bluuebunny/crossref_metadata_2025 huggingface dataset:
Holotoxin Activity of Botulinum Neurotoxin Subtype A4 Originating from a Nontoxigenic Clostridium botulinum Expression System
Authors: Bradshaw Marite , Tepp William H. , Whitemarsh Regina C. M. , Pellett Sabine , Johnson Eric A.
Published: September 2014

Clostridium botulinum
subtype A4 neurotoxin (BoNT/A4) is naturally expressed in the dual-toxin-producing
C. botulinum
strain 657Ba at 100× lower titers than BoNT/B. In this study, we describe purification of recombinant BoNT/A4 (rBoNT/A4) expressed in a nonsporulating and nontoxigenic
C. botulinum
expression host strain. The rBoNT/A4 copurified with nontoxic toxin complex components provided in
trans
by the expression host and was proteolytically cleaved to the active dichain form. Activity of the recombinant BoNT/A4 in mice and in human neuronal cells was about 1,000-fold lower than that of BoNT/A1, and the recombinant BoNT/A4 was effectively neutralized by botulism heptavalent antitoxin. A previous report using recombinant truncated BoNT/A4 light chain (LC) expressed in
Escherichia coli
has indicated reduced stability and activity of BoNT/A4 LC compared to BoNT/A1 LC, which was surmounted by introduction of a single-amino-acid substitution, I264R. In order to determine whether this mutation would also affect the holotoxin activity of BoNT/A4, a recombinant full-length BoNT/A4 carrying this mutation as well as a second mutation predicted to increase solubility (L260F) was produced in the clostridial expression system. Comparative analyses of the
in vitro
, cellular, and
in vivo
activities of rBoNT/A4 and rBoNT/A4-L260F I264R showed 1,000-fold-lower activity than BoNT/A1 in both the mutated and nonmutated BoNT/A4. This indicates that these mutations do not alter the activity of BoNT/A4 holotoxin. In summary, a recombinant BoNT from a dual-toxin-producing strain was expressed and purified in an endogenous clostridial expression system, allowing analysis of this toxin.
Routes of Acquisition of the Gut Microbiota of the Honey Bee Apis mellifera
Authors: Powell J. Elijah , Martinson Vincent G. , Urban-Mead Katherine , Moran Nancy A.
Published: September 2014

Studies of newly emerged
Apis mellifera
worker bees have demonstrated that their guts are colonized by a consistent core microbiota within several days of eclosure. We conducted experiments aimed at illuminating the transmission routes and spatiotemporal colonization dynamics of this microbiota. Experimental groups of newly emerged workers were maintained in cup cages and exposed to different potential transmission sources. Colonization patterns were evaluated using quantitative real-time PCR (qPCR) to assess community sizes and using deep sequencing of 16S rRNA gene amplicons to assess community composition. In addition, we monitored the establishment of the ileum and rectum communities within workers sampled over time from natural hive conditions. The study verified that workers initially lack gut bacteria and gain large characteristic communities in the ileum and rectum within 4 to 6 days within hives. Typical communities, resembling those of workers within hives, were established in the presence of nurse workers or nurse worker fecal material, and atypical communities of noncore or highly skewed compositions were established when workers were exposed only to oral trophallaxis or hive components (comb, honey, bee bread). The core species of Gram-negative bacteria,
Snodgrassella alvi
,
Gilliamella apicola
, and
Frischella perrara
, were dependent on the presence of nurses or hindgut material, whereas some Gram-positive species were more often transferred through exposure to hive components. These results indicate aspects of the colony life cycle and behavior that are key to the propagation of the characteristic honey bee gut microbiota.
Expanding the Halohydrin Dehalogenase Enzyme Family: Identification of Novel Enzymes by Database Mining
Authors: Schallmey Marcus , Koopmeiners Julia , Wells Elizabeth , Wardenga Rainer , Schallmey Anett
Published: September 2014

Halohydrin dehalogenases are very rare enzymes that are naturally involved in the mineralization of halogenated xenobiotics. Due to their catalytic potential and promiscuity, many biocatalytic reactions have been described that have led to several interesting and industrially important applications. Nevertheless, only a few of these enzymes have been made available through recombinant techniques; hence, it is of general interest to expand the repertoire of these enzymes so as to enable novel biocatalytic applications. After the identification of specific sequence motifs, 37 novel enzyme sequences were readily identified in public sequence databases. All enzymes that could be heterologously expressed also catalyzed typical halohydrin dehalogenase reactions. Phylogenetic inference for enzymes of the halohydrin dehalogenase enzyme family confirmed that all enzymes form a distinct monophyletic clade within the short-chain dehydrogenase/reductase superfamily. In addition, the majority of novel enzymes are substantially different from previously known phylogenetic subtypes. Consequently, four additional phylogenetic subtypes were defined, greatly expanding the halohydrin dehalogenase enzyme family. We show that the enormous wealth of environmental and genome sequences present in public databases can be tapped for
in silico
identification of very rare but biotechnologically important biocatalysts. Our findings help to readily identify halohydrin dehalogenases in ever-growing sequence databases and, as a consequence, make even more members of this interesting enzyme family available to the scientific and industrial community.
Prebiotic Oligosaccharides: Comparative Evaluation Using
In Vitro
Cultures of Infants' Fecal Microbiomes
Authors: Stiverson J. , Williams T. , Chen J. , Adams S. , Hustead D. , Price P. , Guerrieri J. , Deacon J. , Yu Z.
Published: September 2014

The objective of this study was to systematically assess the bifidogenic effect of three commonly used prebiotic products using
in vitro
cultures of infant fecal samples. Fresh stool samples collected from six term infants, each exclusively fed human milk (
n
= 3) or infant formula (
n
= 3), at 28 days of age were used as inocula. The following prebiotic products were added at concentrations applicable to infant formula: Vivinal GOS 15 (containing 28.5% galacto-oligosaccharide [GOS]) at 7.2 g/liter, Beneo HP (99.5% long-chain inulin [IN]) at 0.8 g/liter, Beneo Synergy 1 (enriched oligofructose and inulin [OF-IN]) at 4 g/liter, and a combination of Vivinal GOS 15 (7.2 g/liter) and Beneo HP (0.8 g/liter) (GOS-IN). The growth of total bacteria,
Bifidobacterium
,
Bacteroides
,
Bifidobacterium longum
, and
Escherichia coli
was quantified using specific quantitative PCR (qPCR).
Bifidobacterium
was also enumerated on selective Beerens agar plates, with representative colonies identified by sequencing of their 16S rRNA genes. Volatile fatty acids (VFA) and pH in the cultures were also determined. Irrespective of the feeding methods, the GOS product, either alone or in combination with Beneo HP, resulted in substantially higher growth of total bifidobacteria, and much of this growth was attributed to growth of
B. longum
. Beneo Synergy 1 also increased the abundance of total bifidobacteria and
B. longum
. Corresponding to the increases in these two bacterial groups, acetic acid concentrations were higher, while there was a trend of lower
E. coli
levels and pH. The lower pH and higher acetic acid concentration might be directly responsible for the lower
E. coli
population. At the concentrations studied, the GOS product was more bifidogenic and potent in inhibiting
E. coli
than the other products tested. These results suggest that supplementation of infant formula with GOS may increase intestinal bifidobacteria and benefit infant health.
Microbial Synthesis of the Forskolin Precursor Manoyl Oxide in an Enantiomerically Pure Form
Authors: Nielsen Morten T. , Ranberg Johan Andersen , Christensen Ulla , Christensen Hanne Bjerre , Harrison Scott J. , Olsen Carl Erik , Hamberger Björn , Møller Birger Lindberg , Nørholm Morten H. H.
Published: September 2014

Forskolin is a promising medicinal compound belonging to a plethora of specialized plant metabolites that constitute a rich source of bioactive high-value compounds. A major obstacle for exploitation of plant metabolites is that they often are produced in small amounts and in plants difficult to cultivate. This may result in insufficient and unreliable supply leading to fluctuating and high sales prices. Hence, substantial efforts and resources have been invested in developing sustainable and reliable supply routes based on microbial cell factories. Here, we report microbial synthesis of (13
R
)-manoyl oxide, a proposed intermediate in the biosynthesis of forskolin and other medically important labdane-type terpenoids. Process optimization enabled synthesis of enantiomerically pure (13
R
)-manoyl oxide as the sole metabolite, providing a pure compound in just two steps with a yield of 10 mg/liter. The work presented here demonstrates the value of a standardized bioengineering pipeline and the large potential of microbial cell factories as sources for sustainable synthesis of complex biochemicals.
Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma
Authors: Gong Hongli , Shi Yi , Zhou Xia , Wu Chunping , Cao Pengyu , Xu Chen , Hou Dongsheng , Wang Yuezhu , Zhou Liang
Published: September 2014

The compositions and abundances of the microbiota in the ecological niche of the human throat and the possible relationship between the microbiota and laryngeal cancer are poorly understood. To obtain insight into this, we enrolled 27 laryngeal carcinoma patients and 28 subjects with vocal cord polyps as controls. For each subject, we simultaneously collected swab samples from the upper throat near the epiglottis (site I) and tissue samples from the vestibulum laryngis to the subglottic region (site II). The microbiota of the throat were fully characterized by pyrosequencing of barcoded 16S rRNA genes. We found 14 phyla, 20 classes, 38 orders, 85 families, and 218 genera in the throats of enrolled subjects. The main phyla were
Firmicutes
(54.7%),
Fusobacteria
(14.8%),
Bacteroidetes
(12.7%), and
Proteobacteria
(10.6%).
Streptococcus
(37.3%),
Fusobacterium
(11.3%), and
Prevotella
(10.6%) were identified as the three most predominant genera in the throat. The relative abundances of 23 bacterial genera in site I were significantly different from those in site II (
P
< 0.05). The relative proportions of 12 genera largely varied between laryngeal cancer patients and control subjects (
P
< 0.05). Collectively, this study outlined the spatial structure of microbial communities in the human throat. The spatial structure of bacterial communities significantly varied in two anatomical sites of the throat. The bacterial profiles of the throat of laryngeal cancer patients were strongly different from those of control subjects, and several of these microorganisms may be related to laryngeal carcinoma.
Conversion of the Pseudomonas aeruginosa Quinolone Signal and Related Alkylhydroxyquinolines by Rhodococcus sp. Strain BG43
Authors: Müller Christine , Birmes Franziska S. , Niewerth Heiko , Fetzner Susanne
Published: September 2014

A bacterial strain, which based on the sequences of its 16S rRNA,
gyrB
,
catA
, and
qsdA
genes, was identified as a
Rhodococcus
sp. closely related to
Rhodococcus erythropolis
, was isolated from soil by enrichment on the
Pseudomonas
quinolone signal [PQS; 2-heptyl-3-hydroxy-4(1
H
)-quinolone], a quorum sensing signal employed by the opportunistic pathogen
Pseudomonas aeruginosa
. The isolate, termed
Rhodococcus
sp. strain BG43, cometabolically degraded PQS and its biosynthetic precursor 2-heptyl-4(1
H
)-quinolone (HHQ) to anthranilic acid. HHQ degradation was accompanied by transient formation of PQS, and HHQ hydroxylation by cell extracts required NADH, indicating that strain BG43 has a HHQ monooxygenase isofunctional to the biosynthetic enzyme PqsH of
P. aeruginosa
. The enzymes catalyzing HHQ hydroxylation and PQS degradation were inducible by PQS, suggesting a specific pathway. Remarkably,
Rhodococcus
sp. BG43 is also capable of transforming 2-heptyl-4-hydroxyquinoline-
N
-oxide to PQS. It thus converts an antibacterial secondary metabolite of
P. aeruginosa
to a quorum sensing signal molecule.
Fine-Tuning of the Fatty Acid Pathway by Synthetic Antisense RNA for Enhanced (2
S
)-Naringenin Production from
l
-Tyrosine in Escherichia coli
Authors: Wu Junjun , Yu Oliver , Du Guocheng , Zhou Jingwen , Chen Jian
Published: September 2014

Malonyl coenzyme A (malonyl-CoA) is an important precursor for the synthesis of natural products, such as polyketides and flavonoids. The majority of this cofactor often is consumed for producing fatty acids and phospholipids, leaving only a small amount of cellular malonyl-CoA available for producing the target compound. The tuning of malonyl-CoA into heterologous pathways yields significant phenotypic effects, such as growth retardation and even cell death. In this study, fine-tuning of the fatty acid pathway in
Escherichia coli
with antisense RNA (asRNA) to balance the demands on malonyl-CoA for target-product synthesis and cell health was proposed. To establish an efficient asRNA system, the relationship between sequence and function for asRNA was explored. It was demonstrated that the gene-silencing effect of asRNA could be tuned by directing asRNA to different positions in the 5′-UTR (untranslated region) of the target gene. Based on this principle, the activity of asRNA was quantitatively tailored to balance the need for malonyl-CoA in cell growth and the production of the main flavonoid precursor, (2
S
)-naringenin. Appropriate inhibitory efficiency of the anti-
fabB
/
fabF
asRNA improved the production titer by 431% (391 mg/liter). Therefore, the strategy presented in this study provided a useful tool for the fine-tuning of endogenous gene expression in bacteria.
Novel Broad-Spectrum Antimicrobial Photoinactivation of
In Situ
Oral Biofilms by Visible Light plus Water-Filtered Infrared A
Authors: Karygianni L. , Ruf S. , Follo M. , Hellwig E. , Bucher M. , Anderson A. C. , Vach K. , Al-Ahmad A.
Published: September 2014

Antimicrobial photodynamic therapy (APDT) has gained increased attention as an alternative treatment approach in various medical fields. However, the effect of APDT using visible light plus water-filtered infrared A (VIS + wIRA) on oral biofilms remains unexplored. For this purpose, initial and mature oral biofilms were obtained
in situ
; six healthy subjects wore individual upper jaw acrylic devices with bovine enamel slabs attached to their proximal sites for 2 h or 3 days. The biofilms were incubated with 100 μg ml
−1
toluidine blue O (TB) or chlorin e6 (Ce6) and irradiated with VIS + wIRA with an energy density of 200 mW cm
−2
for 5 min. After cultivation, the CFU of half of the treated biofilm samples were quantified, whereas following live/dead staining, the other half of the samples were monitored by confocal laser scanning microscopy (CLSM). TB- and Ce6-mediated APDT yielded a significant decrease of up to 3.8 and 5.7 log
10
CFU for initial and mature oral biofilms, respectively. Quantification of the stained photoinactivated microorganisms confirmed these results. Overall, CLSM revealed the diffusion of the tested photosensitizers into the deepest biofilm layers after exposure to APDT. In particular, Ce6-aided APDT presented elevated permeability and higher effectiveness in eradicating 89.62% of biofilm bacteria compared to TB-aided APDT (82.25%) after 3 days. In conclusion, antimicrobial photoinactivation using VIS + wIRA proved highly potent in eradicating oral biofilms. Since APDT excludes the development of microbial resistance, it could supplement the pharmaceutical treatment of periodontitis or peri-implantitis.
Trimethylamine and Organic Matter Additions Reverse Substrate Limitation Effects on the δ
13
C Values of Methane Produced in Hypersaline Microbial Mats
Authors: Kelley Cheryl A. , Nicholson Brooke E. , Beaudoin Claire S. , Detweiler Angela M. , Bebout Brad M.
Published: September 2014

Methane production has been observed in a number of hypersaline environments, and it is generally thought that this methane is produced through the use of noncompetitive substrates, such as the methylamines, dimethylsulfide and methanol. Stable isotope measurements of the produced methane have also suggested that the methanogens are operating under conditions of substrate limitation. Here, substrate limitation in gypsum-hosted endoevaporite and soft-mat hypersaline environments was investigated by the addition of trimethylamine, a noncompetitive substrate for methanogenesis, and dried microbial mat, a source of natural organic matter. The δ
13
C values of the methane produced after amendments were compared to those in unamended control vials. At all hypersaline sites investigated, the δ
13
C values of the methane produced in the amended vials were statistically lower (by 10 to 71‰) than the unamended controls, supporting the hypothesis of substrate limitation at these sites. When substrates were added to the incubation vials, the methanogens within the vials fractionated carbon isotopes to a greater degree, resulting in the production of more
13
C-depleted methane. Trimethylamine-amended samples produced lower methane δ
13
C values than the mat-amended samples. This difference in the δ
13
C values between the two types of amendments could be due to differences in isotope fractionation associated with the dominant methane production pathway (or substrate used) within the vials, with trimethylamine being the main substrate used in the trimethylamine-amended vials. It is hypothesized that increased natural organic matter in the mat-amended vials would increase fermentation rates, leading to higher H
2
concentrations and increased CO
2
/H
2
methanogenesis.
Activities of Alkyl Hydroperoxide Reductase Subunits C1 and C2 of Vibrio parahaemolyticus against Different Peroxides
Authors: Chung Chun-Hui , Ma Tsung-yong , Fen Shin-yuan , Wong Hin-chung
Published: September 2014

Alkyl hydroperoxide reductase subunit C gene (
ahpC
) functions were characterized in
Vibrio parahaemolyticus
, a commonly occurring marine food-borne enteropathogenic bacterium. Two
ahpC
genes,
ahpC1
(VPA1683) and
ahpC2
(VP0580), encoded putative two-cysteine peroxiredoxins, which are highly similar to the homologous proteins of
Vibrio vulnificus
. The responses of deletion mutants of
ahpC
genes to various peroxides were compared with and without gene complementation and at different incubation temperatures. The growth of the
ahpC1
mutant and
ahpC1 ahpC2
double mutant in liquid medium was significantly inhibited by organic peroxides, cumene hydroperoxide and
tert
-butyl hydroperoxide. However, inhibition was higher at 12°C and 22°C than at 37°C. Inhibiting effects were prevented by the complementary
ahpC1
gene. Inconsistent detoxification of H
2
O
2
by
ahpC
genes was demonstrated in an agar medium but not in a liquid medium. Complementation with an
ahpC2
gene partially restored the peroxidase effect in the double
ahpC1 ahpC2
mutant at 22°C. This investigation reveals that
ahpC1
is the chief peroxidase gene that acts against organic peroxides in
V. parahaemolyticus
and that the function of the
ahpC
genes is influenced by incubation temperature.
A High-Throughput Fatty Acid Profiling Screen Reveals Novel Variations in Fatty Acid Biosynthesis in Chlamydomonas reinhardtii and Related Algae
Authors: Pflaster Erin L. , Schwabe Michael J. , Becker Joyanne , Wilkinson Melissa S. , Parmer Ashley , Clemente Thomas E. , Cahoon Edgar B. , Riekhof Wayne R.
Published: September 2014

Analysis of fatty acid methyl esters (FAMEs) by gas chromatography (GC) is a common technique for the quantitative and qualitative analysis of acyl lipids. Methods for FAME preparation are typically time-consuming and labor-intensive and require multiple transfers of reagents and products between reaction tubes and autosampler vials. In order to increase throughput and lower the time and materials costs required for FAME preparation prior to GC analysis, we have developed a method in which 10-to-20-mg samples of microbial biomass are transferred to standard GC autosampler vials, transesterified using an emulsion of methanolic trimethylsulfonium hydroxide and hexane, and analyzed directly by GC without further sample handling. This method gives results that are essentially identical to those obtained by the more labor- and material-intensive FAME preparation methods, such as transmethylation with methanolic HCl. We applied this method to the screening of laboratory and environmental isolates of the green alga
Chlamydomonas
for variations in fatty acid composition. This screening method facilitated two novel discoveries. First, we identified a common laboratory strain of
C. reinhardtii
, CC-620, completely lacking all ω-3 fatty acids normally found in this organism and showed that this strain contains an inactivating mutation in the CrFAD7 gene, encoding the sole ω-3 desaturase activity in this organism. Second, we showed that some species of
Chlamydomonas
make Δ6-unsaturated polyunsaturated fatty acids (PUFA) rather than the Δ5 species normally made by the previously characterized laboratory strains of
Chlamydomonas
, suggesting that there is species-specific variation in the regiospecificity and substrate selectivity of front-end desaturases in this algal genus.
Genomic Insights into Processes Driving the Infection of Alexandrium tamarense by the Parasitoid Amoebophrya sp
Authors: Lu Yameng , Wohlrab Sylke , Glöckner Gernot , Guillou Laure , John Uwe
Published: September 2014

The regulatory circuits during infection of dinoflagellates by their parasites are largely unknown on the molecular level. Here we provide molecular insights into these infection dynamics.Alexandrium tamarenseis one of the most prominent harmful algal bloom dinoflagellates. Its pathogen, the dinoflagellate parasitoidAmoebophryasp., has been observed to infect and control the blooms of this species. We generated a data set of transcripts from three time points (0, 6, and 96 h) during the infection of this parasite-host system. Assembly of all transcript data from the parasitoid (>900,000 reads/313 Mbp with 454/Roche next-generation sequencing [NGS]) yielded 14,455 contigs, to which we mapped the raw transcript reads of each time point of the infection cycle. We show that particular surface lectins are expressed at the beginning of the infection cycle which likely mediate the attachment to the host cell. In a later phase, signal transduction-related genes together with transmembrane transport and cytoskeleton proteins point to a high integration of processes involved in host recognition, adhesion, and invasion. At the final maturation stage, cell division- and proliferation-related genes were highly expressed, reflecting the fast cell growth and nuclear division of the parasitoid. Our molecular insights into dinoflagellate parasitoid interactions point to general mechanisms also known from other eukaryotic parasites, especially from the Alveolata. These similarities indicate the presence of fundamental processes of parasitoid infection that have remained stable throughout evolution within different phyla.
Successful Transient Expression of Cas9 and Single Guide RNA Genes in Chlamydomonas reinhardtii
Authors: Jiang Wenzhi , Brueggeman Andrew J. , Horken Kempton M. , Plucinak Thomas M. , Weeks Donald P.
Published: September 2014

The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system has become a powerful and precise tool for targeted gene modification (e.g., gene knockout and gene replacement) in numerous eukaryotic organisms. Initial attempts to apply this technology to a model, the single-cell alga,
Chlamydomonas reinhardtii
, failed to yield cells containing edited genes. To determine if the Cas9 and single guide RNA (sgRNA) genes were functional in
C. reinhardtii
, we tested the ability of a codon-optimized Cas9 gene along with one of four different sgRNAs to cause targeted gene disruption during a 24-h period immediately following transformation. All three exogenously supplied gene targets as well as the endogenous
FKB12
(rapamycin sensitivity) gene of
C. reinhardtii
displayed distinct Cas9/sgRNA-mediated target site modifications as determined by DNA sequencing of cloned PCR amplicons of the target site region. Success in transient expression of Cas9 and sgRNA genes contrasted with the recovery of only a single rapamycin-resistant colony bearing an appropriately modified
FKB12
target site in 16 independent transformation experiments involving >10
9
cells. Failure to recover transformants with intact or expressed Cas9 genes following transformation with the Cas9 gene alone (or even with a gene encoding a Cas9 lacking nuclease activity) provided strong suggestive evidence for Cas9 toxicity when Cas9 is produced constitutively in
C. reinhardtii
. The present results provide compelling evidence that Cas9 and sgRNA genes function properly in
C. reinhardtii
to cause targeted gene modifications and point to the need for a focus on development of methods to properly stem Cas9 production and/or activity following gene editing.
Complete Genome Sequence of Klebsiella pneumoniae Strain ATCC 43816 KPPR1, a Rifampin-Resistant Mutant Commonly Used in Animal, Genetic, and Molecular Biology Studies
Authors: Broberg Christopher A. , Wu Weisheng , Cavalcoli James D. , Miller Virginia L. , Bachman Michael A.
Published: September 2014

Klebsiella pneumoniae
is an urgent public health threat due to the spread of carbapenem-resistant strains causing serious, and frequently fatal, infections. To facilitate genetic, molecular, and immunological studies of this pathogen, we report the complete chromosomal sequence of a genetically tractable, prototypical strain used in animal models.
Complete Genome Sequence of
Chryseobacterium
sp. Strain StRB126, an
N
-Acylhomoserine Lactone-Degrading Bacterium Isolated from Potato Root
Authors: Morohoshi Tomohiro , Wang Wen-Zhao , Someya Nobutaka , Ikeda Tsukasa
Published: September 2014

Chryseobacterium
sp. strain StRB126 was isolated from a potato root and showed
N
-acylhomoserine lactone-degrading activity. Here, we present the complete 5,503,743-bp genome sequence of StRB126, which has a G+C content of 35.6% and carries 4,828 protein-coding genes, six rRNA operons, and 80 tRNA genes.
Draft Genome Assembly of Ralstonia pickettii Type Strain K-288 (ATCC 27853)
Authors: Daligault H. E. , Davenport K. W. , Minogue T. D. , Broomall S. M. , Bruce D. C. , Chain P. S. , Coyne S. R. , Gibbons H. S. , Jaissle J. , Lo C.-C. , Meincke L. , Munk A. C. , Rosenzweig C. N. , Johnson S. L.
Published: September 2014

We present the genome assembly of
Ralstonia pickettii
K-288 (ATCC 27511), consisting of 27 contigs placed into a single scaffold. This 4.76-Mbp genome has 64.0% G+C content and 4,425 coding sequences. Because this is the type strain, inclusion of its data set among other
Ralstonia
genomes should provide a historical genomic perspective.
Complete Genome Sequence of Stenotrophomonas maltophilia Type Strain 810-2 (ATCC 13637)
Authors: Davenport K. W. , Daligault H. E. , Minogue T. D. , Broomall S. M. , Bruce D. C. , Chain P. S. , Coyne S. R. , Gibbons H. S. , Jaissle J. , Li P.-E. , Rosenzweig C. N. , Scholz M. B. , Johnson S. L.
Published: September 2014

An emerging nosocomial pathogen,
Stenotrophomonas maltophila
has a high mortality rate in those it infects. Here, we present the complete genome sequence of
Stenotrophomonas maltophilia
810-2 (ATCC 13637), the type strain of the species. The 5-Mb (66.1% G+C content) genome has been deposited in NCBI under accession number CP008838.
HIV status and sexual behaviour among gay men in Ottawa: considerations for public health
Authors: O'Byrne Patrick , Phillips J Craig , Kitson Cynthia , Bryan Alyssa
Published: September 2014

Objectives

HIV prevention efforts, particularly among men who have sex with men (MSM), have not achieved maximum effectiveness. A survey of MSM in Ottawa, Canada was completed to ascertain whether there were differences in how the perceived HIV status of participants and their partners influenced sexual practices.

Methods

Self-directed surveys were administered to a convenience sample of 721 MSM in Ottawa, Canada from November 2011 through May 2012. Data collection occurred at 14 sites. The survey identified whether participants identified as HIV positive, negative or unsure of their HIV status.

Results

The findings indicated variation between HIV-negative MSM and those who are unsure of their HIV status. Men who were unsure of their HIV status were less likely to report that they asked sexual partners or have had their partners ask about HIV status.

Conclusions

The results of this study indicate that some MSM may base decisions about HIV prevention on discussion about HIV status with their partners, rather than condom use. These practices may increase, rather than decrease, HIV transmission. Survey findings and extant literature demonstrate a need to inform MSM about the limitations of serosorting as a prevention strategy, and to provide facilitated access to sexually transmitted infection testing and treatment to further reduce onward HIV transmission.
State-specific, racial and ethnic heterogeneity in trends of firearm-related fatality rates in the USA from 2000 to 2010
Authors: Kalesan Bindu , Vasan Sowmya , Mobily Matthew E , Villarreal Marcos D , Hlavacek Patrick , Teperman Sheldon , Fagan Jeffrey A , Galea Sandro
Published: September 2014

Objectives

To document overall, racial, ethnic and intent-specific spatiotemporal trends of firearm-related fatality rates (FRF rates) in the USA.

Design

Cross-sectional study per year from 2000 to 2010.

Setting

USA.

Participants

Aggregate count of all people in the USA from 2000 to 2010.

Outcome measures

Data from the Web-based Injury Statistics Query and Reporting System from 2000 to 2010 was used to determine annual FRF rates per 100 000 and by states, race, ethnicity and intent.

Results

The average national 11-year FRF rate was 10.21/100 000, from 3.02 in Hawaii to 18.62 in Louisiana: 60% of states had higher than national rates and 41 states showed no temporal change. The average national FRF rates among African-Americans and Caucasians were 18.51 and 9.05/100 000 and among Hispanics and non-Hispanics were 7.13 and 10.13/100 000; Hispanics had a decreasing change of −0.18, p trend<0.0001. In states with increasing trends (Florida and Massachusetts), Caucasians and non-Hispanics drove the rise; while in states with decreasing trends (California, North Carolina, Arizona, Nevada, New York, Illinois, Maryland), Hispanics and African-Americans drove the fall. The average national FRF rates due to homicides (4.1/100 000) and suicides (5.8/100 000) remained constant, but varied between states.

Conclusions

Endemic national FRF rates mask a wide variation in time trends between states. FRF rates were twice as high in African-Americans than Caucasians but decreased among Hispanics. Efforts to identify state-specific best practices can contribute to changes in national FRF rates that remain high.
Are schoolteachers able to teach first aid to children younger than 6 years? A comparative study
Authors: Ammirati Christine , Gagnayre Rémi , Amsallem Carole , Némitz Bernard , Gignon Maxime
Published: September 2014

Objectives

This study was designed to assess the knowledge acquired by very young children (<6 years) trained by their own teachers at nursery school. This comparative study assessed the effect of training before the age of 6 years compared with a group of age-matched untrained children.

Setting

Some schoolteachers were trained by emergency medical teams to perform basic first aid.

Participants

Eighteen classes comprising 315 pupils were randomly selected: nine classes of trained pupils (cohort C1) and nine classes of untrained pupils (cohort C2).

Primary and secondary outcome measures

The test involved observing and describing three pictures and using the phone to call the medical emergency centre. Assessment of each child was based on nine criteria, and was performed by the teacher 2 months after completion of first aid training.

Results

This study concerned 285 pupils: 140 trained and 145 untrained. The majority of trained pupils gave the expected answers for all criteria and reacted appropriately by assessing the situation and alerting emergency services (55.7−89.3% according to the questions). Comparison of the two groups revealed a significantly greater ability of trained pupils to describe an emergency situation (p<0.005) and raise the alert (p<0.0001).

Conclusions

This study shows the ability of very young children to assimilate basic skills as taught by their own schoolteachers.
A longitudinal study to identify the influence of quality of chronic care delivery on productive interactions between patients and (teams of) healthcare professionals within disease management programmes
Authors: Cramm Jane Murray , Nieboer Anna Petra
Published: September 2014

Objective

The chronic care model is an increasingly used approach to improve the quality of care through system changes in care delivery. While theoretically these system changes are expected to increase productive patient–professional interaction empirical evidence is lacking. This study aims to identify the influence of quality of care on productive patient–professional interaction.

Setting

Longitudinal study in 18 Dutch regions.

Participants

Questionnaires were sent to all 5076 patients participating in 18 Disease Management Programmes (DMPs) in 2010 (2676 (53%) respondents). One year later (T1), 4693 patients still participating in the DMPs received a questionnaire (2191 (47%) respondents) and 2 years later (in 2012; T2) 1722 patients responded (out of 4350; 40% response).

Interventions

DMPs

Primary outcome measure

Patients’ perceptions of the productivity of interactions (measured as relational coordination/coproduction of care) with professionals. Patients were asked about communication dimensions (frequent, accurate, and problem-solving communication) and relationship dimensions (shared goals and mutual respect).

Findings

After controlling for background characteristics these results clearly show that quality of chronic care (T0), first-year changes in quality of chronic care (T1—T0) and second-year changes in quality of chronic care (T2—T1) predicted productive interactions between patients and professionals at T2 (all at p≤0.001). Furthermore, we found a negative relationship between lower educational level and productive interactions between patients and professionals 2 years later.

Conclusions

We can conclude that successfully dealing with the consequences of chronic illnesses requires proactive patients who are able to make productive decisions together with their healthcare providers. Since patients and professionals share responsibility for management of the chronic illness, they must also share control of interactions and decisions. The importance of patient-centeredness is growing and this study reports a first example of how quality of chronic care stimulates productive interactions between patients and professionals.
A systematic review of qualitative research on the contributory factors leading to medicine-related problems from the perspectives of adult patients with cardiovascular diseases and diabetes mellitus
Authors: Al Hamid A , Ghaleb M , Aljadhey H , Aslanpour Z
Published: September 2014

Objectives

To synthesise contributing factors leading to medicine-related problems (MRPs) in adult patients with cardiovascular diseases and/or diabetes mellitus from their perspectives.

Design

A systematic literature review of qualitative studies regarding the contributory factors leading to MRPs, medication errors and non-adherence, followed by a thematic synthesis of the studies.

Data sources

We screened Pubmed, EMBASE, ISI Web of Knowledge, PsycInfo, International Pharmaceutical Abstract and PsycExtra for qualitative studies (interviews, focus groups and questionnaires of a qualitative nature).

Review methods

Thematic synthesis was achieved by coding and developing themes from the findings of qualitative studies.

Results

The synthesis yielded 21 studies that satisfied the inclusion and exclusion criteria. Three themes emerged that involved contributing factors to MRPs: patient-related factors including socioeconomic factors (beliefs, feeling victimised, history of the condition, lack of finance, lack of motivation and low self-esteem) and lifestyle factors (diet, lack of exercise/time to see the doctor, obesity, smoking and stress), medicine-related factors (belief in natural remedies, fear of medicine, lack of belief in medicines, lack of knowledge, non-adherence and polypharmacy) and condition-related factors (lack of knowledge/understanding, fear of condition and its complications, and lack of control).

Conclusions

MRPs represent a major health threat, especially among adult patients with cardiovascular diseases and/or diabetes mellitus. The patients’ perspectives uncovered hidden factors that could cause and/or contribute to MRPs in these groups of patients.
Management of behavioural change in patients presenting with a diagnosis of dementia: a video vignette study with Australian general practitioners
Authors: Jiwa Moyez , Nichols Pam , Magin Parker , Pagey Georgina , Meng Xingqiong , Parsons Richard , Pillai Vinita
Published: September 2014

Objective

To test the impact of feedback on the proposed management of standardised patients presenting with behavioural change with a diagnosis of dementia in Australian primary care.

Materials and methods

A video vignette study was performed with Australian general practitioners (GPs) in 2013. Participants viewed six pairs of matched videos depicting people presenting changed behaviour in the context of a dementia diagnosis in two phases. In both phases GPs indicated their diagnosis and management. After phase 1, GPs were offered feedback on management strategies for the patients depicted. Analyses focused on identification of change in management between the two phases of the study. Factors impacting on the intention to coordinate care for such patients were tested in a questionnaire based on the Theory of Planned Behaviour.

Results

Forty-five GPs completed the study. There was significant improvement in the proposed management of three of the six scenarios after the intervention. Older GPs were more likely to refer appropriately (OR=1.11 (1.01 to 1.23), p=0.04.). Overall referral to support agencies was more likely after the intervention (OR=2.52 (1.53 to 4.14), p<0.001). Older GPs were less likely to intend to coordinate care for such patients (OR=0.89 (0.81 to 0.98) p=0.02). Participants who felt confident about their ability to coordinate care were more likely to do so (OR=3.79 (1.08 to 13.32) p=0.04).

Conclusions

The intervention described in this study promoted multidisciplinary management of patients with behavioural problems with a diagnosis of dementia. Increasing practitioner confidence in their ability to coordinate care may increase the proportion of GPs who will respond to patients and carers in this context. Older GPs may benefit in particular.
Improving cardiac assessment and monitoring in methadone prescribing at an addiction service
Authors: Ramage Mark , Fadaka Kate
Published: September 2014

The assessment and monitoring of cardiac risk in patients prescribed methadone is important for patient safety. Although uncommon, QTc interval prolongation is potentially life-threatening. Known risk factors for QTc prolongation include methadone, particularly at doses above 100 milligrams daily. This project aimed to improve the cardiac assessment and monitoring at Barnet Drug and Alcohol Service through raising the awareness of this clinically importance issue as well as through amending the medical assessment guidance to promote the comprehensive assessment of QTc prolongation risk factors and ensure the identification of cardiac risk in patients prescribed methadone.

The project also provided guidance on QTc prolongation management and monitoring (including performance of an electrocardiogram) at the service to provide a baseline measurement and arrangement of annual monitoring. Prior to the intervention, a randomised sample of 26 patients that had been prescribed methadone revealed no comprehensive cardiac risk assessments. Analysing 52 medical assessments in the month following the intervention suggested an improvement in assessment and management of QTc interval prolongation risk, with seven comprehensive cardiac risks assessments performed and one patient having QTc interval prolongation identified following an electrocardiogram and appropriately managed. This project was limited by small sample sizes and the relatively low incidence of QTc prolongation. The poor rate of attendance for requested electrocardiograms in this population was noted as a challenge that needed further consideration.
Top 10 ideas to improve your bedside teaching in a busy emergency department
Authors: Green Gary M , Chen Esther H
Published: September 2014

Physicians are called upon to teach students, residents, patients and their families in the clinical environment every day as part of clinical care. A fast-paced emergency department offers a unique set of challenges that require the physician to be an effective communicator. We present a top 10 list of ideas selected from the literature for the busy clinician to use on that next shift to improve bedside teaching.
Transport cyclists and road rules: what influences the decisions they make?
Authors: Shaw Louise , Poulos Roslyn G , Hatfield Julie , Rissel Chris
Published: September 2014

Objective

To determine the level of adherence by transport cyclists to road rules in traffic situations and their reasons for non-adherence.

Design

The Safer Cycling Study was a prospective cohort study of transport and recreational cyclists. Over 2000 cyclists were recruited between March and November 2011.

Subjects and Setting

770 Transport cyclists aged 18 years and older, who lived in New South Wales, Australia. Participants completed a baseline questionnaire plus provided data during a further six survey weeks over 12 months. In one of their survey weeks, cyclists were asked how often they infringed road rules and what contributory factors led to their road rule infringement. Data were collected via web-based online questionnaires.

Methods

Quantitative data were analysed descriptively. Qualitative data were analysed to identify themes derived from the text.

Results

Riding on the footpath and red light infringement were the most commonly reported road rule breaches. Poor infrastructure design was the most frequently identified contributing factor to road rule breaches, followed by the speed of motorised traffic and the behaviour of other road users.

Conclusions

A transport network needs to facilitate cyclists of all capabilities to reach their required destination in a safe and timely manner, and encourage compliance with the road rules.
Use of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME)
Authors: Shimosako Nana , Kerr Jonathan R
Published: September 2014

Aims

We have reported gene expression changes in patients with chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) and the fact that such gene expression data can be used to identify subtypes of CFS/ME with distinct clinical phenotypes. Due to the difficulties in using a comparative gene expression method as an aid to CFS/ME disease and subtype-specific diagnosis, we have attempted to develop such a method based on single-nucleotide polymorphism (SNP) analysis.

Methods

To identify SNP allele associations with CFS/ME and CFS/ME subtypes, we tested genomic DNA of patients with CFS/ME (n=108), patients with endogenous depression (n=17) and normal blood donors (n=68) for 504 human SNP alleles located within 88 CFS-associated human genes using the SNP Genotyping GoldenGate Assay (Illumina, San Diego, California, USA). 360 ancestry informative markers (AIM) were also examined.

Results

21 SNPs were significantly associated with CFS/ME compared with depression and normal groups. 148 SNP alleles had a significant association with one or more CFS/ME subtypes. For each subtype, associated SNPs tended to be grouped together within particular genes. AIM SNPs indicated that 4 subjects were of Asian origin while the remainder were Caucasian. Hierarchical clustering of AIM data revealed the relatedness between 2 couples of patients with CFS only and confirmed the overall heterogeneity of all subjects.

Conclusions

This study provides evidence that human SNPs located within CFS/ME associated genes are associated with particular genomic subtypes of CFS/ME. Further work is required to develop this into a clinically useful subtype-specific diagnostic test.
Impact of the Great East Japan earthquake on out-of-hospital cardiac arrest with cardiac origin in non-disaster reas
Authors: Kiyohara Kosuke , Kitamura Tetsuhisa , Iwami Taku , Nishiyama Chika , Kawamura Takashi
Published: September 2014

Background

To examine changes in the incidence of out-of-hospital cardiac arrest (OHCA) with cardiac origin in the non-disaster areas of Japan before and after the Great East Japan Earthquake of 11 March 2011.

Methods

The 35 prefectures in Japan with no dead or missing caused directly by the earthquake were defined as the non-disaster areas. Data of adult OHCA patients in the non-disaster areas from March 4 to 24 each year from 2005 to 2011 were obtained from the All-Japan Utstein Registry. Risk ratios (RRs) of OHCA incidence and 95% CIs were estimated for three specific weeks in 2011 (1 week before and 2 weeks after the earthquake) by applying multivariable Poisson regression model. Incidence in the corresponding periods of March 4–24 from 2005 to 2010 was set as the baseline risk.

Results

In the analyses from a total of 17 353 OHCA patients, the incidence statistically significantly increased in the first week after the earthquake in all adults (adjusted-RR=1.13, 95% CI=1.05 to 1.22, p=0.001) and in elderly women (adjusted-RR=1.23, 95% CI=1.11 to 1.37, p<0.001).

Conclusions

The Great East Japan Earthquake caused the increase of OHCA among elderly women even in the non-disaster areas.
A Constrained, Possibilistic Logical Approach for Software System Survivability Evaluation
Authors: Zuo Yanjun
Published: September 2014

In this paper, we present a logical framework to facilitate users in assessing a software system in terms of the required survivability features. Survivability evaluation is essential in linking foreign software components to an existing system or obtaining software systems from external sources. It is important to make sure that any foreign components/systems will not compromise the current system's survivability properties. Given the increasing large scope and complexity of modern software systems, there is a need for an evaluation framework to accommodate uncertain, vague, or even ill-known knowledge for a robust evaluation based on multi-dimensional criteria. Our framework incorporates user-defined constrains on survivability requirements. Necessity-based possibilistic uncertainty and user survivability requirement constraints are effectively linked to logic reasoning. A proof-of-concept system has been developed to validate the proposed approach. To our best knowledge, our work is the first attempt to incorporate vague, imprecise information into software system survivability evaluation.
Traffic, crowds, and dynamics of self-organized particles: New trends and challenges
Authors: Bellomo N. , Brezzi F.
Published: September 2014

This brief note is an introduction to the special issue devoted to modeling, qualitative analysis and simulations of vehicular traffic, crowds and swarms, viewed as living, hence complex, systems. The first part focuses on the conceptual difficulties to be tackled when dealing with the most challenging topics of this subject, mainly on interactions and complexity features. The second part provides a brief overview and critical analysis of the contents. Finally, some perspective ideas on conceivable future research objectives are brought to the reader's attention.