bluuebunny/crossref_metadata_2025 huggingface dataset:
Polyphasic Screening, Homopolysaccharide Composition, and Viscoelastic Behavior of Wheat Sourdough from a Leuconostoc lactis and Lactobacillus curvatus Exopolysaccharide-Producing Starter Culture
Authors: Palomba Simona , Cavella Silvana , Torrieri Elena , Piccolo Alessandro , Mazzei Pierluigi , Blaiotta Giuseppe , Ventorino Valeria , Pepe Olimpia
Published: February 2012

After isolation from different doughs and sourdoughs, 177 strains of lactic acid bacteria were screened at the phenotypic level for exopolysaccharide production on media containing different carbohydrate sources. Two exopolysaccharide-producing lactic acid bacteria (
Lactobacillus curvatus
69B2 and
Leuconostoc lactis
95A) were selected through quantitative analysis on solid media containing sucrose and yeast extract. The PCR detection of homopolysaccharide (
gtf
and
lev
) and heteropolysaccharide (
epsA
,
epsB
,
epsD
and
epsE
, and
epsEFG
) genes showed different distributions within species and strains of the lactic acid bacteria studied. Moreover, in some strains both homopolysaccharide and heteropolysaccharide genes were detected. Proton nuclear magnetic resonance spectra suggest that
Lactobacillus curvatus
69B2 and
Leuconostoc lactis
95A produced the same exopolysaccharide, which was constituted by a single repeating glucopyranosyl unit linked by an α-(1→6) glycosidic bond in a dextran-type carbohydrate. Microbial growth, acidification, and viscoelastic properties of sourdoughs obtained by exopolysaccharide-producing and nonproducing lactic acid bacterial strains were evaluated. Sourdough obtained after 15 h at 30°C with exopolysaccharide-producing lactic acid bacteria reached higher total titratable acidity as well as elastic and dissipative modulus curves with respect to the starter not producing exopolysaccharide, but they showed similar levels of pH and microbial growth. On increasing the fermentation time, no difference in the viscoelastic properties of exopolysaccharide-producing and nonproducing samples was observed. This study suggests that dextran-producing
Leuconostoc lactis
95A and
Lactobacillus curvatus
69B2 can be employed to prepare sourdough, and this would be particularly useful to improve the quality of baked goods while avoiding the use of commercially available hydrocolloids as texturizing additives.
Effect of Soybean Coumestrol on Bradyrhizobium japonicum Nodulation Ability, Biofilm Formation, and Transcriptional Profile
Authors: Lee Hae-In , Lee Jin-Hwan , Park Ki-Hun , Sangurdekar Dipen , Chang Woo-Suk
Published: February 2012

Flavonoids, secondary plant metabolites which mainly have a polyphenolic structure, play an important role in plant-microbe communications for nitrogen-fixing symbiosis. Among 10 polyphenolic compounds isolated from soybean roots in our previous study, coumestrol showed the highest antioxidant activity. In this study, its effect on the soybean nodulation was tested. The soybean symbiont
Bradyrhizobium japonicum
USDA110 pretreated with 20 μM coumestrol enhanced soybean nodulation by increasing the number of nodules 1.7-fold compared to the control. We also tested the effect of coumestrol on
B. japonicum
biofilm formation. At a concentration of 2 μM, coumestrol caused a higher degree of biofilm formation than two major soybean isoflavonoids, genistein and daidzein, although no biofilm formation was observed at a concentration of 20 μM each compound. A genome-wide transcriptional analysis was performed to obtain a comprehensive snapshot of the
B. japonicum
response to coumestrol. When the bacterium was incubated in 20 μM coumestrol for 24 h, a total of 371 genes (139 upregulated and 232 downregulated) were differentially expressed at a 2-fold cutoff with a
q
value of less than 5%. No common
nod
gene induction was found in the microarray data. However, quantitative reverse transcription-PCR (qRT-PCR) data showed that incubation for 12 h resulted in a moderate induction (ca. 2-fold) of
nodD1
and
nodABC
, indicating that soybean coumestrol is a weak inducer of common
nod
genes. In addition, disruption of
nfeD
(bll4952) affected the soybean nodulation by an approximate 30% reduction in the average number of nodules.
Temperature-Dependent Production of Various PlcR-Controlled Virulence Factors in Bacillus weihenstephanensis Strain KBAB4
Authors: Réjasse A. , Gilois N. , Barbosa I. , Huillet E. , Bevilacqua C. , Tran S. , Ramarao N. , Stenfors Arnesen L. P. , Sanchis V.
Published: February 2012

The
Bacillus cereus
sensu lato complex has recently been divided into several phylogenetic groups with clear differences in growth temperature range. However, only a few studies have investigated the actual pathogenic potential of the psychrotolerant strains of the
B. cereus
group at low temperature, and little information is available concerning gene expression at low temperature. We found that vegetative cells of the psychrotolerant
B. weihenstephanensis
strain KBAB4 were pathogenic against the model insect
Galleria mellonella
at 15°C but not at 30°C. A similar temperature-dependent difference also was observed for the supernatant, which was cytotoxic to Vero epithelial cell lines and to murine macrophage J774 cells at 15°C but not at 30°C. We therefore determined the effect of low temperature on the production of various proteins putatively involved in virulence using two-dimensional protein gel electrophoresis, and we showed that the production of the Hbl enterotoxin and of two proteases, NprB and NprP2, was greater at a growth temperature of 15°C than at 30°C. The quantification of the mRNA levels for these virulence genes by real-time quantitative PCR at both temperatures showed that there was also more mRNA present at 15°C than at 30°C. We also found that at 15°C,
hbl
mRNA levels were maximal in the mid- to late exponential growth phase. In conclusion, we found that the higher virulence of the
B. cereus
KBAB4 strain at low temperature was accompanied by higher levels of the production of various known PlcR-controlled virulence factors and by a higher transcriptional activity of the corresponding genes.
Rapid and Simple Cryopreservation of Anaerobic Ammonium-Oxidizing Bacteria
Authors: Heylen Kim , Ettwig Katharina , Hu Ziye , Jetten Mike , Kartal Boran
Published: February 2012

A quick and simple protocol for long-term cryopreservation of anaerobic ammonium-oxidizing bacteria (anammox bacteria) was developed. After 29 weeks of preservation at −80°C, activity recovery for all tested cultures under at least one of the applied sets of preservation conditions was observed. Growth recovery was also demonstrated for a single-cell culture of “
Candidatus
Kuenenia stuttgartiensis.”
Identification of a
pheA
Gene Associated with Streptococcus mitis by Using Suppression Subtractive Hybridization
Authors: Park Hee Kuk , Dang Hien Thanh , Myung Soon Chul , Kim Wonyong
Published: February 2012

We performed suppression subtractive hybridization to identify genomic differences between
Streptococcus mitis
and
Streptococcus pneumoniae
. Based on the
pheA
gene, a primer set specific to
S. mitis
detection was found in 18 out of 103
S. mitis
-specific clones. Our findings would be useful for discrimination of
S. mitis
from other closely related cocci in the oral environment.
Vibrio parahaemolyticus in Rhode Island Coastal Ponds and the Estuarine Environment of Narragansett Bay
Authors: Cox Annie M. , Gomez-Chiarri Marta
Published: February 2012

Quantification of the abundance of
Vibrio parahaemolyticus
in water and oysters from Rhode Island showed the presence of environmental strains and low levels of potentially pathogenic strains when water temperatures were ≥18°C, with peak levels in late July to early August. A higher abundance of the
trh
gene than of the
tdh
gene was observed.
Seropathotypes, Phylogroups, Stx Subtypes, and Intimin Types of Wildlife-Carried, Shiga Toxin-Producing Escherichia coli Strains with the Same Characteristics as Human-Pathogenic Isolates
Authors: Mora Azucena , López Cecilia , Dhabi Ghizlane , López-Beceiro Ana M. , Fidalgo Luís E. , Díaz Eduardo A. , Martínez-Carrasco Carlos , Mamani Rosalía , Herrera Alexandra , Blanco Jesús E. , Blanco Miguel , Blanco Jorge
Published: February 2012

The objectives of this study were to investigate the presence of Shiga toxin-producingEscherichia coli(STEC) strains in wildlife that have spread in Europe, living near human settlements; to analyze their epidemiological role in maintenance and transmission to domestic livestock; and to assess the potential health risk of wildlife-carried strains. STEC strains were recovered from 53% of roe deer, 8.4% of wild boars, and 1.9% of foxes sampled in the northwest of Spain (Galicia). Of the 40 serotypes identified, 21 were classified as seropathotypes associated with human disease, accounting for 81.5% of the wildlife-carried STEC strains, including the enterohemorrhagic serotypes O157:H7-D-eae-γ1, O26:[H11]-B1-eae-β1, O121:H19-B1-eae-ε1, and O145:[H28]-D-eae-γ1. None of the wildlife-carried strains belonged to the highly pathogenic serotype O104:H4-B1 from the recent Germany outbreak. Forty percent of wildlife-carried STEC strains shared serotypes, phylogroups, intimin types, and Stx profiles with isolates from human patients from the same geographic area. Furthermore, wildlife-carried strains belonging to serotypes O5:HNM-A, O26:[H11]-B1, O76:H19-B1, O145:[H28]-D, O146:H21-B1, and O157:H7-D showed pulsed-field gel electrophoresis (PFGE) profiles with >85% similarity to human-pathogenic STEC strains. We also found a high level of similarity among STEC strains of serotypes O5:HNM-A, O26:[H11]-B1, and O145:HNM-D of bovine (feces and beef) and wildlife origins. Interestingly, O146:H21-B1, the second most frequently detected serotype in this study, is commonly associated with human diarrhea and isolated from beef and vegetables sold in Galicia. Importantly, at least 3 STEC isolates from foxes (O5:HNM-A-eae-β1, O98:[H21]-B1-eae-ζ1, and O146:[H21]-B1) showed characteristics similar to those of human STEC strains. In conclusion, roe deer, wild boar, and fox in Galicia are confirmed to be carriers of STEC strains potentially pathogenic for humans and seem to play an important role in the maintenance of STEC.
Listeria monocytogenes Shows Temperature-Dependent and -Independent Responses to Salt Stress, Including Responses That Induce Cross-Protection against Other Stresses
Authors: Bergholz Teresa M. , Bowen Barbara , Wiedmann Martin , Boor Kathryn J.
Published: February 2012

The food-borne pathogen
Listeria monocytogenes
experiences osmotic stress in many habitats, including foods and the gastrointestinal tract of the host. During transmission,
L. monocytogenes
is likely to experience osmotic stress at different temperatures and may adapt to osmotic stress in a temperature-dependent manner. To understand the impact of temperature on the responses this pathogen uses to adapt to osmotic stress, we assessed genome-wide changes in the
L. monocytogenes
H7858 transcriptome during short-term and long-term adaptation to salt stress at 7°C and 37°C. At both temperatures, the short-term response to salt stress included increased transcript levels of
sigB
and SigB-regulated genes, as well as
mrpABCDEFG
, encoding a sodium/proton antiporter. This antiporter was found to play a role in adaptation to salt stress at both temperatures; Δ
mrpABCDEFG
had a significantly longer lag phase than the parent strain in BHI plus 6% NaCl at 7°C and 37°C. The short-term adaptation to salt stress at 7°C included increased transcript levels of two genes encoding carboxypeptidases that modify peptidoglycan. These carboxypeptidases play a role in the short-term adaptation to salt stress only at 7°C, where the deletion mutants had significantly different lag phases than the parent strain. Changes in the transcriptome at both temperatures suggested that exposure to salt stress could provide cross-protection to other stresses, including peroxide stress. Short-term exposure to salt stress significantly increased H
2
O
2
resistance at both temperatures. These results provide information for the development of knowledge-based intervention methods against this pathogen, as well as provide insight into potential mechanisms of cross-protection.
Characterization of Esterase A, a Pseudomonas stutzeri A15 Autotransporter
Authors: Nicolay Toon , Devleeschouwer Ken , Vanderleyden Jos , Spaepen Stijn
Published: February 2012

Autotransporters are a widespread family of proteins, generally known as virulence factors produced by Gram-negative bacteria. In this study, the esterase A (EstA) autotransporter of the rice root-colonizing beneficial bacterium
Pseudomonas stutzeri
A15 was characterized. A multiple sequence alignment identified EstA as belonging to clade II of the GDSL esterase family. Autologous overexpression allowed the investigation of several features of both autotransporter proteins and GDSL esterases. First, the correctly folded autotransporter was shown to be present in the membrane fraction. Unexpectedly, after separation of the membrane fraction, EstA was detected in the
N
-laurylsarcosine soluble fraction. However, evidence is presented for the surface exposure of EstA based on fluorescent labeling with EstA specific antibodies. Another remarkable feature is the occurrence of a C-terminal leucine residue instead of the canonical phenylalanine or tryptophan residue. Replacement of this residue with a phenylalanine residue reduced the stability of the β-barrel. Regarding the esterase passenger domain, we show the importance of the catalytic triad residues, with the serine and histidine residues being more critical than the aspartate residue. Furthermore, the growth of an
estA
-negative mutant was not impaired and cell mobility was not disabled compared to the wild type. No specific phenotype was detected for an
estA
-negative mutant. Overall,
P. stutzeri
A15 EstA is a new candidate for the surface display of proteins in environmentally relevant biotechnological applications.
Longitudinal Study of the Persistence of Antimicrobial-Resistant Campylobacter Strains in Distinct Swine Production Systems on Farms, at Slaughter, and in the Environment
Authors: Quintana-Hayashi Macarena P. , Thakur Siddhartha
Published: February 2012

The objectives of this study were to compare and characterize the prevalence of antimicrobial-resistant (AR)
Campylobacter
in conventional and antimicrobial-free (ABF) production systems on farms, at slaughter, and in the environment. Fecal and environmental samples were collected from ABF farms (pigs, 1,239; environment, 797) and conventional farms (pigs, 1,650; environment, 1,325). At slaughter, we collected samples from carcasses, including postevisceration swabs, postchill swabs, and mesenteric lymph nodes from ABF systems (postevisceration swabs, 182; postchill swabs, 199; mesenteric lymph nodes, 184) and conventional systems (postevisceration swabs, 272; postchill swabs, 271; mesenteric lymph nodes, 255) at separate processing facilities. We also sampled the processing plant environment, including truck and lairage floor swab samples (ABF, 115; conventional, 90). Overall, a total of 2,908
Campylobacter
isolates, including
Campylobacter coli
(farm, 2,557, 99.8%; slaughter, 341, 98.3%) and
Campylobacter jejuni
(farm, 4, 0.2%; slaughter, 6, 1.7%), were isolated in the study. There was no significant difference in the prevalence of
Campylobacter
between ABF and conventionally raised pigs (farrowing,
P
= 0.20; nursery,
P
= 0.06; finishing,
P
= 0.24) and the environment (
P
= 0.37). At slaughter,
Campylobacter
was isolated from all of the stages, including postchill. The highest frequencies of resistance were exhibited against tetracycline (ABF, 48.2%; conventional, 88.3%). Ciprofloxacin-resistant
C. coli
isolates were observed in conventionally raised (17.1%) and ABF (1.2%) pigs (
P
= 0.11). Antimicrobial use data from conventional farms indicated significant associations between oxytetracycline use and tetracycline resistance in the nursery pigs (
P
= 0.01), between tiamulin exposure and azithromycin and erythromycin resistance in nursery (
P
< 0.01) and finishing (
P
< 0.01) pigs, and between enrofloxacin exposure and ciprofloxacin and nalidixic acid resistance in farrowing (
P
< 0.01) and nursery (
P
< 0.01) pigs. Identical antimicrobial resistance profiles were observed in the pigs and their environments on farms and at slaughter. In summary, our results highlight the persistence and dissemination of AR
Campylobacter
from farm to slaughter in ABF and conventionally raised pigs and their environments.
Piglets Are a Source of Pathogenic Yersinia enterocolitica on Fattening-Pig Farms
Authors: Virtanen Sonja , Salonen Laura , Laukkanen-Ninios Riikka , Fredriksson-Ahomaa Maria , Korkeala Hannu
Published: February 2012

To study the origin and spread of
Yersinia enterocolitica
among pigs, fecal and blood samples were repeatedly taken on a fattening farm. A few piglets were found to be already infected on breeding farms. After the piglets were mixed, the infection spread through the whole unit. Eventually, all the pigs excreted the pathogen.
Rerouting Carbon Flux To Enhance Photosynthetic Productivity
Authors: Ducat Daniel C. , Avelar-Rivas J. Abraham , Way Jeffrey C. , Silver Pamela A.
Published: February 2012

The bioindustrial production of fuels, chemicals, and therapeutics typically relies upon carbohydrate inputs derived from agricultural plants, resulting in the entanglement of food and chemical commodity markets. We demonstrate the efficient production of sucrose from a cyanobacterial species,
Synechococcus elongatus
, heterologously expressing a symporter of protons and sucrose (
cscB
).
cscB
-expressing cyanobacteria export sucrose irreversibly to concentrations of >10 mM without culture toxicity. Moreover, sucrose-exporting cyanobacteria exhibit increased biomass production rates relative to wild-type strains, accompanied by enhanced photosystem II activity, carbon fixation, and chlorophyll content. The genetic modification of sucrose biosynthesis pathways to minimize competing glucose- or sucrose-consuming reactions can further improve sucrose production, allowing the export of sucrose at rates of up to 36.1 mg liter
−1
h illumination
−1
. This rate of production exceeds that of previous reports of targeted, photobiological production from microbes. Engineered
S. elongatus
produces sucrose in sufficient quantities (up to ∼80% of total biomass) such that it may be a viable alternative to sugar synthesis from terrestrial plants, including sugarcane.
Evidence of an Evolutionarily Conserved LMBR1 Domain-Containing Protein That Associates with Endocytic Cups and Plays a Role in Cell Migration in Dictyostelium discoideum
Authors: Kelsey Jessica S. , Fastman Nathan M. , Blumberg Daphne D.
Published: February 2012

The
ampA
gene plays a role in
Dictyostelium discoideum
cell migration. Loss of
ampA
function results in reduced ability of growing cells to migrate to folic acid and causes small plaques on bacterial lawns, while overexpression of AmpA results in a rapid-migration phenotype and correspondingly larger plaques than seen with wild-type cells. To help understand how the
ampA
gene functions, second-site suppressors were created by restriction enzyme-mediated integration (REMI) mutagenesis. These mutants were selected for their ability to reduce the large plaque size of the AmpA overexpresser strain. The
lmbd2B
gene was identified as a suppressor of an AmpA-overexpressing strain. The
lmbd2B
gene product belongs to the evolutionarily conserved LMBR1 protein family, some of whose known members are endocytic receptors associated with human diseases, such as anemia. In order to understand
lmbd2B
function, mRFP fusion proteins were created and
lmbd2B
knockout cell lines were established. Our findings indicate that the LMBD2B protein is found associated with endocytic cups. It colocalizes with proteins that play key roles in endocytic events and is localized to ruffles on the dorsal surfaces of growing cells. Vegetative
lmbd2B
-null cells display defects in cell migration. These cells have difficulty sensing the chemoattractant folic acid, as indicated by a decrease in their chemotactic index.
lmbd2B
-null cells also appear to have difficulty establishing a front/back orientation to facilitate migration. A role for
lmbd2B
in development is also suggested. Our research gives insight into the function of a previously uncharacterized branch of the LMBR1 family of proteins. We provide evidence of an LMBR1 family plasma membrane protein that associates with endocytic cups and plays a role in chemotaxis.
Delta-Aminolevulinate-Induced Host-Parasite Porphyric Disparity for Selective Photolysis of Transgenic Leishmania in the Phagolysosomes of Mononuclear Phagocytes: a Potential Novel Platform for Vaccine Delivery
Authors: Dutta Sujoy , Chang Celia , Kolli Bala Krishna , Sassa Shigeru , Yousef Malik , Showe Michael , Showe Louise , Chang Kwang-Poo
Published: February 2012

Leishmaniadouble transfectants (DTs) expressing the 2nd and 3rd enzymes in the heme biosynthetic pathway were previously reported to show neogenesis of uroporphyrin I (URO) when induced with delta-aminolevulinate (ALA), the product of the 1st enzyme in the pathway. The ensuing accumulation of URO in DT promastigotes rendered them light excitable to produce reactive oxygen species (ROS), resulting in their cytolysis. Evidence is presented showing that the DTs retained wild-type infectivity to their host cells and that the intraphagolysosomal/parasitophorous vacuolar (PV) DTs remained ALA inducible for uroporphyrinogenesis/photolysis. Exposure of DT-infected cells to ALA was noted by fluorescence microscopy to result in host-parasite differential porphyrinogenesis: porphyrin fluorescence emerged first in the host cells and then in the intra-PV amastigotes. DT-infected and control cells differed qualitatively and quantitatively in their porphyrin species, consistent with the expected multi- and monoporphyrinogenic specificities of the host cells and the DTs, respectively. After ALA removal, the neogenic porphyrins were rapidly lost from the host cells but persisted as URO in the intra-PV DTs. These DTs were thus extremely light sensitive and were lysed selectively by illumination under nonstringent conditions in the relatively ROS-resistant phagolysosomes. Photolysis of the intra-PV DTs returned the distribution of major histocompatibility complex (MHC) class II molecules and the global gene expression profiles of host cells to their preinfection patterns and, when transfected with ovalbumin, released this antigen for copresentation with MHC class I molecules. TheseLeishmaniamutants thus have considerable potential as a novel model of a universal vaccine carrier for photodynamic immunotherapy/immunoprophylaxis.
The TonB3 System in the Human Pathogen Vibrio vulnificus Is under the Control of the Global Regulators Lrp and Cyclic AMP Receptor Protein
Authors: Alice Alejandro F. , Crosa Jorge H.
Published: February 2012

TonB systems transduce the proton motive force of the cytoplasmic membrane to energize substrate transport through a specific TonB-dependent transporter across the outer membrane.
Vibrio vulnificus
, an opportunistic marine pathogen that can cause a fatal septicemic disease in humans and eels, possesses three TonB systems. While the TonB1 and TonB2 systems are iron regulated, the TonB3 system is induced when the bacterium grows in human serum. In this work we have determined the essential roles of the leucine-responsive protein (Lrp) and cyclic AMP (cAMP) receptor protein (CRP) in the transcriptional activation of this system. Whereas Lrp shows at least four very distinctive DNA binding regions spread out from position −59 to −509, cAMP-CRP binds exclusively in a region centered at position −122.5 from the start point of the transcription. Our results suggest that both proteins bind simultaneously to the region closer to the RNA polymerase binding site. Importantly, we report that the TonB3 system is induced not only by serum but also during growth in minimal medium with glycerol as the sole carbon source and low concentrations of Casamino Acids. In addition to catabolite repression by glucose,
l
-leucine acts by inhibiting the binding of Lrp to the promoter region, hence preventing transcription of the TonB3 operon. Thus, this TonB system is under the direct control of two global regulators that can integrate different environmental signals (i.e., glucose starvation and the transition between “feast” and “famine”). These results shed light on new mechanisms of regulation for a TonB system that could be widespread in other organisms.
Evidence that a Single Monomer of Spx Can Productively Interact with RNA Polymerase in Bacillus subtilis
Authors: Lin Ann A. , Zuber Peter
Published: February 2012

Spx activates transcription initiation in
Bacillus subtilis
by directly interacting with the C-terminal domain of the RNA polymerase (RNAP) holoenzyme α subunit, which generates a complex that recognizes the promoter regions of genes within the Spx regulon. Many Gram-positive species possess multiple paralogs of Spx, suggesting that two paralogous forms of Spx could simultaneously contact RNAP. The composition of Spx/RNAP was examined
in vitro
using an Spx variant (SpxΔCHA) bearing a 12-amino-acid deletion of the C terminus (SpxΔC) and a hemagglutinin (HA) epitope tag and Spxc-Myc, a full-length Spx with a C-terminal myelocytomatosis oncoprotein (c-Myc) epitope tag. All Spx/RNAP complexes bearing deletion or C-terminal-tagged variants were transcriptionally active
in vivo
and
in vitro
. Reaction mixtures containing SpxΔCHA and Spxc-Myc combined with RNAP were applied to either anti-HA or anti-c-Myc affinity columns. Eluted fractions contained RNAP with only one of the epitope-tagged Spx derivatives. The resin-bound RNAP complex bearing a single epitope-tagged Spx derivative was transcriptionally active.
In vivo
production of SpxΔC and SpxΔCHA followed by anti-HA affinity column chromatography of a cleared lysate resulted in retrieval of Spx/RNAP with only the SpxΔCHA derivative. Binding reactions that combined active Spxc-Myc, inactive Spx(R60E)ΔCHA, and RNAP, when applied to the anti-HA affinity column, yielded only inactive Spx(R60E)ΔCHA/RNAP complexes. The results strongly argue for a model in which a single Spx monomer engages RNAP to generate an active transcriptional complex.
Genome-Wide Definition of the SigF Regulon in Mycobacterium tuberculosis
Authors: Hartkoorn Ruben C. , Sala Claudia , Uplekar Swapna , Busso Philippe , Rougemont Jacques , Cole Stewart T.
Published: February 2012

In
Mycobacterium tuberculosis
the alternative sigma factor SigF controls the expression of a particular subset of genes by altering RNA polymerase specificity. Here, we utilize two genome-wide approaches to identify SigF-binding sites: chromatin immunoprecipitation (ChIP-on-chip) and microarray analysis of SigF-mediated transcripts. Since SigF is not an abundant protein in the logarithmic phase of growth, a pristinamyin IA-inducible system was used to control its expression. We identified 67 high-affinity SigF-binding sites and 16 loci where a SigF promoter directs the expression of a transcript. These loci include
sigF
itself, genes involved in lipid and intermediary metabolism and virulence, and at least one transcriptional regulator (
Rv2884
), possibly acting downstream of SigF. In addition, SigF was also found to direct the transcription of the gene for small RNA F6. Many loci were also found where SigF may be involved in antisense transcription, and in two cases (
Rv1358
and
Rv1870c
) the SigF-dependent promoter was located within the predicted coding sequence. Quantitative PCR confirmed the microarray findings and 5′-rapid amplification of cDNA ends was used to map the SigF-specific transcriptional start points. A canonical SigF consensus promoter sequence GGTTT-N
(15-17)
-GGGTA was found prior to 11 genes. Together, these data help to define the SigF regulon and show that SigF not only governs expression of proteins such as the virulence factor, HbhA, but also impacts novel functions, such as noncoding RNAs and antisense transcripts.
A cross-sectional study of glucose regulation in young adults with very low birth weight: impact of male gender on hyperglycaemia
Authors: Sato Ryosuke , Watanabe Hiroshi , Shirai Kenji , Ohki Shigeru , Genma Rieko , Morita Hiroshi , Inoue Eisuke , Takeuchi Masahiro , Maekawa Masato , Nakamura Hirotoshi
Published: February 2012

Objectives

To investigate glucose regulation in young adults with very low birth weight (VLBW; <1500 g) in an Asian population.

Design

Cross-sectional observational study.

Setting

A general hospital in Hamamatsu, Japan.

Participants

111 young adults (42 men and 69 women; aged 19–30 years) born with VLBW between 1980 and 1990. Participants underwent standard 75 g oral glucose tolerance test (OGTT).

Primary and secondary outcome measures

The primary outcomes were glucose and insulin levels during OGTT and risk factors for a category of hyperglycaemia defined as follows: diabetes mellitus, impaired glucose tolerance (IGT), impaired fasting glycaemia (IFG) and non-diabetes/IGT/IFG with elevated 1 h glucose levels (>8.6 mmol/l). The secondary outcomes were the pancreatic β cell function (insulinogenic index and homeostasis model of assessment for beta cell (HOMA-β)) and insulin resistance (homeostasis model of assessment for insulin resistance (HOMA-IR)).

Results

Of 111 young adults with VLBW, 21 subjects (19%) had hyperglycaemia: one had type 2 diabetes, six had IGT, one had IFG and 13 had non-diabetes/IGT/IFG with elevated 1 h glucose levels. In logistic regression analysis, male gender was an independent risk factor associated with hyperglycaemia (OR 3.34, 95% CI 1.08 to 10.3, p=0.036). Male subjects had significantly higher levels of glucose and lower levels of insulin during OGTT than female subjects (p<0.001 for glucose and p=0.005 for insulin by repeated measures analysis of variance). Pancreatic β cell function was lower in men (insulinogenic index: p=0.002; HOMA-β: p=0.001), although no gender difference was found in insulin resistance (HOMA-IR: p=0.477). In male subjects, logistic regression analysis showed that small for gestational age was an independent risk factor associated with hyperglycaemia (OR 33.3, 95% CI 1.67 to 662.6, p=0.022).

Conclusions

19% of individuals with VLBW already had hyperglycaemia in young adulthood, and male gender was a significant independent risk factor of hyperglycaemia. In male young adults with VLBW, small for gestational age was associated with hyperglycaemia.
Emergency and surgery services of primary hospitals in the United Republic of Tanzania
Authors: Penoyar Tom , Cohen Hillary , Kibatala P , Magoda A , Saguti G , Noel L , Groth S , Mwakyusa D H , Cherian M
Published: February 2012

Objective

The primary objective was to evaluate the capacity of first-referral health facilities in Tanzania to perform basic surgical procedures. The intent was to assist in planning strategies for universal access to life-saving and disability-preventing surgical services.

Design

Cross-sectional survey.

Setting

First-referral health facilities in the United Republic of Tanzania.

Participants

48 health facilities.

Measures

The WHO Tool for Situational Analysis to Assess Emergency and Essential Surgical Care was employed to capture a health facility's capacity to perform basic surgical (including obstetrics and trauma) and anaesthesia interventions by investigating four categories of data: infrastructure, human resources, interventions available and equipment. The tool queried the availability of eight types of care providers, 35 surgical interventions and 67 items of equipment.

Results

The 48 facilities surveyed served 18.6 million residents (46% of the population). Supplies for basic airway management were inconsistently available. Only 42% had consistent access to oxygen, and only six functioning pulse oximeters were located in all facilities surveyed. 37.5% of facilities reported both consistent running water and electricity. While very basic interventions (suturing, wound debridement, incision and drainage) were provided in nearly all facilities, more advanced life-saving procedures including chest tube thoracostomy (30/48), open fracture management (29/48) and caesarean section delivery (32/48) were not consistently available.

Conclusions

Based on the results in this WHO country survey, significant gaps exist in the capacity for emergency and essential surgical services in Tanzania including deficits in human resources, essential equipment and infrastructure. The information in this survey will provide a foundation for evidence-based decisions in country-level policy regarding the allocation of resources and provision of emergency and essential surgical services.
Short sleep and obesity in a large national cohort of Thai adults
Authors: Yiengprugsawan Vasoontara , Banwell Cathy , Seubsman Sam-ang , Sleigh Adrian C ,   Thai Cohort Study Team
Published: February 2012

Objective

To investigate the relationship between short sleep and obesity among Thai adults.

Design

Both 4-year longitudinal and cross-sectional analyses of a large national cohort.

Setting

Thai adults residing nationwide from 2005 to 2009.

Participants

Cohort members were enrolled as distance learners at Sukhothai Thammathirat Open University (N=87 134 in 2005 and 60 569 at 2009 follow-up). At 2005 baseline, 95% were between 20 and 49 years of age.

Measures

Self-reported sleep duration was categorised as <6, 6, 7, 8 and ≥9 h. For all analyses (2005 and 2009 cross-sectional and 2005–2009 longitudinal), we used multinomial logistic regression models to assess the effect of sleep duration on abnormal body size (underweight, overweight-at-risk, obese). Results were adjusted for an array of relevant covariates.

Results

At the last cohort follow-up in 2009, cross-sectional associations linked short sleep (<6 h) and obesity: adjusted ORs (AOR) =1.49, 95% CIs 1.32 to 1.68 for women and AOR=1.36, 95% CI 1.21 to 1.52 for men. The earlier cross-sectional baseline results in 2005 were quite similar. Longitudinal analysis (2005–2009) of 4-year incremental weight gain (5 to <10%, 10 to <20% and 20%+) strongly supported the short sleep–obesity relationship (significant AORs of 1.10, 1.30 and 1.69, respectively).

Conclusions

The results are internally consistent (2005 and 2009) and longitudinally confirmatory of a short sleep effect on obesity among Thai adults. Further research is needed to elucidate causal mechanisms underlying the sleep–obesity relationship.
Lifestyle counselling targeting infant's mother during the child's first year and offspring weight development until 4 years of age: a follow-up study of a cluster RCT
Authors: Mustila Taina , Raitanen Jani , Keskinen Päivi , Saari Antti , Luoto Riitta
Published: February 2012

Objective

To investigate the effect of intensified lifestyle counselling targeting infants' mothers on offspring weight development during the first 4 years of life.

Design and setting

Follow-up of a cluster-randomised controlled trial in primary care child health clinics during 2004–2006 in Finland. Participants received a follow-up survey during 2010 concerning weight and height measurements of their offspring. Number of clusters was six and the response rate to the follow-up 71.9% (N=64/89).

Participants

The participants (N=89) were mothers of infants aged 2–10 months.

Intervention

The intervention included individual counselling on diet and physical activity when the infant was 2–10 months of age and an option to attend supervised group exercise sessions.

Primary and secondary outcome measures

The authors analysed the secondary outcome of the intervention study: the weight development of the offspring. The primary outcome was the proportion of women returning to their prepregnancy weight by 10 months post partum, reported earlier.

Results

Multilevel mixed effect non-linear regression models included group, age of the child and interaction between group and age of the child. The increase of BMI z-score between 24 and 48 months was slower among the intervention group offspring (−0.034 to −0.002, p=0.028) as compared with control group. Z-scores for weight-for-length/height did not differ between groups when the period 0–48 months was analysed (p=0.23) but for the period of 24–48 months, between-group differences were significant (p=0.012).

Conclusions

Lifestyle counselling targeting mothers during the child's first year may be effective in slowing offspring weight gain until 4 years of age. However, larger studies are needed to confirm the findings which may have the potential in combatting the obesity epidemic.

Trial registration number

Current Controlled TrialsISRCTN21512277.
A prospective follow-up study of the association of radiation exposure with fatal and non-fatal stroke among atomic bomb survivors in Hiroshima and Nagasaki (1980–2003)
Authors: Takahashi Ikuno , Abbott Robert D , Ohshita Tomohiko , Takahashi Tetsuya , Ozasa Kotaro , Akahoshi Masazumi , Fujiwara Saeko , Kodama Kazunori , Matsumoto Masayasu
Published: February 2012

Objective

Use of medical radiotherapy has increased markedly in recent decades. Whether the consequence includes an increased risk of cardiovascular disease remains to be determined. The purpose of this study was to examine the association between radiation exposure and the incidence of stroke among Japanese atomic bomb survivors.

Design

A prospective follow-up study.

Setting and participants

Radiation exposure from the atomic bombing was assessed in 9515 subjects (34.8% men) with 24-year follow-up from 1980. Subjects were free of prevalent stroke when follow-up began.

Outcome measures

Stroke events and the underlying cause of death were reviewed to confirm the first-ever stroke. Subtypes (ischaemic and haemorrhagic events) were categorised based on established criteria according to the definitions of typical/atypical stroke symptoms.

Results

Overall mean radiation dose (±SD) in units of gray (Gy) was 0.38±0.58 (range: 0–3.5). During the study period, 235 haemorrhagic and 607 ischaemic events were identified. For men, after adjusting for age and concomitant risk factors, the risk of haemorrhagic stroke rose consistently from 11.6 to 29.1 per 10 000 person-years as doses increased from <0.05 to ≥2 Gy (p=0.009). Incidence also rose within the dose range <1 Gy (p=0.004) with no dose threshold. In women, the risk of haemorrhagic stroke rose with increasing radiation exposure but not until doses reached a threshold of 1.3 Gy (95% CI 0.5 to 2.3). Among women, for doses <1.3 Gy, differences in stroke risk were modest (13.5 per 10 000 person-years), while it increased to 20.3 per 10 000 person-years for doses that ranged from 1.3 to <2.2 Gy and to 48.6 per 10 000 person-years for doses that were higher (p=0.002). In both sexes, dose was unrelated to ischaemic stroke.

Conclusion

While the risk of haemorrhagic stroke increases with rising radiation exposure for both sexes, effects in women are less apparent until doses exceed a threshold at 1.3 Gy.
Detecting and measuring deprivation in primary care: development, reliability and validity of a self-reported questionnaire: the DiPCare-Q
Authors: Vaucher Paul , Bischoff Thomas , Diserens Esther-Amélie , Herzig Lilli , Meystre-Agustoni Giovanna , Panese Francesco , Favrat Bernard , Sass Catherine , Bodenmann Patrick
Published: February 2012

Objectives

Advances in biopsychosocial science have underlined the importance of taking social history and life course perspective into consideration in primary care. For both clinical and research purposes, this study aims to develop and validate a standardised instrument measuring both material and social deprivation at an individual level.

Methods

We identified relevant potential questions regarding deprivation using a systematic review, structured interviews, focus group interviews and a think-aloud approach. Item response theory analysis was then used to reduce the length of the 38-item questionnaire and derive the deprivation in primary care questionnaire (DiPCare-Q) index using data obtained from a random sample of 200 patients during their planned visits to an ambulatory general internal medicine clinic. Patients completed the questionnaire a second time over the phone 3 days later to enable us to assess reliability. Content validity of the DiPCare-Q was then assessed by 17 general practitioners. Psychometric properties and validity of the final instrument were investigated in a second set of patients. The DiPCare-Q was administered to a random sample of 1898 patients attending one of 47 different private primary care practices in western Switzerland along with questions on subjective social status, education, source of income, welfare status and subjective poverty.

Results

Deprivation was defined in three distinct dimensions: material (eight items), social (five items) and health deprivation (three items). Item consistency was high in both the derivation (Kuder-Richardson Formula 20 (KR20) =0.827) and the validation set (KR20 =0.778). The DiPCare-Q index was reliable (interclass correlation coefficients=0.847) and was correlated to subjective social status (rs=−0.539).

Conclusion

The DiPCare-Q is a rapid, reliable and validated instrument that may prove useful for measuring both material and social deprivation in primary care.
Evaluating the travel, physical activity and carbon impacts of a ‘natural experiment’ in the provision of new walking and cycling infrastructure: methods for the core module of the iConnect study
Authors: Ogilvie David , Bull Fiona , Cooper Ashley , Rutter Harry , Adams Emma , Brand Christian , Ghali Karen , Jones Tim , Mutrie Nanette , Powell Jane , Preston John , Sahlqvist Shannon , Song Yena
Published: February 2012

Introduction

Improving infrastructure to support walking and cycling is often regarded as fundamental to encouraging their widespread uptake. However, there is little evidence that specific provision of this kind has led to a significant increase in walking or cycling in practice, let alone wider impacts such as changes in overall physical activity or carbon emissions. Connect2 is a major new project that aims to promote walking and cycling in the UK by improving local pedestrian and cycle routes. It therefore provides a useful opportunity to contribute new evidence in this field by means of a natural experimental study.

Methods and analysis

iConnect is an independent study that aims to integrate the perspectives of public health and transport research on the measurement and evaluation of the travel, physical activity and carbon impacts of the Connect2 programme. In this paper, the authors report the study design and methods for the iConnect core module. This comprised a cohort study of residents living within 5 km of three case study Connect2 projects in Cardiff, Kenilworth and Southampton, supported by a programme of qualitative interviews with key informants about the projects. Participants were asked to complete postal questionnaires, repeated before and after the opening of the new infrastructure, which collected data on demographic and socioeconomic characteristics, travel, car fuel purchasing and physical activity, and potential psychosocial and environmental correlates and mediators of those behaviours. In the absence of suitable no-intervention control groups, the study design drew on heterogeneity in exposure both within and between case study samples to provide for a counterfactual.

Ethics and dissemination

The study was approved by the University of Southampton Research Ethics Committee. The findings will be disseminated through academic presentations, peer-reviewed publications and the study website (http://www.iconnect.ac.uk) and by means of a national seminar at the end of the study.
Emergency department management of undifferentiated abdominal pain with hyoscine butylbromide and paracetamol: a randomised control trial
Authors: Remington-Hobbs Jennifer , Petts Gemma , Harris Tim
Published: February 2012

Objective

To compare the effectiveness of paracetamol, hyoscine butylbromide and the combination of paracetamol plus hyoscine butylbromide (paracetamol + hyoscine butylbromide) in the management of patients with acute undifferentiated abdominal pain attending the emergency department (ED).

Setting

A large teaching hospital with an annual ED census of 120 000 adult patients.

Methods

A prospective, randomised placebo controlled trial of a convenience sample of patients attending the ED. The trial compared the analgesic effect of intravenous hyoscine butylbromide, oral paracetamol and the combination of both drugs using a Visual Analogue Scale pain scoring tool. Rescue analgesia was administered when pain was inadequately controlled by trial medication.

Results

132 patients were recruited to the trial. At 30 min, all analgesic combinations produced significant similar levels of pain relief. At 60 min after administration of the trial medication, mean reductions in pain scores for patients receiving paracetamol only were significantly greater than those receiving paracetamol + hyoscine butylbromide (ANCOVA model, p=0.0180). No relationship was seen between treatment arm and the need for rescue analgesia (χ2, p value=0.846).

Conclusion

The trial data suggest that oral paracetamol is at least as effective as intravenous hyoscine butylbromide and a combination of both drugs in the management of acute undifferentiated abdominal pain presenting to the ED. Based on these results and factors such as cost and tolerability, we recommend single agent paracetamol as the agent of choice for the management of acute mild to moderate undifferentiated abdominal pain.

Trial registration number

MHRA Ref: 19717/0226/001-0001; European Clinical Trials Database. EUDRAct No: 2006-005395-40.
Intervention to reduce C-reactive protein determination requests for acute infections at an emergency department
Authors: Santos I S , Benseñor I M , Machado J B A , Fedeli L M G , Lotufo P A
Published: February 2012

Introduction

C-reactive protein (CRP) levels rise during inflammatory processes and have been ordered for rheumatic disease follow-up since the 1950s. The number of tests ordered in the emergency setting has increased, but without evident improvement in medical care quality.

Objective

To determine the pattern of CRP determinations in the emergency department (ED) of a university hospital in Sao Paulo, Brazil, and to evaluate the effect of an intervention with staff and students about the best use of the test in the ED.

Methods

Data regarding CRP testing requests, related diagnoses and the number of monthly consultations in the hospital ED were analysed before and after the intervention. Because of an increase in CRP measurement requests from 2007 to 2009, the author started discussing the role of CRP determinations in the medical decision-making process in early 2010. Staff and faculty members openly discussed the pattern of requests in the hospital and related current medical literature. During 2010, the medical staff worked as multipliers to change the behaviour of new students and residents. The results of the first 4 months after the intervention were presented at another general meeting in July 2010.

Results

From 2007 to 2009, there were 11 786 CRP measurement requests with a clear exponential trend. After the intervention, during the calendar year 2010, there was a 48% reduction in adjusted annual CRP requests. Pneumonia, fever and urinary tract infections were the most common reasons for CRP requests.

Discussion

Inexpensive, well-directed, interactive educational interventions may affect professional behaviour and curb rates of laboratory tests.