bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct water and fat determination in two‐point Dixon imaging with flexible echo times
Authors: Rambow Olen , Hazle John , Clark John , Ma Jingfei 
Published: October 2013

Purpose:Identifying water and fat unambiguously in multipoint Dixon imaging often requires phase correction, which can be challenging and may fail. The purpose of this work is to present a geometric interpretation of the two‐point Dixon method with flexible echo times (TEs) and to investigate the conditions under which water and fat can be determined directly without phase correction.Methods:Geometrically, the equation for the magnitude of the acquired signal at a givenTE represents an ellipse in the water–fat plane centered at the origin. Determining water and fat in two‐point Dixon imaging thus amounts to finding the correct intercept between two ellipses from the signals at two TEs. At the right TE combinations, the physicality requirement that water and fat be non‐negative can be used to select a unique water and fat solution. Systematic computer simulations were conducted to examine the ranges of the TEs for which this approach is feasible and how different noise levels impact the feasibility. Phantom and in vivo experiments on a 1.5‐T whole‐body MRI scanner were used to validate the computer simulations.Results:In simulation and phantom experiments, nearly all pixels of pure water or pure fat were reliably identified based on the physicality requirement alone for a range of practically usefulTE combinations (e.g., around 3 ms/6 ms at 1.5 T) and at moderate to high SNR levels (≥25). At other TE combinations, finding the correct solution based on the physicality requirement alone was not feasible or became sensitive to noise. In vivo findings were in overall agreement with the simulation and phantom studies, although the percentage of pixels that were correctly determined was lower.Conclusions:The problem of direct water and fat determination without phase correction can be understood geometrically. Using the physicality requirement, it is possible to identify the differentTE combinations and imaging conditions under which water and fat imaging can be performed either completely without phase correction or by generating a first‐pass solution that can be used to improve the processing reliability of a phase‐correction based method.
Rapid Detection and Identification of Nontuberculous Mycobacterial Pathogens in Fish by Using High-Resolution Melting Analysis
Authors: Phung Thu Nguyet , Caruso Domenico , Godreuil Sylvain , Keck Nicolas , Vallaeys Tatiana , Avarre Jean-Christophe 
Published: October 2013

ABSTRACT

Mycobacterial infections in fish are commonly referred to as piscine mycobacteriosis, irrespectively of the specific identity of the causal organism. They usually cause a chronic disease and sometimes may result in high mortalities and severe economic losses. Nearly 20 species of
Mycobacterium
have been reported to infect fish. Among them,
Mycobacterium marinum
,
M. fortuitum
, and
M. chelonae
are generally considered the major agents responsible for fish mycobacteriosis. As no quick and inexpensive diagnostic test exists, we tested the potential of high-resolution melting analysis (HRMA) to rapidly identify and differentiate several
Mycobacterium
species involved in fish infections. By analyzing both the melting temperature and melting profile of the 16S-23S rRNA internal transcribed spacer (ITS), we were able to discriminate 12 different species simultaneously. Sensitivity tests conducted on purified
M. marinum
and
M. fortuitum
DNA revealed a limit of detection of 10 genome equivalents per reaction. The primers used in this procedure did not lead to any amplification signal with 16 control non-
Mycobacterium
species, thereby demonstrating their specificity for the genus
Mycobacterium
.
Characterization of Bacteriophages Cp1 and Cp2, the Strain-Typing Agents for Xanthomonas axonopodis pv. citri
Authors: Ahmad Abdelmonim Ali , Ogawa Megumi , Kawasaki Takeru , Fujie Makoto , Yamada Takashi 
Published: October 2013

ABSTRACT

The strains of
Xanthomonas axonopodis
pv. citri, the causative agent of citrus canker, are historically classified based on bacteriophage (phage) sensitivity. Nearly all
X. axonopodis
pv. citri strains isolated from different regions in Japan are lysed by either phage Cp1 or Cp2; Cp1-sensitive (Cp1
s
) strains have been observed to be resistant to Cp2 (Cp2
r
) and
vice versa
. In this study, genomic and molecular characterization was performed for the typing agents Cp1 and Cp2. Morphologically, Cp1 belongs to the
Siphoviridae
. Genomic analysis revealed that its genome comprises 43,870-bp double-stranded DNA (dsDNA), with 10-bp 3′-extruding cohesive ends, and contains 48 open reading frames. The genomic organization was similar to that of
Xanthomonas
phage phiL7, but it lacked a group I intron in the DNA polymerase gene. Cp2 resembles morphologically
Escherichia coli
T7-like phages of
Podoviridae
. The 42,963-bp linear dsDNA genome of Cp2 contained terminal repeats. The Cp2 genomic sequence has 40 open reading frames, many of which did not show detectable homologs in the current databases. By proteomic analysis, a gene cluster encoding structural proteins corresponding to the class III module of T7-like phages was identified on the Cp2 genome. Therefore, Cp1 and Cp2 were found to belong to completely different virus groups. In addition, we found that Cp1 and Cp2 use different molecules on the host cell surface as phage receptors and that host selection of
X. axonopodis
pv. citri strains by Cp1 and Cp2 is not determined at the initial stage by binding to receptors.
The Novel BacterialN-Demethylase PdmAB Is Responsible for the Initial Step ofN,N-Dimethyl-Substituted Phenylurea Herbicide Degradation
Authors: Gu Tao , Zhou Chaoyang , Sørensen Sebastian R. , Zhang Ji , He Jian , Yu Peiwen , Yan Xin , Li Shunpeng 
Published: October 2013

ABSTRACTThe environmental fate of phenylurea herbicides has received considerable attention in recent decades. The microbial metabolism ofN,N-dimethyl-substituted phenylurea herbicides can generally be initiated by mono-N-demethylation. In this study, the molecular basis for this process was revealed. ThepdmABgenes inSphingobiumsp. strain YBL2 were shown to be responsible for the initial mono-N-demethylation of commonly usedN,N-dimethyl-substituted phenylurea herbicides. PdmAB is the oxygenase component of a bacterial Rieske non-heme iron oxygenase (RO) system. The genespdmAB, encoding the α subunit PdmA and the β subunit PdmB, are organized in a transposable element flanked by two direct repeats of an insertion element resembling ISRh1. Furthermore, this transposable element is highly conserved among phenylurea herbicide-degrading sphingomonads originating from different areas of the world. However, there was no evidence of a gene for an electron carrier (a ferredoxin or a reductase) located in the immediate vicinity ofpdmAB. Without its cognate electron transport components, expression of PdmAB inEscherichia coli,Pseudomonas putida, and other sphingomonads resulted in a functional enzyme. Moreover, coexpression of a putative [3Fe-4S]-type ferredoxin fromSphingomonassp. strain RW1 greatly enhanced the catalytic activity of PdmAB inE. coli. These data suggested that PdmAB has a low specificity for electron transport components and that its optimal ferredoxin may be the [3Fe-4S] type. PdmA exhibited low homology to the α subunits of previously characterized ROs (less than 37% identity) and did not cluster with the RO group involved inO- orN-demethylation reactions, indicating that PdmAB is a distinct bacterial RON-demethylase.
A Novel Gene Involved in the Survival of Streptococcus mutans under Stress Conditions
Authors: Li Dan , Shibata Yukie , Takeshita Toru , Yamashita Yoshihisa 
Published: October 2013

ABSTRACT

A
Streptococcus mutans
mutant defective in aciduricity was constructed by random-insertion mutagenesis. Sequence analysis of the mutant revealed a mutation in
gidA
, which is known to be involved in tRNA modification in
Streptococcus pyogenes
. Complementation of
gidA
by
S. pyogenes
gidA
recovered the acid tolerance of
S. mutans
. Although the
gidA
-inactivated
S. pyogenes
mutant exhibited significantly reduced expression of multiple extracellular virulence proteins, the
S. mutans
mutant did not. On the other hand, the
gidA
mutant of
S. mutans
showed reduced ability to withstand exposure to other stress conditions (high osmotic pressure, high temperature, and bacitracin stress) besides an acidic environment. In addition, loss of GidA decreased the capacity for glucose-dependent biofilm formation by over 50%. This study revealed that
gidA
plays critical roles in the survival of
S. mutans
under stress conditions, including lower pH.
Genomic Overview and Biological Functions of Exopolysaccharide Biosynthesis in Bifidobacterium spp
Authors: Hidalgo-Cantabrana Claudio , Sánchez Borja , Milani Christian , Ventura Marco , Margolles Abelardo , Ruas-Madiedo Patricia 
Published: October 2013

ABSTRACT

For many years, bacterial exopolysaccharides (EPS) have received considerable scientific attention, mainly due to their contribution to biofilm formation and, above all, because EPS are potential virulence factors. In recent times, interest in EPS research has enjoyed a welcome boost thanks to the discovery of their ability to mediate communication processes with their surrounding environment and to their contribution to host health maintenance. In this review, we provide a fresh perspective on the genetics and activity of these polymers in members of the
Bifidobacterium
genus, a common gut inhabitant of humans and animals that has been associated with several health-promoting effects. Bifidobacteria can use EPS to protect themselves against the harsh conditions of the gastrointestinal tract, thus improving their persistence in the host. Indeed, the relevant function of EPS for bifidobacteria is underlined by the fact that most genomes sequenced until now contain genes related to EPS biosynthesis. A high interspecies variability in the number of genes and structural organization is denoted among species/subspecies; thus,
eps
clusters in this genus do not display a consensus genetic architecture. Their different G+C content compared to that of the whole genome suggests that
eps
genes have been acquired by horizontal transfer. From the host perspective, EPS-producing bifidobacteria are able to trigger both innate and adaptive immune responses, and they are able to modulate the composition and activity of the gut microbiota. Thus, these polymers seem to be critical in understanding the physiology of bifidobacteria and their interaction with the host.
Interaction between the Microbial Community and Invading Escherichia coli O157:H7 in Soils from Vegetable Fields
Authors: Yao Zhiyuan , Wang Haizhen , Wu Laosheng , Wu Jianjun , Brookes Philip C. , Xu Jianming 
Published: October 2013

ABSTRACT

The survival of
Escherichia coli
O157:H7 in soils can contaminate vegetables, fruits, drinking water, etc. However, data on the impact of
E. coli
O157:H7 on soil microbial communities are limited. In this study, we monitored the changes in the indigenous microbial community by using the phospholipid fatty acid (PLFA) method to investigate the interaction of the soil microbial community with
E. coli
O157:H7 in soils. Simple correlation analysis showed that the survival of
E. coli
O157:H7 in the test soils was negatively correlated with the ratio of Gram-negative (G
−
) to Gram-positive (G
+
) bacterial PLFAs (G
−
/G
+
ratio). In particular, levels of 14 PLFAs were negatively correlated with the survival time of
E. coli
O157:H7. The contents of actinomycetous and fungal PLFAs in the test soils declined significantly (
P
, <0.05) after 25 days of incubation with
E. coli
O157:H7. The G
−
/G
+
ratio declined slightly, while the ratio of bacterial to fungal PLFAs (B/F ratio) and the ratio of normal saturated PLFAs to monounsaturated PLFAs (S/M ratio) increased, after
E. coli
O157:H7 inoculation. Principal component analysis results further indicated that invasion by
E. coli
O157:H7 had some effects on the soil microbial community. Our data revealed that the toxicity of
E. coli
O157:H7 presents not only in its pathogenicity but also in its effect on soil microecology. Hence, close attention should be paid to the survival of
E. coli
O157:H7 and its potential for contaminating soils.
Contributions of Aspergillus fumigatus ATP-Binding Cassette Transporter Proteins to Drug Resistance and Virulence
Authors: Paul Sanjoy , Diekema Daniel , Moye-Rowley W. Scott 
Published: October 2013

ABSTRACT

In yeast cells such as those of
Saccharomyces cerevisiae
, expression of ATP-binding cassette (ABC) transporter proteins has been found to be increased and correlates with a concomitant elevation in azole drug resistance. In this study, we investigated the roles of two
Aspergillus fumigatus
proteins that share high sequence similarity with
S. cerevisiae
Pdr5, an ABC transporter protein that is commonly overproduced in azole-resistant isolates in this yeast. The two
A. fumigatus
genes encoding the ABC transporters sharing the highest sequence similarity to
S. cerevisiae
Pdr5 are called
abcA
and
abcB
here. We constructed deletion alleles of these two different ABC transporter-encoding genes in three different strains of
A. fumigatus
. Loss of
abcB
invariably elicited increased azole susceptibility, while
abcA
disruption alleles had variable phenotypes. Specific antibodies were raised to both AbcA and AbcB proteins. These antisera allowed detection of AbcB in wild-type cells, while AbcA could be visualized only when overproduced from the
hspA
promoter in
A. fumigatus
. Overproduction of AbcA also yielded increased azole resistance. Green fluorescent protein fusions were used to provide evidence that both AbcA and AbcB are localized to the plasma membrane in
A. fumigatus
. Promoter fusions to firefly luciferase suggested that expression of both ABC transporter-encoding genes is inducible by azole challenge. Virulence assays implicated AbcB as a possible factor required for normal pathogenesis. This work provides important new insights into the physiological roles of ABC transporters in this major fungal pathogen.
Laccases Involved in 1,8-Dihydroxynaphthalene Melanin Biosynthesis in Aspergillus fumigatus Are Regulated by Developmental Factors and Copper Homeostasis
Authors: Upadhyay Srijana , Torres Guadalupe , Lin Xiaorong 
Published: October 2013

ABSTRACT

Aspergillus fumigatus
produces heavily melanized infectious conidia. The conidial melanin is associated with fungal virulence and resistance to various environmental stresses. This 1,8-dihydroxynaphthalene (DHN) melanin is synthesized by enzymes encoded in a gene cluster in
A. fumigatus
, including two laccases, Abr1 and Abr2. Although this gene cluster is not conserved in all aspergilli, laccases are critical for melanization in all species examined. Here we show that the expression of
A. fumigatus
laccases Abr1/2 is upregulated upon hyphal competency and drastically increased during conidiation. The Abr1 protein is localized at the surface of stalks and conidiophores, but not in young hyphae, consistent with the gene expression pattern and its predicted role. The induction of Abr1/2 upon hyphal competency is controlled by BrlA, the master regulator of conidiophore development, and is responsive to the copper level in the medium. We identified a developmentally regulated putative copper transporter, CtpA, and found that CtpA is critical for conidial melanization under copper-limiting conditions. Accordingly, disruption of CtpA enhanced the induction of
abr1
and
abr2
, a response similar to that induced by copper starvation. Furthermore, nonpigmented
ctpA
Δ conidia elicited much stronger immune responses from the infected invertebrate host
Galleria mellonella
than the pigmented
ctpA
Δ or wild-type conidia. Such enhancement in eliciting
Galleria
immune responses was independent of the
ctpA
Δ conidial viability, as previously observed for the DHN melanin mutants. Taken together, our findings indicate that both copper homeostasis and developmental regulators control melanin biosynthesis, which affects conidial surface properties that shape the interaction between this pathogen and its host.
Lactobacillus reuteri-Specific Immunoregulatory Gene
rsiR
Modulates Histamine Production and Immunomodulation by Lactobacillus reuteri
Authors: Hemarajata P. , Gao C. , Pflughoeft K. J. , Thomas C. M. , Saulnier D. M. , Spinler J. K. , Versalovic J. 
Published: October 2013

ABSTRACT

Human microbiome-derived strains of
Lactobacillus reuteri
potently suppress proinflammatory cytokines like human tumor necrosis factor (TNF) by converting the amino acid
l
-histidine to the biogenic amine histamine. Histamine suppresses mitogen-activated protein (MAP) kinase activation and cytokine production by signaling via histamine receptor type 2 (H
2
) on myeloid cells. Investigations of the gene expression profiles of immunomodulatory
L. reuteri
ATCC PTA 6475 highlighted numerous genes that were highly expressed during the stationary phase of growth, when TNF suppression is most potent. One such gene was found to be a regulator of genes involved in histidine-histamine metabolism by this probiotic species. During the course of these studies, this gene was renamed the
Lactobacillus reuteri
-specific immunoregulatory (
rsiR
) gene. The
rsiR
gene is essential for human TNF suppression by
L. reuteri
and expression of the histidine decarboxylase (
hdc
) gene cluster on the
L. reuteri
chromosome. Inactivation of
rsiR
resulted in diminished TNF suppression
in vitro
and reduced anti-inflammatory effects
in vivo
in a trinitrobenzene sulfonic acid (TNBS)-induced mouse model of acute colitis. A
L. reuteri
strain lacking an intact
rsiR
gene was unable to suppress colitis and resulted in greater concentrations of serum amyloid A (SAA) in the bloodstream of affected animals. The P

hdcAB

promoter region targeted by
rsiR
was defined by reporter gene experiments. These studies support the presence of a regulatory gene,
rsiR
, which modulates the expression of a gene cluster known to mediate immunoregulation by probiotics at the transcriptional level. These findings may point the way toward new strategies for controlling gene expression in probiotics by dietary interventions or microbiome manipulation.
Structure and Function of a Novel
ld
-Carboxypeptidase A Involved in Peptidoglycan Recycling
Authors: Das Debanu , Hervé Mireille , Elsliger Marc-André , Kadam Rameshwar U. , Grant Joanna C. , Chiu Hsiu-Ju , Knuth Mark W. , Klock Heath E. , Miller Mitchell D. , Godzik Adam , Lesley Scott A. , Deacon Ashley M. , Mengin-Lecreulx Dominique , Wilson Ian A. 
Published: October 2013

ABSTRACT

Approximately 50% of cell wall peptidoglycan in Gram-negative bacteria is recycled with each generation. The primary substrates used for peptidoglycan biosynthesis and recycling in the cytoplasm are GlcNAc-MurNAc(anhydro)-tetrapeptide and its degradation product, the free tetrapeptide. This complex process involves ∼15 proteins, among which the cytoplasmic enzyme
ld
-carboxypeptidase A (LdcA) catabolizes the bond between the last two
l
- and
d
-amino acid residues in the tetrapeptide to form the tripeptide, which is then utilized as a substrate by murein peptide ligase (Mpl). LdcA has been proposed as an antibacterial target. The crystal structure of
Novosphingobium aromaticivorans
DSM 12444 LdcA (
Na
LdcA) was determined at 1.89-Å resolution. The enzyme was biochemically characterized and its interactions with the substrate modeled, identifying residues potentially involved in substrate binding. Unaccounted electron density at the dimer interface in the crystal suggested a potential site for disrupting protein-protein interactions should a dimer be required to perform its function in bacteria. Our analysis extends the identification of functional residues to several other homologs, which include enzymes from bacteria that are involved in hydrocarbon degradation and destruction of coral reefs. The
Na
LdcA crystal structure provides an alternate system for investigating the structure-function relationships of LdcA and increases the structural coverage of the protagonists in bacterial cell wall recycling.
What helps children to move more at school recess and lunchtime? Mid-intervention results from Transform-Us! cluster-randomised controlled trial
Authors: Yıldırım Mine , Arundell Lauren , Cerin Ester , Carson Valerie , Brown Helen , Crawford David , Hesketh Kylie D , Ridgers Nicola D , Te Velde Saskia J , Chinapaw Mai J M , Salmon Jo 
Published: October 2013

BackgroundTo investigate the interpersonal and physical environment mediators of the Transform-Us! mid-intervention effects on physical activity (PA) during recess and lunchtime.MethodsTransform-Us! is a clustered randomised school-based intervention with four groups: sedentary behaviour intervention (SB-I), PA intervention (PA-I), combined PA+SB-I and control group. All children in grade 3 from 20 participating primary schools in Melbourne, Australia were eligible to complete annual evaluation assessments. The outcomes were the proportion of time spent in moderate-to-vigorous PA (MVPA) and light PA (LPA) during recess and lunchtime assessed by accelerometers. Potential mediators included: perceived social support from teachers; perceived availability of line markings; perceived accessibility of sports equipment; and perceived school play environment. Generalised linear models were used and mediation effects were estimated by product-of-coefficients (a·b) approach.Results268 children (8.2 years, 57% girls at baseline) provided complete data at both time points. A significant intervention effect on MVPA during recess in the SB-I and PA-I groups compared with the control group (proportional difference in MVPA time; 38% (95% CI 21% to 57%) and 40% (95% CI 20% to 62%), respectively) was found. The perceived school play environment was significantly positively associated with MVPA at recess among girls. An increase in perceived social support from teachers suppressed the PA+SB-I effect on light PA during recess (a·b= −0.03, 95% CI −0.06 to −0.00). No significant mediating effects on PA during recess and lunchtime were observed.ConclusionsA positive perception of the school play environment was associated with higher MVPA during recess among girls. Future studies should conduct mediation analyses to explore underlying mechanisms of PA interventions.