA of
Sulfolobus acidocaldarius
.

IMPORTANCE
Sulfolobales
species increase their fitness after UV stress by a UV-inducible pilus system that enables high rates of DNA exchange between cells. Downstream of the pilus operon, three genes that seem to play a role in the repair or transfer of the DNA between
Sulfolobus
cells were identified, and their possible functions are discussed. Next to the previously described role of UV-inducible pili in the exchange of DNA, we have thereby increased our knowledge of DNA transfer at the level of DNA processing. This paper therefore contributes to the overall understanding of the DNA exchange mechanism among
Sulfolobales
cells.
Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli
Authors: Hengge Regine , Galperin Michael Y. , Ghigo Jean-Marc , Gomelsky Mark , Green Jeffrey , Hughes Kelly T. , Jenal Urs , Landini Paolo
Published: July 2015

In recent years,
Escherichia coli
has served as one of a few model bacterial species for studying cyclic di-GMP (c-di-GMP) signaling. The widely used
E. coli
K-12 laboratory strains possess 29 genes encoding proteins with GGDEF and/or EAL domains, which include 12 diguanylate cyclases (DGC), 13 c-di-GMP-specific phosphodiesterases (PDE), and 4 “degenerate” enzymatically inactive proteins. In addition, six new GGDEF and EAL (GGDEF/EAL) domain-encoding genes, which encode two DGCs and four PDEs, have recently been found in genomic analyses of commensal and pathogenic
E. coli
strains. As a group of researchers who have been studying the molecular mechanisms and the genomic basis of c-di-GMP signaling in
E. coli
, we now propose a general and systematic
dgc
and
pde
nomenclature for the enzymatically active GGDEF/EAL domain-encoding genes of this model species. This nomenclature is intuitive and easy to memorize, and it can also be applied to additional genes and proteins that might be discovered in various strains of
E. coli
in future studies.
Eccentric apical hypertrophic cardiomyopathy unmasked by multimodality imaging: an uncommon but missed cause of out of hospital cardiac arrest
Authors: Towe Eric , Sharma Saurabh , Geske Jeffrey , Ackerman Michael J
Published: July 2015

A woman in her late 50s experienced a witnessed, sudden out of hospital cardiac arrest. Initial workup included coronary angiography, transthoracic echocardiogram and a CT scan of the chest to rule out pulmonary embolus. She was subsequently discharged home without an implantable cardioverter defibrillator (ICD) or a life vest. On follow-up at another facility, an ICD was placed and a Holter monitor showed no ventricular ectopy. Further transthoracic echocardiographic images were obtained, which were suggestive of apical hypertrophic cardiomyopathy. A limited transthoracic echocardiogram with contrast was performed, which did not elucidate the hypertrophy. However, eccentric left ventricular apical wall hypertrophy was visualised by a coronary CT scan.
Treatment resistant somatic delusions in bipolar disorder
Authors: Slattery Hannah , Nance Michael
Published: July 2015

Two patients each developed a single, fixed somatic delusion complicating their existing bipolar disorder. Both failed to respond to a range of antidepressant and antipsychotic medications. They each showed a partial response to clozapine and to electroconvulsive therapy, with resolution of mood symptoms and diminution of their ongoing somatic preoccupation. A review of case reports suggests a possible relationship between somatic delusions and affective disorders.
Novel use of videolaryngoscopy to remove a foreign body
Authors: Ho Geoffrey , Singh Neeraj , Andrews Jonathan , Westhead Peter
Published: July 2015

We present a case where a C-MAC video laryngoscope was used to remove a duodenal stent that was inadvertently dislodged in the patient's proximal oesophagus during an interventional radiology procedure, causing upper airway obstruction. Using the C-MAC and a pair of Magill forceps, we were able to successfully remove the stent. Video feed allowed for further communication between us and the ENT (ear, nose and throat) surgeons.
Pacemaker lead-associated thrombosis in cardiac resynchronisation therapy
Authors: Buttigieg Jesmar , Asciak Rachelle , Mallia Azzopardi Charles
Published: July 2015

Pacemaker lead-associated thrombosis is a possible complication of any cardiac implantable electronic device. We present a case of a middle-aged woman with a history of ischaemic left ventricular failure, who presented with fever and other non-specific symptoms 4 months after cardiac resynchronisation therapy. A transoesophageal echocardiogram confirmed a vegetation-like structure originating from the pacemaker lead in the right atrium. The patient was treated with intravenous antibiotics followed by open heart surgery in order to remove this mass as well as the pacing device, including all three pacing leads. Histology and culture of the retrieved mass confirmed a sterile thrombus with no features to suggest an infected mass (vegetation). The patient made an uncomplicated recovery and there were no long-term sequelae on follow-up during the 2 years after the event.
Aborted sudden cardiac death associated with an anomalous right coronary artery
Authors: Diaz Rienzi A , Valdés Julio
Published: July 2015

Coronary artery anomalies arising from the opposite sinus of Valsalva and having an interarterial course between the aorta (AO) and pulmonary artery (PA) are the second most common cause of sudden cardiac death among young athletes, after hypertrophic cardiomyopathy. The right coronary artery (RCA) originating from the AO above the left sinus of Valsalva (LSV) is an extremely rare anomaly. We report the first case of a RCA arising from the AO above the LSV that subsequently runs between the AO and the PA, discovered by a 64-slice multidetector coronary CT, in a patient who was successfully resuscitated from ventricular fibrillation (VF) cardiac arrest while running in a marathon race.
Late neonatal presentation of reduced arm movement due to painful infective lymphadenopathy
Authors: Stokes Victoria , Fertleman Caroline
Published: July 2015

We report two cases of 21-day-old male infants, Baloo and Bagheera, both admitted with unilateral reduced arm movement secondary to painful lymphadenopathy, which is a presentation previously unreported in the paediatric literature. The only abnormal finding following investigations in both neonates was infective lymphadenopathy; we hypothesise that the inflamed lymph nodes were tender when the surrounding muscles, fascia or skin were moved, so that the infants learnt to reduce arm movement to minimise pain. This report explores the differential diagnoses for reduced arm movement in neonates, and highlights the importance of sepsis with painful lymphadenopathy as a differential diagnosis in neonates presenting with reduced arm movement.
Pulmonary aspergillosis presenting with recurrent haemoptysis
Authors: Betancourt Blas Y , Garofoli Adrian C , Sandhu Jagbir S , Boma Noella , Sy Alexander M
Published: July 2015

Pulmonary aspergillosis presents with a variety of clinical forms including invasive pulmonary aspergillosis, chronic necrotising aspergillosis, aspergilloma, chronic cavitary pulmonary aspergillosis and allergic bronchopulmonary aspergillosis. Haemoptysis is a devastating complication of pulmonary aspergillosis and a common indication for surgery. We report a case of a 54-year-old man with a history of pulmonary tuberculosis and diabetes mellitus, who presented with productive cough and haemoptysis for 2 months. Chest CT revealed a 30 mm diameter soft tissue mass in the upper lobe of the right lung. Haemoptysis subsided with conservative measures, but 2 weeks later the patient developed a new episode of persistent haemoptysis, which was only partially controlled with bronchial arterial embolisation. He underwent right upper and middle lobectomy. Histology examination confirmed the presence of a fungal cavitary lesion. The patient was started on voriconazole, and recovered with no recurrence at 18 months follow-up.
Development of a computerised decisions support system for renal risk drugs targeting primary healthcare
Authors: Helldén Anders , Al-Aieshy Fadiea , Bastholm-Rahmner Pia , Bergman Ulf , Gustafsson Lars L , Höök Hans , Sjöviker Susanne , Söderström Anders , Odar-Cederlöf Ingegerd
Published: July 2015

Objectives

To assess general practitioners (GPs) experience from the implementation and use of a renal computerised decision support system (CDSS) for drug dosing, developed for primary healthcare, integrated into the patient’s electronic health record (EHR), and building on estimation of the patient's creatinine clearance (ClCG).

Design

Qualitative research design by a questionnaire and a focus group discussion.

Setting and participants

Eight GPs at two primary healthcare centres (PHCs).

Interventions

The GP at PHC 1, and the project group, developed and tested the technical solution of the CDSS. Proof-of-concept was tested by seven GPs at PHC 2. They also participated in a group discussion and answered a questionnaire. A web window in the EHR gave drug and dosage in relation to ClCG. Each advice was according to three principles: If? Why? Because.

Outcome measures

(1) The GPs’ experience of ‘easiness to use’ and ‘perceived usefulness’ at PHC 2, based on loggings of use, answers from a questionnaire using a 5-point Likert scale, and answers from a focus group discussion. (2) The number of patients aged 65 years and older with an estimation of ClCGbefore and after the implementation of the CDSS.

Results

The GPs found the CDSS fast, simple and easy to use. They appreciated the automatic presentation of the CICGstatus on opening the medication list, and the ability to actively look up specific drug recommendations in two steps. The CDSS scored high on the Likert scale. All GPs wanted to continue the use of the CDSS and to recommend it to others. The number of patients with an estimated ClCGincreased 1.6-fold.

Conclusions

Acceptance of the simple graphical interface of this push and pull renal CDSS was high among the primary care physicians evaluating this proof of concept. The graphical model should be useful for further development of renal decision support systems.
How effective are patient safety initiatives? A retrospective patient record review study of changes to patient safety over time
Authors: Baines Rebecca , Langelaan Maaike , de Bruijne Martine , Spreeuwenberg Peter , Wagner Cordula
Published: July 2015

Objectives

To assess whether, compared with previous years, hospital care became safer in 2011/2012, expressing itself in a fall in preventable adverse event (AE) rates alongside patient safety initiatives.

Design

Retrospective patient record review at three points in time.

Setting

In three national AE studies, patient records of 2004, 2008 and 2011/2012 were reviewed in, respectively, 21 hospitals in 2004, 20 hospitals in 2008 and 20 hospitals in 2011/2012. In each hospital, 400, 200 and 200 patient records were sampled, respectively.

Participants

In total, 15 997 patient admissions were included in the study, 7926 patient admissions from 2004, 4023 from 2008 and 4048 from 2011/2012.

Interventions

The main patient safety initiatives in hospital care at a national level between 2004 and 2012 have been small as well as large-scale multifaceted programmes.

Main outcome measures

Rates of both AEs and preventable AEs.

Results

Uncorrected crude overall AE rates showed no change in 2011/2012 in comparison with 2008, whereas preventable AE rates showed a reduction of 45%. After multilevel corrections, the decrease in preventable AE rate in 2011/2012 was still clearly visible with a decrease of 30% in comparison to 2008 (p=0.10). In 2011/2012, fewer preventable AEs were found in older age groups, or related to the surgical process, in comparison with 2008.

Conclusions

Our study shows some improvements in preventable AEs in the areas that were addressed during the comprehensive national safety programme. There are signs that such a programme has a positive impact on patient safety.
Discovery of potential negative allosteric modulators of mGluR5 from natural products using pharmacophore modeling, molecular docking, and molecular dynamics simulation studies
Authors: Jiang Ludi , Li Yong , Qiao Liansheng , Chen Xi , He Yusu , Zhang Yanling , Li Gongyu
Published: July 2015

mGluR5, which belongs to the G-protein-coupled receptor superfamily, is believed to be associated with many human diseases, such as a wide range of neurological disorders, gastroesophageal reflux disease, and cancer. Comparing with compounds that target on the orthosteric binding site, significant roles have been established for mGluR5 negative allosteric modulators (NAMs) due to their higher subtype selectivity and more suitable pharmacokinetic profiles. Nevertheless, to date, none of them have come to market for various reasons. In this study, a 3D quantitative pharmacophore model was generated by using the HypoGen module in Discovery Studio 4.0. With several validation methods ultilized, the optimal pharmacophore model Hypo2 was selected to discover potential mGluR5 NAMs from natural products. Two hundred and seventeen potential NAMs were obtained after being filtered by Lipinski’s rule (≥4). Then, molecular docking was used to refine the pharmacophore-based screening results and analyze the binding mode of NAMs and mGluR5. Three compounds, aglaiduline, 5-O-ethyl-hirsutanonol, and yakuchinone A, with good ADMET properties, acceptable Fit value and estimated value, and high docking score, were reserved for a molecular dynamics simulation study. All of them have stability of ligand binding. From our computational results, there might exhibit drug-like negative allosteric moderating effects on mGluR5 in these natural products. This work provides a reliable method for discovering mGluR5 NAMs from natural products.
Induction and viability of tetraploids in brook trout (Salvelinus fontinalis)
Authors: Weber Gregory M. , Hostuttler Mark A. , Semmens Kenneth J. , Beers Brian A.
Published: July 2015

Brook trout (Salvelinus fontinalis) populations are threatened by introduction of invasive species, habitat loss, and habitat degradation in their native range and are a problem invasive species in western Unites States and Canada and in Europe. Stocking sterile triploids has been promoted as an approach to reduce negative effects of stocking of brook trout for recreational fishing on native fish populations. Crossing a tetraploid with a diploid is a method of triploid production that may help hatcheries meet demand. We induced tetraploidy in brook trout by application of 633 kg·cm−2 of hydrostatic pressure for 8 min at 70%–72.5% of the first cleavage interval. Yields of above 50% tetraploid progeny at hatching were readily achieved, although few animals reached 1 year of age. We crossed a male tetraploid with female diploid fish and produced interploid-triploids with eyeing rates in excess of 50%, demonstrating male tetraploids are fertile and capable of siring triploid progeny. Female tetraploid fish were reared to 16 months posthatching and possessed follicles in secondary vitellogenesis, suggesting tetraploid females are also fertile. Tetraploid induction rates in excess of 96% were achieved applying the same hydrostatic pressure treatment to zygotes of tetraploid × diploid crosses at 30 min postfertilization.
Isolating causal pathways between flow and fish in the regulated river hierarchy
Authors: McManamay Ryan A. , Peoples Brandon K. , Orth Donald J. , Dolloff Charles A. , Matthews David C.
Published: July 2015

Unregulated river systems are organized in a hierarchy in which large-scale factors (i.e., landscape and segment scales) influence local habitats (i.e., reach, meso-, and microhabitat scales), and both differentially exert selective pressures on biota. Dams, however, create discontinua in these processes and change the hierarchical structure. We examined the relative roles of hydrology and other instream factors, within a hierarchical landscape context, in organizing fish communities in regulated and unregulated tributaries to the Upper Tennessee River, USA. We used multivariate regression trees to identify factors that partition fish assemblages based on trait similarities, irrespective of spatial scale. We then used classical path analysis and structural equation modeling to evaluate the most plausible hierarchical causal structure of specific trait-based community components, given the data. Both statistical approaches suggested that river regulation affects stream fishes through a variety of reach-scale variables, not always through hydrology itself. Although we observed different changes in flow, temperature, and biotic responses according to regulation types, the most predominant path in which dam regulation affected biota was via temperature alterations. Diversion dams had the strongest effects on fish assemblages. Diversion dams reduced flow magnitudes, leading to declines in fish richness but increased temperatures, leading to lower abundances in equilibrium species and nest guarders. Peaking and run-of-river dams increased flow variability, leading to lower abundances in nest-guarding fishes. Flow displayed direct relationships with biotic responses; however, results indicated that changes in temperature and substrate had equal, if not stronger, effects on fish assemblage composition. The strength and nature of relationships depended on whether flow metrics were standardized for river size. We suggest that restoration efforts in regulated rivers focus on improving flow conditions in conjunction with temperature and substrate restoration.
Weak vs. Self vs. Probabilistic Stabilization
Authors: Devismes Stéphane , Tixeuil Sébastien , Yamashita Masafumi
Published: July 2015

Self-stabilization is a strong property, which guarantees that a distributed system always resumes a correct behavior starting from an arbitrary initial state. Since it is a strong property, some problems cannot have self-stabilizing solutions. Weaker guarantees hence have been later introduced to cope with impossibility results, e.g., probabilistic self-stabilization only guarantees probabilistic convergence to a correct behavior, and weak stabilization only guarantees the possibility of convergence. In this paper, we investigate the relative power of self, probabilistic, and weak stabilization, with respect to the set of problems that can be solved. Weak stabilization is by definition stronger than self-stabilization and probabilistic self-stabilization in that precise sense. We first show that weak stabilization allows to solve problems having no self-stabilizing solution. We then show that any finite state deterministic weak stabilizing algorithm to solve a problem under the strongly fair scheduler is always a probabilistic self-stabilizing algorithm to solve the same problem under the randomized scheduler. Unfortunately, this good property does not hold in general for infinite state algorithms. We however show that for some classes of infinite state algorithms, this property holds. These results hint at more practical use of weak stabilizing algorithms, as they are easier to design and prove their correctness than their self-stabilizing and probabilistic self-stabilizing counterparts.
Automatic Sets of Rational Numbers
Authors: Rowland Eric , Shallit Jeffrey
Published: July 2015

The notion of a [Formula: see text]-automatic set of integers is well-studied. We develop a new notion — the [Formula: see text]-automatic set of rational numbers — and prove basic properties of these sets, including closure properties and decidability.