bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of the germination kinetics of individual Bacillus subtilis spores treated with hydrogen peroxide or sodium hypochlorite
Authors: Setlow B. , Yu J. , Li Y.-Q. , Setlow P.
Published: June 2013

More than 95% of individuals in populations of Bacillus subtilis spores killed approximately 95% by hydrogen peroxide or hypochlorite germinated with a nutrient, although the germination of the treated spores was slower than that of untreated spores. The slow germination of individual oxidizing agent-treated spores was due to: (i) 3- to 5-fold longer lag times (Tlag) between germinant addition and initiation of fast release of spores' large dipicolinic acid (DPA) depot (ii) 2- to 10-fold longer times (ΔTrelease) for rapid DPA release, once this process had been initiated; and (iii) 3- to 7-fold longer times needed for lysis of spores' peptidoglycan cortex. These results indicate that effects of oxidizing agent treatment on subsequent spore germination are on: (i) nutrient germinant receptors in spores' inner membrane (ii) components of the DPA release process, possibly SpoVA proteins also in spores' inner membrane, or the cortex-lytic enzyme CwlJ; and (iii) the cortex-lytic enzyme SleB, also largely in spores' inner membrane. This study further indicates that rapid assays of spore viability based on measurement of DPA release in spore germination can give false-positive readings.

Significance and Impact of the Study

This work shows that with Bacillus subtilis spore populations in which approximately 95% of individual spores were killed by several oxidizing agents, >95% of the spores in these populations germinated with nutrients, albeit slowly. This is important, as assay of an early germination event, release of dipicolinic acid, has been suggested as a rapid assay for spore viability and would give false-positive readings for the level of the killing of oxidizing agent-treated spore populations. Analysis of the germination kinetics of multiple individual untreated or oxidizing agent-treated spores also provides new information on proteins damaged by oxidizing agent treatment, and at least some of which are in spores' inner membrane.
The development of a new risk model: The Threat Matrix
Authors: Jones Emma , Harkins Leigh , Beech Anthony R.
Published: June 2013

The risk assessment of sex offenders has evolved rapidly over a 20‐year period. However, there is still disparity between empirically evaluated approaches and the needs within the applied context. This article discusses the division between the current needs in the applied setting of sex offender risk assessment, and the existing approaches to risk assessment. It highlights key needs that ought to be responded to, to continue the evolution of sex offender risk assessment (i.e., increased automation of processes, additional emphasis on early identification and prevention, and the targeting of resources towards risk). A new risk assessment model termed the Threat Matrix is introduced as a proposed response to these needs. The new model uses information derived from police systems to make proactive assessments of those who may pose a risk of sexual violence, but who have not been convicted of sexual offences. The practical and ethical implications of implementing and testing this model are discussed.
Work, Family, and Accounts of Mothers’ Lives Using Discourse to Navigate Intensive Mothering Ideals
Authors: Damaske Sarah
Published: June 2013

Despite the dramatic increase in women’s employment since the 1970s, mothers’ decisions about work remain closely scrutinized. The intensive mothering ethos in which “good” mothers are highly involved in the minutiae of their children’s lives, continues to be the prevailing parenting paradigm in the United States. This article asks: How do women use discourse to navigate the demands of intensive motherhood? First, this article reviews literature on ideologies of intensive mothering. The article then considers research on how accounts are used to navigate the moral dilemmas surrounding women’s work and motherhood. This article provides us with a better understanding of how traditional gender divides remain culturally relevant, how people use discourse to expand cultural schemas to fit their own social location, and how the process of expanding the framework of a schema through this negotiation process can allow traditional gender schemas to remain salient even while different actions are incorporated.
Improving medication adherence through technology: analyzing the managing meds video challenge
Authors: Laffer Matthew S. , Feldman Steven R.
Published: June 2013

Background

Poor adherence to medication is an enormous problem. While many measures to improve adherence have been proposed, patients may be a good source of novel approaches. The Managing Meds Video Challenge was designed, by the U.S. Department of Health and Human Services (HHS), in collaboration with the National Consumers League Script Your Future campaign, for patients to create short videos containing ideas on how to better take medications as directed.

Purpose

Determine what forms of technology patients use to help adhere to their medication regimens.

Methods

The 17 available videos from the Managing Meds Video Challenge were analyzed to determine what forms of technology patients use to help adhere to their medication regimens.

Results

Approaches to improve adherence included calendar and reminder applications, and third‐party applications such as MedCoach Medication Reminder, Walgreens Pharmacy, and CVS/Pharmacy. Patients also improved adherence by using the Internet to access websites such as www.rememberitnow.com to manage medications, access electronic health records, and to order medications from online pharmacies.

Limitations

This study only analyzes the 17 available videos from the Managing Meds Video Challenge.

Conclusions

Patients are using a variety of technology to manage their medications. They appear to rely primarily on reminder systems.
Cross‐reaction and co‐sensitization among related and unrelated allergens in canine intradermal tests
Authors: Buckley Laura , Schmidt Vanessa , McEwan Neil , Nuttall Tim
Published: June 2013

Background

Intradermal tests are used to identify allergens for avoidance and immunotherapy in atopic dogs.

Hypothesis/Objectives

To evaluate cross‐reaction or co‐sensitization among 53 intradermal test allergens.

Animals

Six hundred and fifty‐one client‐owned dogs with atopic dermatitis.

Methods

Intradermal tests were performed with 53 house dust/storage mite, epidermal, insect, tree, weed and grass pollen and mould allergens. Pairwise comparisons were used to calculate the odds ratios (ORs), 95% confidence intervals (CIs) and statistical significance for the results of each allergen pair, with significance at P < 0.0006 (Holm–Bonferroni correction to reduce the false‐detection rate).

Results

Apart from cotton, cockroach, red clover, grain smut and Penicillium, the results for the allergens within each group were statistically associated [ORs from 4.7 (CI 2.5–8.9) to 1229.4 (CI 166.5–1795.1); P = 0.0005 to P < 0.0001]. Excluding red clover and cotton, 94% of results between tree, weed and grass pollens were also statistically associated [ORs from 8.3 (CI 3.6–24.7) to 117 (CI 29.1–341); P = 0.0005 to P < 0.0001]. In contrast, few allergens from unrelated groups were statistically associated [ORs from 0.12 (CI 0.03–1.1) to 27.7 (CI 0.2–93); P = 1.0 to P < 0.0001]. The mean (SD) of the log e transformed ORs for the related and statistically associated allergens [5.3 (1.3)] was significantly greater than those for related but nonstatistically associated [1.7 (1.6)] or unrelated allergens [1.4 (1.4); P < 0.0001].

Conclusions and clinical importance

This suggests that there is cross‐reaction or co‐sensitization between related allergens. This could have implications for allergen selection in testing and immunotherapy, but further studies are required to differentiate cross‐reaction from co‐sensitization.
Elevated blood pressure, heart rate and body temperature in mice lacking the XLαs protein of the Gnas locus is due to increased sympathetic tone
Authors: Nunn Nicolas , Feetham Claire H. , Martin Jennifer , Barrett‐Jolley Richard , Plagge Antonius
Published: June 2013

New Findings

What is the central question of this study?

Previously, we showed that Gnasxl knock‐out mice are lean and hypermetabolic, with increased sympathetic stimulation of adipose tissue. Do these mice also display elevated sympathetic cardiovascular tone? Is the brain glucagon‐like peptide‐1 system involved?

What is the main finding and its importance?

Gnasxl knock‐outs have increased blood pressure, heart rate and body temperature. Heart rate variability analysis suggests an elevated sympathetic tone. The sympatholytic reserpine had stronger effects on blood pressure, heart rate and heart rate variability in knock‐out compared with wild‐type mice. Stimulation of the glucagon‐like peptide‐1 system inhibited parasympathetic tone to a similar extent in both genotypes, with a stronger associated increase in heart rate in knock‐outs. Deficiency of Gnasxl increases sympathetic cardiovascular tone.

Imbalances of energy homeostasis are often associated with cardiovascular complications. Previous work has shown that Gnasxl‐deficient mice have a lean and hypermetabolic phenotype, with increased sympathetic stimulation of adipose tissue. The Gnasxl transcript from the imprinted Gnas locus encodes the trimeric G‐protein subunit XLαs, which is expressed in brain regions that regulate energy homeostasis and sympathetic nervous system (SNS) activity. To determine whether Gnasxl knock‐out (KO) mice display additional SNS‐related phenotypes, we have now investigated the cardiovascular system. The Gnasxl KO mice were ∼20 mmHg hypertensive in comparison to wild‐type (WT) littermates (P≤ 0.05) and hypersensitive to the sympatholytic drug reserpine. Using telemetry, we detected an increased waking heart rate in conscious KOs (630 ± 10 versus 584 ± 12 beats min−1, KO versus WT, P≤ 0.05). Body temperature was also elevated (38.1 ± 0.3 versus 36.9 ± 0.4°C, KO versus WT, P≤ 0.05). To investigate autonomic nervous system influences, we used heart rate variability analyses. We empirically defined frequency power bands using atropine and reserpine and verified high‐frequency (HF) power and low‐frequency (LF) LF/HF power ratio to be indicators of parasympathetic and sympathetic activity, respectively. The LF/HF power ratio was greater in KOs and more sensitive to reserpine than in WTs, consistent with elevated SNS activity. In contrast, atropine and exendin‐4, a centrally acting agonist of the glucagon‐like peptide‐1 receptor, which influences cardiovascular physiology and metabolism, reduced HF power equally in both genotypes. This was associated with a greater increase in heart rate in KOs. Mild stress had a blunted effect on the LF/HF ratio in KOs consistent with elevated basal sympathetic activity. We conclude that XLαs is required for the inhibition of sympathetic outflow towards cardiovascular and metabolically relevant tissues.
Euler–Lagrange Two-Phase Model for Simulating Live-Bed Scour Beneath Marine Pipelines
Authors: Yeganeh-Bakhtiary A. , Zanganeh M. , Kazemi E. , Cheng L. , Abd Wahab A. K.
Published: June 2013

In this study, an Euler–Lagrange coupling two-phase flow model, namely movable bed simulator (MBS)-two-dimensional (2D) model was employed to explore the current-induced live-bed scour beneath marine pipelines. The fluid phase characteristics, such as velocity and pressure, were obtained by the Reynolds-averaged Navier–Stokes (RANS) equations with a k-ε turbulence closure model in a two-dimensional Eulerian grid, whereas the seabed beneath pipelines was traced as an assembly of discrete sand grains from the Lagrangian point of view. The live-bed scour was evolved as the motion of a granular media based on distinct element method (DEM) formulation, in which the frequent interparticle collision was described with a spring and dashpot system. The fluid flow was coupled to the sediment phase, considering the acting drag forces between. Comparison between the numerical result and experimental measurement confirms that the numerical model successfully estimates the bed profile and flow velocity field. It is evident that the fluid shear stress decreases with the increasing of gap ratio e/D. The numerical model provides a useful approach to improve mechanistic understanding of hydrodynamic and sediment transport in live-bed scour beneath a marine pipeline.
Critical assessment of intramodality 3D ultrasound imaging for prostate IGRT compared to fiducial markers
Authors: van der Meer Skadi , Bloemen‐van Gurp Esther , Hermans Jolanda , Voncken Robert , Heuvelmans Denys , Gubbels Carol , Fontanarosa Davide , Visser Peter , Lutgens Ludy , van Gils Francis , Verhaegen Frank
Published: June 2013

Purpose:

A quantitative 3D intramodality ultrasound (US) imaging system was verified for daily in‐room prostate localization, and compared to prostate localization based on implanted fiducial markers (FMs).

Methods:

Thirteen prostate patients underwent multiple US scans during treatment. A total of 376 US‐scans and 817 matches were used to determine the intra‐ and interoperator variability. Additionally, eight other patients underwent daily prostate localization using both US and electronic portal imaging (EPI) with FMs resulting in 244 combined US‐EPI scans. Scanning was performed with minimal probe pressure and a correction for the speed of sound aberration was performed. Uncertainties of both US and FM methods were assessed. User variability of the US method was assessed.

Results:

The overall US user variability is 2.6 mm. The mean differences between US and FM are: 2.5 ± 4.0 mm (LR), 0.6 ± 4.9 mm (SI), and −2.3 ± 3.6 mm (AP). The intramodality character of this US system mitigates potential errors due to transducer pressure and speed of sound aberrations.

Conclusions:

The overall accuracy of US (3.0 mm) is comparable to our FM workflow (2.2 mm). Since neither US nor FM can be considered a gold standard no conclusions can be drawn on the superiority of either method. Because US imaging captures the prostate itself instead of surrogates no invasive procedure is required. It requires more effort to standardize US imaging than FM detection. Since US imaging does not involve a radiation burden, US prostate imaging offers an alternative for FM EPI positioning.
A high amplitude, time reversal acoustic non-contact excitation (trance)
Authors: Le Bas Pierre-Yves , Ulrich T. J. , Anderson Brian E. , Esplin J. James
Published: June 2013

This paper describes the principle behind a high amplitude non-contact acoustic source based on the principle of time reversal (TR), a process to focus energy at a point in space. By doing the TR in an air filled, hollow cavity and using a laser vibrometer in the calibration of the system, a non-contact source may be created. This source is proven to be more energetic than an off the shelf focused ultrasound transducer. A scaled up version of the proposed source has the potential to allow nondestructive evaluation processes that require high amplitude, such as nonlinear elastic wave spectroscopy (NEWS) techniques.
Identification and Characterization of a Novel Flagellum-Dependent Salmonella-Infecting Bacteriophage, iEPS5
Authors: Choi Younho , Shin Hakdong , Lee Ju-Hoon , Ryu Sangryeol
Published: June 2013

A novel flagellatropic phage of
Salmonella enterica
serovar Typhimurium, called iEPS5, was isolated and characterized. iEPS5 has an icosahedral head and a long noncontractile tail with a tail fiber. Genome sequencing revealed a double-stranded DNA of 59,254 bp having 73 open reading frames (ORFs). To identify the receptor for iEPS5, Tn
5
transposon insertion mutants of
S
. Typhimurium SL1344 that were resistant to the phage were isolated. All of the phage-resistant mutants were found to have mutations in genes involved in flagellar formation, suggesting that the flagellum is the adsorption target of this phage. Analysis of phage infection using the Δ
motA
mutant, which is flagellated but nonmotile, demonstrated the requirement of flagellar rotation for iEPS5 infection. Further analysis of phage infection using the Δ
cheY
mutant revealed that iEPS5 could infect host bacteria only when the flagellum is rotating counterclockwise (CCW). These results suggested that the CCW-rotating flagellar filament is essential for phage adsorption and required for successful infection by iEPS5. In contrast to the well-studied flagellatropic phage Chi, iEPS5 cannot infect the Δ
fliK
mutant that makes a polyhook without a flagellar filament, suggesting that these two flagellatropic phages utilize different infection mechanisms. Here, we present evidence that iEPS5 injects its DNA into the flagellar filament for infection by assessing DNA transfer from SYBR gold-labeled iEPS5 to the host bacteria.
Broad Distribution of Diverse Anaerobic Ammonium-Oxidizing Bacteria in Chinese Agricultural Soils
Authors: Shen Li-dong , Liu Shuai , Lou Li-ping , Liu Wei-ping , Xu Xiang-yang , Zheng Ping , Hu Bao-lan
Published: June 2013

Anaerobic ammonium-oxidizing (anammox) bacteria have been detected in many marine and freshwater ecosystems. However, little is known about the distribution, diversity, and abundance of anammox bacteria in terrestrial ecosystems. In this study, anammox bacteria were found to be present in various agricultural soils collected from 32 different locations in China. Phylogenetic analysis of the 16S rRNA genes showed “
Candidatus
Brocadia,” “
Candidatus
Kuenenia,” “
Candidatus
Anammoxoglobus,” and “
Candidatus
Jettenia” in the collected soils, with “
Candidatus
Brocadia” being the dominant genus. Quantitative PCR showed that the abundance of anammox bacteria ranged from 6.38 × 10
4
± 0.42 × 10
4
to 3.69 × 10
6
± 0.25 × 10
6
copies per gram of dry weight. Different levels of diversity, composition, and abundance of the anammox bacterial communities were observed, and redundancy analysis indicated that the soil organic content and the distribution of anammox communities were correlated in the soils examined. Furthermore, Pearson correlation analysis showed that the diversity of the anammox bacteria was positively correlated with the soil ammonium content and the organic content, while the anammox bacterial abundance was positively correlated with the soil ammonium content. These results demonstrate the broad distribution of diverse anammox bacteria and its correlation with the soil environmental conditions within an extensive range of Chinese agricultural soils.
An Improved Method for
oriT
-Directed Cloning and Functionalization of Large Bacterial Genomic Regions
Authors: Kvitko Brian H. , McMillan Ian A. , Schweizer Herbert P.
Published: June 2013

We have made significant improvements to a broad-host-range system for the cloning and manipulation of large bacterial genomic regions based on site-specific recombination between directly repeated
oriT
sites during conjugation. Using two suicide capture vectors carrying flanking homology regions,
oriT
sites are recombined on either side of the target region. Using a broad-host-range conjugation helper plasmid, the region between the
oriT
sites is conjugated into an
Escherichia coli
recipient strain, where it is circularized and maintained as a chimeric mini-F vector. The cloned target region is functionalized in multiple ways to accommodate downstream manipulation. The target region is flanked with Gateway
attB
sites for recombination into other vectors and by rare 18-bp I-SceI restriction sites for subcloning. The Tn
7
-functionalized target can also be inserted at a naturally occurring chromosomal
att
Tn
7
site(s) or maintained as a broad-host-range plasmid for complementation or heterologous expression studies. We have used the oriTn
7
capture technique to clone and complement
Burkholderia pseudomallei
genomic regions up to 140 kb in size and have created isogenic
Burkholderia
strains with various combinations of genomic islands. We believe this system will greatly aid the cloning and genetic analysis of genomic islands, biosynthetic gene clusters, and large open reading frames.
Proposed Model for the High Rate of Rearrangement and Rapid Migration Observed in Some IncA/C Plasmid Lineages
Authors: Meinersmann R. J. , Lindsey R. L. , Bono J. L. , Smith T. P. , Oakley B. B.
Published: June 2013

IncA/C plasmids are a class of plasmids from the
Enterobacteriaceae
that are relatively large (49 to >180 kbp), that are readily transferred by conjugation, and that carry multiple antimicrobial resistance genes. Reconstruction of the phylogeny of these plasmids has been difficult because of the high rate of remodeling by recombination-mediated horizontal gene transfer (HGT). We hypothesized that evaluation of nucleotide polymorphisms relative to the rate of HGT would help to develop a clock to show whether anthropic practices have had significant influences on the lineages of the plasmid. A system was developed to rapidly sequence up to 191 known open reading frames from each of 39 recently isolated IncA/C plasmids from a diverse panel of
Salmonella enterica
and
Escherichia coli
strains. With these data plus sequences from GenBank, we were able to distinguish six distinct lineages that had extremely low numbers of polymorphisms within each lineage, especially among the largest group designated as group 1. Two regions, each about half the plasmid in size, could be distinguished with a separate lineal pattern. The distribution of group 1 showed that it has migrated extremely rapidly with fewer polymorphisms than can be expected in 2,000 years. Remodeling by frequent HGT was evident, with a pattern that appeared to have the highest rate just upstream of the putative conjugation origin of transfer (oriT). It seems likely that when an IncA/C plasmid is transferred by conjugation there is an opportunity for plasmid remodeling adjacent to the oriT, which was also adjacent to a multiple antimicrobial resistance gene cassette.
Bacterial Cell Wall Synthesis GeneuppPIs Required for Burkholderia Colonization of the Stinkbug Gut
Authors: Kim Jiyeun Kate , Lee Ho Jin , Kikuchi Yoshitomo , Kitagawa Wataru , Nikoh Naruo , Fukatsu Takema , Lee Bok Luel
Published: June 2013

To establish a host-bacterium symbiotic association, a number of factors involved in symbiosis must operate in a coordinated manner. In insects, bacterial factors for symbiosis have been poorly characterized at the molecular and biochemical levels, since many symbionts have not yet been cultured or are as yet genetically intractable. Recently, the symbiotic association between a stinkbug,Riptortus pedestris, and its beneficial gut bacterium,Burkholderiasp., has emerged as a promising experimental model system, providing opportunities to study insect symbiosis using genetically manipulated symbiotic bacteria. Here, in search of bacterial symbiotic factors, we targeted cell wall components of theBurkholderiasymbiont by disruption ofuppPgene, which encodes undecaprenyl pyrophosphate phosphatase involved in biosynthesis of various bacterial cell wall components. Under culture conditions, the ΔuppPmutant showed higher susceptibility to lysozyme than the wild-type strain, indicating impaired integrity of peptidoglycan of the mutant. When administered to the host insect, the ΔuppPmutant failed to establish normal symbiotic association: the bacterial cells reached to the symbiotic midgut but neither proliferated nor persisted there. Transformation of the ΔuppPmutant withuppP-encoding plasmid complemented these phenotypic defects: lysozyme susceptibilityin vitrowas restored, and normal infection and proliferation in the midgut symbiotic organ were observedin vivo. The ΔuppPmutant also exhibited susceptibility to hypotonic, hypertonic, and centrifugal stresses. These results suggest that peptidoglycan cell wall integrity is a stress resistance factor relevant to the successful colonization of the stinkbug midgut byBurkholderiasymbiont.
Clostridium perfringens Is Not Suitable for the Indication of Fecal Pollution from Ruminant Wildlife but Is Associated with Excreta from Nonherbivorous Animals and Human Sewage
Authors: Vierheilig J. , Frick C. , Mayer R. E. , Kirschner A. K. T. , Reischer G. H. , Derx J. , Mach R. L. , Sommer R. , Farnleitner A. H.
Published: June 2013

During a 3-year study,Clostridium perfringenswas investigated in defined fecal sources from a temperate alluvial backwater area of a large river system. The results reveal that usingC. perfringensas a conservative water quality indicator for total fecal pollution monitoring is no longer justified but suggest that it can be used as a tracer for excreta from nonherbivorous wildlife and human sewage.
Spatial Reorganization of Saccharomyces cerevisiae Enolase To Alter Carbon Metabolism under Hypoxia
Authors: Miura Natsuko , Shinohara Masahiro , Tatsukami Yohei , Sato Yasuhiko , Morisaka Hironobu , Kuroda Kouichi , Ueda Mitsuyoshi
Published: June 2013

Hypoxia has critical effects on the physiology of organisms. In the yeast
Saccharomyces cerevisiae
, glycolytic enzymes, including enolase (Eno2p), formed cellular foci under hypoxia. Here, we investigated the regulation and biological functions of these foci. Focus formation by Eno2p was inhibited temperature independently by the addition of cycloheximide or rapamycin or by the single substitution of alanine for the Val22 residue. Using mitochondrial inhibitors and an antioxidant, mitochondrial reactive oxygen species (ROS) production was shown to participate in focus formation. Focus formation was also inhibited temperature dependently by an
SNF1
knockout mutation. Interestingly, the foci were observed in the cell even after reoxygenation. The metabolic turnover analysis revealed that [U-
13
C]glucose conversion to pyruvate and oxaloacetate was accelerated in focus-forming cells. These results suggest that under hypoxia,
S. cerevisiae
cells sense mitochondrial ROS and, by the involvement of SNF1/AMPK, spatially reorganize metabolic enzymes in the cytosol via
de novo
protein synthesis, which subsequently increases carbon metabolism. The mechanism may be important for yeast cells under hypoxia, to quickly provide both energy and substrates for the biosynthesis of lipids and proteins independently of the tricarboxylic acid (TCA) cycle and also to fit changing environments.
Lipid Composition of Multilamellar Bodies Secreted by Dictyostelium discoideum Reveals Their Amoebal Origin
Authors: Paquet Valérie E. , Lessire René , Domergue Frédéric , Fouillen Laetitia , Filion Geneviève , Sedighi Ahmadreza , Charette Steve J.
Published: June 2013

When they are fed with bacteria,
Dictyostelium discoideum
amoebae produce and secrete multilamellar bodies (MLBs), which are composed of membranous material. It has been proposed that MLBs are a waste disposal system that allows
D. discoideum
to eliminate undigested bacterial remains. However, the real function of MLBs remains unknown. Determination of the biochemical composition of MLBs, especially lipids, represents a way to gain information about the role of these structures. To allow these analyses, a protocol involving various centrifugation procedures has been developed to purify secreted MLBs from amoeba-bacterium cocultures. The purity of the MLB preparation was confirmed by transmission electron microscopy and by immunofluorescence using H36, an antibody that binds to MLBs. The lipid and fatty acid compositions of pure MLBs were then analyzed by high-performance thin-layer chromatography (HPTLC) and gas chromatography (GC), respectively, and compared to those of amoebae as well as bacteria used as a food source. While the bacteria were devoid of phosphatidylcholine (PC) and phosphatidylinositol (PI), these two polar lipid species were major classes of lipids in MLBs and amoebae. Similarly, the fatty acid composition of MLBs and amoebae was characterized by the presence of polyunsaturated fatty acids, while cyclic fatty acids were found only in bacteria. These results strongly suggest that the lipids constituting the MLBs originate from the amoebal metabolism rather than from undigested bacterial membranes. This opens the possibility that MLBs, instead of being a waste disposal system, have unsuspected roles in
D. discoideum
physiology.
Large Linear Plasmids of Borrelia Species That Cause Relapsing Fever
Authors: Miller Shelley Campeau , Porcella Stephen F. , Raffel Sandra J. , Schwan Tom G. , Barbour Alan G.
Published: June 2013

Borrelia
species of relapsing fever (RF) and Lyme disease (LD) lineages have linear chromosomes and both linear and circular plasmids. Unique to RF species, and little characterized to date, are large linear plasmids of ∼160 kb, or ∼10% of the genome. By a combination of Sanger and next-generation methods, we determined the sequences of large linear plasmids of two New World species:
Borrelia hermsii
, to completion of its 174-kb length, and
B. turicatae
, partially to 114 kb of its 150 kb. These sequences were then compared to corresponding sequences of the Old World species
B. duttonii
and
B. recurrentis
and to plasmid sequences of LD
Borrelia
species. The large plasmids were largely colinear, except for their left ends, about 27 kb of which was inverted in New World species. Approximately 60% of the
B. hermsii
lp174 plasmid sequence was repetitive for 6 types of sequence, and half of its open reading frames encoded hypothetical proteins not discernibly similar to proteins in the database. The central ∼25 kb of all 4 linear plasmids was syntenic for orthologous genes for plasmid maintenance or partitioning in
Borrelia
species. Of all the sequenced linear and circular plasmids in
Borrelia
species, the large plasmid's putative partition/replication genes were most similar to those of the 54-kb linear plasmids of LD species. Further evidence for shared ancestry was the observation that two of the hypothetical proteins were predicted to be structurally similar to the LD species' CspA proteins, which are encoded on the 54-kb plasmids.
The Streptococcus mutans Aminotransferase Encoded by
ilvE
Is Regulated by CodY and CcpA
Authors: Santiago Brendaliz , Marek Maksym , Faustoferri Roberta C. , Quivey Robert G.
Published: June 2013

The aminotransferase IlvE was implicated in the acid tolerance response of
Streptococcus mutans
when a mutation in its gene resulted in an acid-sensitive phenotype (B. Santiago, M. MacGilvray, R. C. Faustoferri, and R. G. Quivey, Jr., J. Bacteriol. 194:2010–2019, 2012). The phenotype suggested that amino acid metabolism is important for acid adaptation, as turnover of branched-chain amino acids (bcAAs) could provide important signals to modulate expression of genes involved in the adaptive process. Previous studies have demonstrated that
ilvE
is regulated in response to the external pH, though the mechanism is not yet established. CodY and CcpA have been shown to regulate expression of branched-chain amino acid biosynthetic genes, suggesting that the ability to sense carbon flow and the nutritional state of the cell also plays a role in the regulation of
ilvE
. Electrophoretic mobility shift assays using the
ilvE
promoter and a purified recombinant CodY protein provided evidence of the physical interaction between CodY and
ilvE
. In order to elucidate the signals that contribute to
ilvE
regulation,
cat
reporter fusions were utilized. Transcriptional assays demonstrated that bcAAs are signaling molecules involved in the repression of
ilvE
through regulation of CodY. In a
codY
deletion background,
ilvE
transcription was elevated, indicating that CodY acts a repressor of
ilvE
transcription. Conversely, in a
ccpA
deletion background,
ilvE
transcription was reduced, showing that CcpA activated
ilvE
transcription. The effects of both regulators were directly relevant for transcription of
ilvE
under conditions of acid stress, demonstrating that both regulators play a role in acid adaptation.
Chemoreceptor Gene Loss and Acquisition via Horizontal Gene Transfer in Escherichia coli
Authors: Borziak Kirill , Fleetwood Aaron D. , Zhulin Igor B.
Published: June 2013

Chemotaxis allows bacteria to more efficiently colonize optimal microhabitats within their larger environment. Chemotaxis in
Escherichia coli
is the best-studied model system, and a large number of
E. coli
strains have been sequenced. The
Escherichia/Shigella
genus encompasses a great variety of commensal and pathogenic strains, but the role of chemotaxis in their association with the host remains poorly understood. Here we show that the core chemotaxis genes are lost in many, but not all, nonmotile strains but are well preserved in all motile strains. The genes encoding the Tar, Tsr, and Aer chemoreceptors, which mediate chemotaxis to a broad spectrum of chemical and physical cues, are also nearly uniformly conserved in motile strains. In contrast, the clade of extraintestinal pathogenic
E. coli
strains apparently underwent an ancestral loss of Trg and Tap chemoreceptors, which sense sugars, dipeptides, and pyrimidines. The broad range of time estimated for the loss of these genes (1 to 3 million years ago) corresponds to the appearance of the genus
Homo
.
In the Absence of RidA, Endogenous 2-Aminoacrylate Inactivates Alanine Racemases by Modifying the Pyridoxal 5′-Phosphate Cofactor
Authors: Flynn Jeffrey M. , Downs Diana M.
Published: June 2013

Members of the RidA (YjgF/YER057c/UK114) protein family are broadly conserved across the domains of life.
In vitro
, these proteins deaminate 3- or 4-carbon enamines that are generated as mechanistic intermediates of pyridoxal 5′-phosphate (PLP)-dependent serine/threonine dehydratases. The three-carbon enamine 2-aminoacrylate can inactivate some enzymes by forming a covalent adduct via a mechanism that has been well characterized
in vitro
. The biochemical activity of RidA suggested that the phenotypes of
ridA
mutant strains were caused by the accumulation of reactive enamine metabolites. The data herein show that in
ridA
mutant strains of
Salmonella enterica
, a stable 2-aminoacrylate (2-AA)/PLP adduct forms on the biosynthetic alanine racemase, Alr, indicating the presence of 2-aminoacrylate
in vivo
. This study confirms the deleterious effect of 2-aminoacrylate generated by metabolic enzymes and emphasizes the need for RidA to quench this reactive metabolite.
The Sinorhizobium meliloti Essential Porin RopA1 Is a Target for Numerous Bacteriophages
Authors: Crook Matthew B. , Draper Alicia L. , Guillory R. Jordan , Griffitts Joel S.
Published: June 2013

The symbiotic nitrogen-fixing bacterium
Sinorhizobium meliloti
harbors a gene,
SMc02396
, which encodes a predicted outer membrane porin that is conserved in many symbiotic and pathogenic bacteria in the order
Rhizobiales
. Here, this gene (renamed
ropA1
) is shown to be required for infection by two commonly utilized transducing bacteriophages (ΦM12 and N3). Mapping of
S. meliloti
mutations conferring resistance to ΦM12, N3, or both phages simultaneously revealed diverse mutations mapping within the
ropA1
open reading frame. Subsequent tests determined that RopA1, lipopolysaccharide, or both are required for infection by all of a larger collection of
Sinorhizobium
-specific phages. Failed attempts to disrupt or delete
ropA1
suggest that this gene is essential for viability. Phylogenetic analysis reveals that
ropA1
homologs in many
Rhizobiales
species are often found as two genetically linked copies and that the intraspecies duplicates are always more closely related to each other than to homologs in other species, suggesting multiple independent duplication events.
Functional Consequences of Substitution Mutations in MepR, a Repressor of the Staphylococcus aureus
mepA
Multidrug Efflux Pump Gene
Authors: Schindler Bryan D. , Seo Susan M. , Jacinto Pauline L. , Kumaraswami Muthiah , Birukou Ivan , Brennan Richard G. , Kaatz Glenn W.
Published: June 2013

The expression of
mepA
, encoding the
Staphylococcus aureus
MepA multidrug efflux protein, is repressed by the MarR homologue MepR. MepR dimers bind differently to operators upstream of
mepR
and
mepA
, with affinity being greatest at the
mepA
operator. MepR substitution mutations may result in
mepA
overexpression, with A103V most common in clinical strains. Evaluation of the functional consequences of this and other MepR substitutions using a
lacZ
reporter gene assay revealed markedly reduced repressor activity in the presence of Q18P, F27L, G97E, and A103V substitutions. Reporter data were generally supported by susceptibility and efflux assays, and electrophoretic mobility shift assays (EMSAs) confirmed compromised affinities of MepR F27L and A103V for the
mepR
and
mepA
operators. One mutant protein contained two substitutions (T94P and T132M); T132M compensated for the functional defect incurred by T94P and also rescued that of A103V but not F27L, establishing it as a limited-range suppressor. The function of another derivative with 10 substitutions was minimally affected, and this may be an extreme example of suppression involving interactions among several residues. Structural correlations for the observed functional effects were ascertained by modeling mutations onto apo-MepR. It is likely that F27L and A103V affect the protein-DNA interaction by repositioning of DNA recognition helices. Negative functional consequences of MepR substitution mutations may result from interference with structural plasticity, alteration of helical arrangements, reduced protein-cognate DNA affinity, or possibly association of MepR protomers. Structural determinations will provide further insight into the consequences of these and other mutations that affect MepR function, especially the T132M suppressor.
Spontaneous free floating carotid artery thrombosis
Authors: Graham Ruth , Blaszczynski Marek
Published: June 2013

A 64-year-old man, with no history of trauma, presented with transient visual loss. He was diagnosed with amaurosis fugax and started on dipyridamole and simvastatin. An inconclusive ultrasound (US) Doppler was followed by CT angiogram (CTA) and MRI, which demonstrated free floating intraluminal thrombus in the distal right common carotid artery. ECG showed sinus rhythm and an echocardiogram showed no cardiac thrombus. Following discussion at the vascular multidisciplinary team the decision was made to treat with intravenous heparin followed by warfarin. He has been regularly followed up with CTA/USS, the most recent (Oct 2012) showing no evidence of thrombus. He has had no further symptoms. Despite no initial aetiology being found we suggest that his undiagnosed oesophageal carcinoma (diagnosed 5 months after initial presentation) could have been responsible for a hypercoagulability state giving an increased risk of thrombosis and leading to the thrombus in the common carotid artery.
Organising pneumonia in common variable immunodeficiency
Authors: Boujaoude Ziad , Arya Rohan , Rafferty William , Dammert Pedro
Published: June 2013

Common variable immunodeficiency (CVID) is the most common of the primary immunodeficiency disorders. Pulmonary manifestations are characterised by recurrent rhinosinusitis, respiratory tract infections and bronchiectasis. Less commonly the lung may be affected by lymphoid disorders and sarcoid-like granulomas. Organising pneumonia (OP) is a rare pulmonary manifestation. We report the case of a 32-year-old woman with CVID who presented with fever, dyspnoea and persistent lung infiltrates despite antibiotic therapy. CT of the chest showed bilateral patchy alveolar infiltrates. Pulmonary function tests revealed moderate restriction and reduction in diffusion capacity. Initial bronchoscopy with transbronchial biopsies did not yield a diagnosis but surgical lung biopsies identified OP. Significant clinical, radiographic and physiological improvement was achieved after institution of corticosteroid therapy.
Unusual breast neoplasm: primary breast lymphoma
Authors: Binesh Fariba , Vahedian Hassanali , Akhavan Ali , Hakiminia Marjan
Published: June 2013

Primary breast lymphoma (PBL) is a rare clinical entity. The clinical and imaging findings in breast lymphoma can mimic those of breast carcinoma. As a result, the diagnosis of PBL relies on histological evaluation and confirmed by immunohistochemical staining. The treatment of choice of this rare disease is controversial. This case report highlights the diagnosis and management of a 48-year-old woman residing in Iran with PBL.
Modified Nance palatal arch appliance for anterior tooth replacement
Authors: Sethi Ntasha , Shanthraj Srinivas L , Muraleedharan Manju , Mallikarjuna Rachappa
Published: June 2013

The following case report presents a new and an innovative technique for the postextraction replacement of maxillary central incisors using the natural teeth as pontics. The novel appliance fabricated fully satisfied the demands of the adolescent patient for a fixed prosthetic, while fulfilling the aesthetic and functional requirements presented by the case.
Successful thrombolytic treatment of prosthetic mitral valve thrombosis
Authors: Gazi Emine , Altun Burak , Temiz Ahmet , Colkesen Yucel
Published: June 2013

Prosthetic heart valve thrombosis is a rare but serious complication. Surgery is the first-line therapy in symptomatic obstructive mechanical valve thrombosis, thrombolytic therapy has been used as an alternative to surgical treatment. In this case report we described a 47-year-old woman who had undergone coronary artery bypass graft and mitral valve replacement operation 9 months ago. A thrombus was detected on the prosthetic mitral valve with high transmitral gradient by transoesophageal echocardiography. Tissue plasminogen activator treatment was administered successfully. The gradient was improved on prosthetic mitral valve and embolic complications or bleeding were not occurred.
Pneumomediastinum secondary to mephedrone inhalation
Authors: McCullough Chris , Keane Margaret Geraldine , Hillman Toby , Elkhodair Samer
Published: June 2013

A 23-year-old man presented to the emergency department with severe, central, pleuritic chest pain. The pain was present on waking and exacerbated by movement. On examination, supraclavicular and anterior chest wall surgical emphysema was noted, otherwise examination and initial observations were normal. A chest x-ray and subsequent chest CT demonstrated a pneumomediastium with significant subcutaneous emphysema. There was no history of vomiting or chest trauma, but the patient had inhaled mephedrone, a synthetic stimulant drug, 36 h prior. Pneumomediastinum is an uncommon complication of inhalational drug use.
How can clinical practice guidelines be adapted to facilitate shared decision making? A qualitative key-informant study
Authors: van der Weijden Trudy , Pieterse Arwen H , Koelewijn-van Loon Marije S , Knaapen Loes , Légaré France , Boivin Antoine , Burgers Jako S , Stiggelbout Anne M , Faber Marjan , Elwyn Glyn
Published: June 2013

Background

To explore how clinical practice guidelines can be adapted to facilitate shared decision making.

Methods

This was a qualitative key-informant study with group discussions and semi-structured interviews. First, 75 experts in guideline development or shared decision making participated in group discussions at two international conferences. Next, health professionals known as experts in depression or breast cancer, experts on clinical practice guidelines and/or shared decision making, and patient representatives were interviewed (N=20). Using illustrative treatment decisions on depression or breast cancer, we asked the interviewees to indicate as specifically as they could how guidelines could be used to facilitate shared decision making.

Results

Interviewees suggested some generic strategies, namely to include a separate chapter on the importance of shared decision making, to use language that encourages patient involvement, and to develop patient versions of guidelines. Recommendation-specific strategies, related to specific decision points in the guideline, were also suggested: These include structuring the presentation of healthcare options to increase professionals' option awareness; structuring the deliberation process between professionals and patients; and providing relevant patient support tools embedded at important decision points in the guideline.

Conclusions

This study resulted in an overview of strategies to adapt clinical practice guidelines to facilitate shared decision making. Some strategies seemed more contentious than others. Future research should assess the feasibility and impact of these strategies to make clinical practice guidelines more conducive to facilitate shared decision making.
The changing pattern of amputations
Authors: Brown Kate V , Clasper J C
Published: June 2013

Introduction

Conflict in the Middle East over the past 10 years has seen a change in warfare tactics from the use of ballistic missiles to blast weapons, which has resulted in a well-documented change in wounding patterns. Due to the severity of these injuries, there have been large numbers of amputations, both as life and limb saving procedures. The purpose of this paper is to retrospectively review all UK service personnel who have undergone limb amputation in the last 8 years of conflict and compare those from the early years with the more recent.

Methods

All UK service personnel scoring more than 1 on the extremity score of the Abbreviated Injury Score were identified from the UK Joint Theatre Trauma Registry and separated into two temporal cohorts (August 2003–February 2008 and August 2008–July 2010). Intheatre medical facility and Role 4 hospital notes from the Queen Elizabeth Hospital Birmingham were examined for details of mechanisms of injury, number of limbs injured, associated injuries, method of amputation, microbiology of contaminating organisms and outcome.

Results

There were significant differences in the nature of the amputations, the number of multiple amputations and soft tissue perineal wounds, as well as a significantly higher Injury Severity Score in the later time period. There were also significant differences in the surgical techniques, with more guillotine amputations in the early group, and mechanism of injury, with more blast injuries in the late group.

Conclusions

This study has confirmed the clinical impression that there has been a significant change in the limb trauma from the Iraq conflict to Afghanistan. These injury patterns have significantly different logistic implications and this must be considered when planning the required medical assets in future conflicts.
Occlusion of M1 segment after superficial temporal artery-middle cerebral artery bypass in a giant M1 aneurysm with Onyx-34 injected via a double-lumen balloon under balloon inflation
Authors: Clarençon Frédéric , Nouet Aurelien , Redondo Aimée , Di Maria Federico , Iosif Christina , Le Jean Lise , Chiras Jacques , Sourour Nader
Published: June 2013

A 29-year-old patient attended our institution for recurrent strokes related to a giant partially thrombosed M1 aneurysm. Superficial temporal artery-middle cerebral artery (STA-MCA) bypass and subsequent occlusion of both the aneurysm and the dysplastic M1 segment were planned. However, owing to the shortness of the non-dysplastic segment of M1 and the risk of occlusion of the lenticulostriate arteries, the use of a double-lumen balloon was considered for coiling and subsequent injection of Onyx. STA-MCA bypass was performed using a regular technique. Endovascular occlusion of both the aneurysm and the parent artery was subsequently performed by means of coils and Onyx-34 that was injected via the Ascent balloon under balloon inflation. No complications were recorded and no stroke was observed on control MRI. The injection of Onyx-34 through a double-lumen balloon under balloon inflation is a quick and safe technique for precise occlusion of a parent artery.