bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a Sequence-Characterized Amplified Region Marker-Targeted Quantitative PCR Assay for Strain-Specific Detection ofOenococcus oeniduring Wine Malolactic Fermentation
Authors: Solieri Lisa , Giudici Paolo
Published: October 2010

Control over malolactic fermentation (MLF) is a difficult goal in winemaking and needs rapid methods to monitorOenococcus oenimalolactic starters (MLS) in a stressful environment such as wine. In this study, we describe a novel quantitative PCR (QPCR) assay enabling the detection of anO. oenistrain during MLF without culturing.O. oenistrain LB221 was used as a model to develop a strain-specific sequence-characterized amplified region (SCAR) marker derived from a discriminatory OPA20-based randomly amplified polymorphic DNA (RAPD) band. The 5′ and 3′ flanking regions and the copy number of the SCAR marker were characterized using inverse PCR and Southern blotting, respectively. Primer pairs targeting the SCAR sequence enabled strain-specific detection without cross amplification of otherO. oenistrains or wine species of lactic acid bacteria (LAB), acetic acid bacteria (AAB), and yeasts. The SCAR-QPCR assay was linear over a range of cell concentrations (7 log units) and detected as few as 2.2 × 102CFU per ml of red wine with good quantification effectiveness, as shown by the correlation of QPCR and plate counting results. Therefore, the cultivation-independent monitoring of a singleO. oenistrain in wine based on a SCAR marker represents a rapid and effective strain-specific approach. This strategy can be adopted to develop easy and rapid detection techniques for monitoring the implantation of inoculatedO. oeniMLS on the indigenous LAB population, reducing the risk of unsuccessful MLF.
Impact of Metal Pollution and
Thlaspi caerulescens
Growth on Soil Microbial Communities
Authors: Epelde Lur , Becerril José M. , Kowalchuk George A. , Deng Ye , Zhou Jizhong , Garbisu Carlos
Published: October 2010

Soil microorganisms drive critical functions in plant-soil systems. As such, various microbial properties have been proposed as indicators of soil functioning, making them potentially useful in evaluating the recovery of polluted soils via phytoremediation strategies. To evaluate microbial responses to metal phytoextraction using hyperaccumulators, a microcosm experiment was carried out to study the impacts of Zn and/or Cd pollution and
Thlaspi caerulescens
growth on key soil microbial properties: basal respiration; substrate-induced respiration (SIR); bacterial community structure as assessed by PCR-denaturing gradient gel electrophoresis (DGGE); community sizes of total bacteria, ammonia-oxidizing bacteria, and chitin-degrading bacteria as assessed by quantitative PCR (Q-PCR); and functional gene distributions as determined by functional gene arrays (GeoChip).
T. caerulescens
proved to be suitable for Zn and Cd phytoextraction: shoots accumulated up to 8,211 and 1,763 mg kg
−1
(dry weight [DW]) of Zn and Cd, respectively. In general, Zn pollution led to decreased levels of basal respiration and ammonia-oxidizing bacteria, while
T. caerulescens
growth increased the values of substrate-induced respiration (SIR) and total bacteria. In soils polluted with 1,000 mg Zn kg
−1
and 250 mg Cd kg
−1
(DW), soil bacterial community profiles and the distribution of microbial functional genes were most affected by the presence of metals. Metal-polluted and planted soils had the highest percentage of unique genes detected via the GeoChip (35%). It was possible to track microbial responses to planting with
T. caerulescens
and to gain insight into the effects of metal pollution on soilborne microbial communities.
Proposed Modifications of Environmental Protection Agency Method 1601 for Detection of Coliphages in Drinking Water, with Same-Day Fluorescence-Based Detection and Evaluation by the Performance-Based Measurement System and Alternative Test Protocol Validation Approaches
Authors: Salter Robert S. , Durbin Gregory W. , Conklin Ernestine , Rosen Jeff , Clancy Jennifer
Published: October 2010

Coliphages are microbial indicators specified in the Ground Water Rule that can be used to monitor for potential fecal contamination of drinking water. The Total Coliform Rule specifies coliform andEscherichia coliindicators for municipal water quality testing; thus, coliphage indicator use is less common and advances in detection methodology are less frequent. Coliphages are viral structures and, compared to bacterial indicators, are more resistant to disinfection and diffuse further distances from pollution sources. Therefore, coliphage presence may serve as a better predictor of groundwater quality. This study describes Fast Phage, a 16- to 24-h presence/absence modification of U.S. Environmental Protection Agency (EPA) Method 1601 for detection of coliphages in 100 ml water. The objective of the study is to demonstrate that the somatic and male-specific coliphage modifications provide results equivalent to those of Method 1601. Five laboratories compared the modifications, featuring same-day fluorescence-based prediction, to Method 1601 by using the performance-based measurement system (PBMS) criterion. This requires a minimum 50% positive response in 10 replicates of 100-ml water samples at coliphage contamination levels of 1.3 to 1.5 PFU/100 ml. The laboratories showed that Fast Phage meets PBMS criteria with 83.5 to 92.1% correlation of the same-day rapid fluorescence-based prediction with the next-day result. Somatic coliphage PBMS data are compared to manufacturer development data that followed the EPA alternative test protocol (ATP) validation approach. Statistical analysis of the data sets indicates that PBMS utilizes fewer samples than does the ATP approach but with similar conclusions. Results support testing the coliphage modifications by using an EPA-approved national PBMS approach with collaboratively shared samples.
Adaptation to Cold and Proteomic Responses of the Psychrotrophic Biopreservative
Lactococcus piscium
Strain CNCM I-4031
Authors: Garnier Matthieu , Matamoros Sebastien , Chevret Didier , Pilet Marie-France , Leroi Francoise , Tresse Odile
Published: October 2010

There is considerable interest in the use of psychrotrophic bacteria for food biopreservation and in the understanding of cold adaptation mechanisms. The psychrotrophic biopreservative
Lactococcus piscium
strain CNCM I-4031 was studied for its growth behavior and proteomic responses after cold shock and during cold acclimation. Growth kinetics highlighted the absence of growth latency after cold shock, suggesting a very high promptness in cold adaptation, a behavior that has never been described before for lactic acid bacteria (LAB). A comparative proteomic analysis was applied with two-dimensional gel electrophoresis (2-DE), and upregulated proteins were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Both cold shock and cold acclimation triggered the upregulation of proteins involved in general and oxidative stress responses and fatty acid and energetic metabolism. However, 2-DE profiles and upregulated proteins were different under both conditions, suggesting a sequence of steps in cold adaptation. In addition, the major 7-kDa Csp protein was identified in the
L. piscium
CNCM I-4031 genome but was not cold regulated. The implication of the identified cold shock proteins and cold acclimation proteins in efficient cold adaptation, the possible regulation of a histidyl phosphocarrier protein, and the roles of a constitutive major 7-kDa Csp are discussed.
Synthetic Riboswitches That Induce Gene Expression in Diverse Bacterial Species
Authors: Topp Shana , Reynoso Colleen M. K. , Seeliger Jessica C. , Goldlust Ian S. , Desai Shawn K. , Murat Dorothée , Shen Aimee , Puri Aaron W. , Komeili Arash , Bertozzi Carolyn R. , Scott June R. , Gallivan Justin P.
Published: October 2010

We developed a series of ligand-inducible riboswitches that control gene expression in diverse species of Gram-negative and Gram-positive bacteria, including human pathogens that have few or no previously reported inducible expression systems. We anticipate that these riboswitches will be useful tools for genetic studies in a wide range of bacteria.
Development of a Versatile Procedure Based on Natural Transformation for Marker-Free Targeted Genetic Modification in
Streptococcus thermophilus
Authors: Fontaine Laetitia , Dandoy Damien , Boutry Céline , Delplace Brigitte , de Frahan Marie Henry , Fremaux Christophe , Horvath Philippe , Boyaval Patrick , Hols Pascal
Published: October 2010

A versatile natural transformation protocol was established for and successfully applied to 18 of the 19
Streptococcus thermophilus
strains tested. The efficiency of the protocol enables the use of
in vitro
-amplified mutagenesis fragments to perform deletion or insertion of large genetic fragments. Depending on the phenotype linked to the mutation, markerless mutants can be selected either in two steps, i.e., resistance marker insertion and excision using an adapted Cre-
loxP
system, or in one step using a powerful positive screening procedure as illustrated here for histidine prototrophy.
Metabolic Engineering of
Corynebacterium glutamicum
for 2-Ketoisovalerate Production
Authors: Krause Felix S. , Blombach Bastian , Eikmanns Bernhard J.
Published: October 2010

2-Ketoisovalerate is used as a therapeutic agent, and a 2-ketoisovalerate-producing organism may serve as a platform for products deriving from this 2-keto acid. We engineered the wild type of
Corynebacterium glutamicum
for the growth-decoupled production of 2-ketoisovalerate from glucose by deletion of the
aceE
gene encoding the E1p subunit of the pyruvate dehydrogenase complex, deletion of the transaminase B gene
ilvE
, and additional overexpression of the
ilvBNCD
genes, encoding the
l
-valine biosynthetic enzymes acetohydroxyacid synthase (AHAS), acetohydroxyacid isomeroreductase, and dihydroxyacid dehydratase. 2-Ketoisovalerate production was further improved by deletion of the pyruvate:quinone oxidoreductase gene
pqo
. In fed-batch fermentations at high cell densities, the newly constructed strains produced up to 188 ± 28 mM (21.8 ± 3.2 g liter
−1
) 2-ketoisovalerate and showed a product yield of about 0.47 ± 0.05 mol per mol (0.3 ± 0.03 g per g) of glucose and a volumetric productivity of about 4.6 ± 0.6 mM (0.53 ± 0.07 g liter
−1
) 2-ketoisovalerate per h in the overall production phase. In studying the influence of the three branched-chain 2-keto acids 2-ketoisovalerate, 2-ketoisocaproate, and 2-keto-3-methylvalerate on the AHAS activity, we observed a competitive inhibition of the AHAS enzyme by 2-ketoisovalerate.
Variability of
Bartonella
Genotypes among Small Mammals in Spain
Authors: Gil H. , García-Esteban C. , Barandika J. F. , Peig J. , Toledo A. , Escudero R. , Jado I. , Rodríguez-Vargas M. , García-Amil C. , Lobo B. , Roales P. , Rodríguez-Moreno I. , Olmeda A. S. , García-Pérez A. L. , Anda P.
Published: October 2010

In order to study which
Bartonella
genotypes are circulating among small mammals in Spain, we analyzed the spleens of 395 animals from three different areas—247 animals from the Basque Country (northern Spain), 121 animals from Catalonia (northeastern Spain), and 27 animals from Madrid (central Spain)—by a triplex PCR combined with a reverse line blot previously described by our group. The prevalence of
Bartonella
was 26.8% (106/395), and in 4.8% (19/395) of the animals more than one
Bartonella
genotype was detected. The study of
gltA
and the intergenic transcribed spacer in the positive samples demonstrated a large diversity, allowing the assignation of them into 22 genotypes. The most prevalent genotypes were 2 and 3, which are closely related to
Bartonella taylorii
. In addition, nine genotypes were associated with specific mammal species. Genotypes close to the zoonotic
Bartonella grahamii
,
Bartonella elizabethae
, and
Bartonella rochalimae
were also detected. Ten genotypes showed a percentage of similarity with known
Bartonella
species lower than 96%, suggesting the presence of potential new species. Further studies of the impact of these pathogens on human health and especially in cases of febrile illness in Spain are strongly recommended. Furthermore, our method has been updated with 21 new probes in a final panel of 36, which represents a robust molecular tool for clinical and environmental
Bartonella
studies.
Derepression ofINO1Transcription Requires Cooperation between the Ino2p-Ino4p Heterodimer and Cbf1p and Recruitment of the ISW2 Chromatin-Remodeling Complex
Authors: Shetty Ameet , Lopes John M.
Published: October 2010

TheSaccharomyces cerevisiaeINO1gene encodes the structural enzyme inositol-3-phosphate synthase for the synthesisde novoof inositol and inositol-containing phospholipids. The transcription ofINO1is completely derepressed in the absence of inositol and choline (I−C−). Derepression requires the binding of the Ino2p-Ino4p basic helix-loop-helix (bHLH) heterodimer to the UASINOpromoter element. We report here the requirement of a third bHLH protein, centromere-binding factor 1 (Cbf1p), for the complete derepression ofINO1transcription. We found that Cbf1p regulatesINO1transcription by binding to sites distal to theINO1promoter and encompassing the upstreamSNA3open reading frame (ORF) and promoter. The binding of Cbf1p requires Ino2p-Ino4p binding to the UASINOsites in theINO1promoter and vice versa, suggesting a cooperative mechanism. Furthermore, Cbf1p binding to the upstream sites was required for the binding of the ISW2 chromatin-remodeling complex to the Ino2p-Ino4p-binding sites on theINO1promoter. Consistent with this, ISW2 was also required for the complete derepression ofINO1transcription.
Suppressor Mutagenesis Identifies a Velvet Complex Remediator of Aspergillus nidulans Secondary Metabolism
Authors: Shaaban Mona I. , Bok Jin Woo , Lauer Carrie , Keller Nancy P.
Published: October 2010

Fungal secondary metabolites (SM) are bioactive compounds that are important in fungal ecology and, moreover, both harmful and useful in human endeavors (e.g., as toxins and pharmaceuticals). Recently a nuclear heterocomplex termed the Velvet complex, characterized in the model ascomyceteAspergillus nidulans, was found to be critical for SM production. Deletion of two members of the Velvet complex,laeAandveA, results in near loss of SM and defective sexual spore production inA. nidulansand other species. Using a multicopy-suppressor genetics approach, we have isolated anAspergillus nidulansgene namedrsmA(remediation of secondary metabolism) based upon its ability to remediate secondary metabolism in ΔlaeAand ΔveAbackgrounds. Overexpression ofrsmA(OE::rsmA) restores production of sterigmatocystin (ST) (a carcinogenic SM) via transcriptional activation of ST biosynthetic genes. However, defects in sexual reproduction in either ΔlaeAor ΔveAstrains cannot be overcome by OE::rsmA. An intact Velvet complex coupled with an OE::rsmAallele increases SM many fold over the wild-type level, but loss ofrsmAdoes not decrease SM. RsmA encodes a putative bZIP basic leucine zipper-type transcription factor.
Stressosomes Formed inBacillus subtilisfrom the RsbR Protein ofListeria monocytogenesAllow σBActivation following Exposure to either Physical or Nutritional Stress
Authors: Martinez Luis , Reeves Adam , Haldenwang William
Published: October 2010

The general stress regulon ofBacillus subtilisis controlled by σB, a transcription factor that is activated by physical or nutritional stress. InB. subtilis, each of these two stresses is communicated to the primary σBregulators by distinct pathways. Physical stress activation of σBinvolves a large-molecular-mass (>106-Da) structure (stressosome) formed by one or more homologous proteins (RsbRA, -B, -C, and -D) onto which the pathway's principal regulators are bound. The RsbR proteins are thought to be potential receptors for stress signaling.Listeria monocytogenesencodes orthologs of σBand its principal regulators; however, unlikeB. subtilis,L. monocytogenesappears to use the stressosome pathway for both physical and nutritional stress activation of σB. In the current work, aB. subtilisstrain that expressedL. monocytogenes rsbR(rsbRLm) in lieu ofB. subtilis rsbR(rsbRBs) was created and was found to display theListeriaphenotype of σBactivation following exposure to either physical or nutritional stress.B. subtilisexpressing either the RsbR paralogrsbRCorrsbRD, but notrsbRAorrsbRB, as the sole source of RsbR also allowed σBinduction following nutritional stress. It is unclear whether the nutritional stress induction seen in these strains is the result of a direct effect of nutritional stress on stressosome activity or a consequence of the background levels of σBactivation in these strains and the effects of diminished ATP on the downstream phosphorylation reaction needed to reinactivate σB.
Silent Mischief: Bacteriophage Mu Insertions Contaminate Products of
Escherichia coli
Random Mutagenesis Performed Using Suicidal Transposon Delivery Plasmids Mobilized by Broad-Host-Range RP4 Conjugative Machinery
Authors: Ferrières Lionel , Hémery Gaëlle , Nham Toan , Guérout Anne-Marie , Mazel Didier , Beloin Christophe , Ghigo Jean-Marc
Published: October 2010

Random transposon mutagenesis is the strategy of choice for associating a phenotype with its unknown genetic determinants. It is generally performed by mobilization of a conditionally replicating vector delivering transposons to recipient cells using broad-host-range RP4 conjugative machinery carried by the donor strain. In the present study, we demonstrate that bacteriophage Mu, which was deliberately introduced during the original construction of the widely used donor strains SM10 λ
pir
and S17-1 λ
pir
, is silently transferred to
Escherichia coli
recipient cells at high frequency, both by
hfr
and by release of Mu particles by the donor strain. Our findings suggest that bacteriophage Mu could have contaminated many random-mutagenesis experiments performed on Mu-sensitive species with these popular donor strains, leading to potential misinterpretation of the transposon mutant phenotype and therefore perturbing analysis of mutant screens. To circumvent this problem, we precisely mapped Mu insertions in SM10 λ
pir
and S17-1 λ
pir
and constructed a new Mu-free donor strain, MFD
pir
, harboring stable
hfr-
deficient RP4 conjugative functions and sustaining replication of Π-dependent suicide vectors. This strain can therefore be used with most of the available transposon-delivering plasmids and should enable more efficient and easy-to-analyze mutant hunts in
E. coli
and other Mu-sensitive RP4 host bacteria.
Crl Binds to Domain 2 of σ
S
and Confers a Competitive Advantage on a Natural
rpoS
Mutant of
Salmonella enterica
Serovar Typhi
Authors: Monteil Véronique , Kolb Annie , Mayer Claudine , Hoos Sylviane , England Patrick , Norel Françoise
Published: October 2010

The RpoS sigma factor (σ
S
) is the master regulator of the bacterial response to a variety of stresses. Mutants in
rpoS
arise in bacterial populations in the absence of stress, probably as a consequence of a subtle balance between self-preservation and nutritional competence. We characterized here one natural
rpoS
mutant of
Salmonella enterica
serovar Typhi (Ty19). We show that the
rpoS
allele of Ty19 (
rpoS
Ty19
) led to the synthesis of a σ
S
Ty19
protein carrying a single glycine-to-valine substitution at position 282 in σ
S
domain 4, which was much more dependent than the wild-type σ
S
protein on activation by Crl, a chaperone-like protein that increases the affinity of σ
S
for the RNA polymerase core enzyme (E). We used the bacterial adenylate cyclase two-hybrid system to demonstrate that Crl bound to residues 72 to 167 of σ
S
domain 2 and that G282V substitution did not directly affect Crl binding. However, this substitution drastically reduced the ability of σ
S
Ty19
to bind E in a surface plasmon resonance assay, a defect partially rescued by Crl. The modeled structure of the Eσ
S
holoenzyme suggested that substitution G282V could directly disrupt a favorable interaction between σ
S
and E. The
rpoS
Ty19
allele conferred a competitive fitness when the bacterial population was wild type for
crl
but was outcompeted in Δ
crl
populations. Thus, these results indicate that the competitive advantage of the
rpoS
Ty19
mutant is dependent on Crl and suggest that
crl
plays a role in the appearance of
rpoS
mutants in bacterial populations.
GlpR Represses Fructose and Glucose Metabolic Enzymes at the Level of Transcription in the HaloarchaeonHaloferax volcanii
Authors: Rawls Katherine S. , Yacovone Shalane K. , Maupin-Furlow Julie A.
Published: October 2010

In this study, a DeoR/GlpR-type transcription factor was investigated for its potential role as a global regulator of sugar metabolism in haloarchaea, usingHaloferax volcaniias a model organism. Common to a number of haloarchaea and Gram-positive bacterial species, the encodingglpRgene was chromosomally linked with genes of sugar metabolism. InH. volcanii,glpRwas cotranscribed with the downstream phosphofructokinase (PFK;pfkB) gene, and the transcript levels of thisglpR-pfkBoperon were 10- to 20-fold higher when cells were grown on fructose or glucose than when they were grown on glycerol alone. GlpR was required for repression on glycerol based on significant increases in the levels of PFK (pfkB) transcript and enzyme activity detected upon deletion ofglpRfrom the genome. Deletion ofglpRalso resulted in significant increases in both the activity and the transcript (kdgK1) levels of 2-keto-3-deoxy-d-gluconate kinase (KDGK), a key enzyme of haloarchaeal glucose metabolism, when cells were grown on glycerol, compared to the levels obtained for media with glucose. Promoter fusions to a β-galactosidasebgaHreporter revealed that transcription ofglpR-pfkBandkdgK1was modulated by carbon source and GlpR, consistent with quantitative reverse transcription-PCR (qRT-PCR) and enzyme activity assays. The results presented here provide genetic and biochemical evidence that GlpR controls both fructose and glucose metabolic enzymes through transcriptional repression of theglpR-pfkBoperon andkdgK1during growth on glycerol.
Regulation of CodY Activity through Modulation of Intracellular Branched-Chain Amino Acid Pools
Authors: Brinsmade Shaun R. , Kleijn Roelco J. , Sauer Uwe , Sonenshein Abraham L.
Published: October 2010

In several Gram-positive bacterial species, the global transcriptional regulatory protein CodY adjusts the expression of many metabolic genes, apparently in response to changes in the pools of specific metabolites, i.e., the branched-chain amino acids (BCAAs) isoleucine, leucine, and valine (ILV) and the nucleoside triphosphate GTP. CodY not only responds to these metabolites as measuredin vitrobut also regulates the genes that direct their synthesis. We have constructed a set of strains lacking binding sites for the CodY protein incisat loci coding for the ILV biosynthetic machinery, effectively overexpressing these genes in an attempt to modulate the ILV input signal to CodY. Metabolite analyses of strains derepressed for genes needed for ILV synthesis revealed more than a 6-fold increase in the valine pool and a 2-fold increase in the isoleucine and leucine pools. Accumulation of the branched-chain amino acids was accompanied by a 24-fold induction of thebkdoperon (required for branched-chain fatty acid synthesis) and 6-fold hyperrepression of the CodY-regulatedyhdGandyufNgenes, demonstrating that CodY perceives intracellular fluctuations in at least one if its input signals. We conclude that changes in the rate of endogenous ILV synthesis serve as an important signal for CodY-mediated gene regulation.
Evolution and Population Structure of
Salmonella enterica
Serovar Newport
Authors: Sangal Vartul , Harbottle Heather , Mazzoni Camila J. , Helmuth Reiner , Guerra Beatriz , Didelot Xavier , Paglietti Bianca , Rabsch Wolfgang , Brisse Sylvain , Weill François-Xavier , Roumagnac Philippe , Achtman Mark
Published: October 2010

Salmonellosis caused by
Salmonella enterica
serovar Newport is a major global public health concern, particularly because
S.
Newport isolates that are resistant to multiple drugs (MDR), including third-generation cephalosporins (MDR-AmpC phenotype), have been commonly isolated from food animals. We analyzed 384
S.
Newport isolates from various sources by a multilocus sequence typing (MLST) scheme to study the evolution and population structure of the serovar. These were compared to the population structure of
S. enterica
serovars Enteritidis, Kentucky, Paratyphi B, and Typhimurium. Our
S.
Newport collection fell into three lineages, Newport-I, Newport-II, and Newport-III, each of which contained multiple sequence types (STs). Newport-I has only a few STs, unlike Newport-II or Newport-III, and has possibly emerged recently. Newport-I is more prevalent among humans in Europe than in North America, whereas Newport-II is preferentially associated with animals. Two STs of Newport-II encompassed all MDR-AmpC isolates, suggesting recent global spread after the acquisition of the
bla
CMY-2
gene. In contrast, most Newport-III isolates were from humans in North America and were pansusceptible to antibiotics. Newport was intermediate in population structure to the other serovars, which varied from a single monophyletic lineage in
S.
Enteritidis or
S.
Typhimurium to four discrete lineages within
S.
Paratyphi B. Both mutation and homologous recombination are responsible for diversification within each of these lineages, but the relative frequencies differed with the lineage. We conclude that serovars of
S. enterica
provide a variety of different population structures.
Genome Sequence of the Polysaccharide-Degrading, Thermophilic AnaerobeSpirochaeta thermophilaDSM 6192
Authors: Angelov Angel , Liebl Susanne , Ballschmiter Meike , Bömeke Mechthild , Lehmann Rüdiger , Liesegang Heiko , Daniel Rolf , Liebl Wolfgang
Published: October 2010

Spirochaeta thermophilais a thermophilic, free-living anaerobe that is able to degrade various α- and β-linked sugar polymers, including cellulose. We report here the complete genome sequence ofS. thermophilaDSM 6192, which is the first genome sequence of a thermophilic, free-living member of theSpirochaetesphylum. The genome data reveal a high density of genes encoding enzymes from more than 30 glycoside hydrolase families, a noncellulosomal enzyme system for (hemi)cellulose degradation, and indicate the presence of a novel carbohydrate-binding module.
Whole-Genome Sequences of Thirteen Isolates of
Borrelia burgdorferi
Authors: Schutzer Steven E. , Fraser-Liggett Claire M. , Casjens Sherwood R. , Qiu Wei-Gang , Dunn John J. , Mongodin Emmanuel F. , Luft Benjamin J.
Published: October 2010

Borrelia burgdorferi
is a causative agent of Lyme disease in North America and Eurasia. The first complete genome sequence of
B. burgdorferi
strain 31, available for more than a decade, has assisted research on the pathogenesis of Lyme disease. Because a single genome sequence is not sufficient to understand the relationship between genotypic and geographic variation and disease phenotype, we determined the whole-genome sequences of 13 additional
B. burgdorferi
isolates that span the range of natural variation. These sequences should allow improved understanding of pathogenesis and provide a foundation for novel detection, diagnosis, and prevention strategies.
Emergence of
Pseudomonas aeruginosa
Strains Producing High Levels of Persister Cells in Patients with Cystic Fibrosis
Authors: Mulcahy Lawrence R. , Burns Jane L. , Lory Stephen , Lewis Kim
Published: October 2010

The majority of cystic fibrosis (CF) patients succumb to a chronic infection of the airway with
Pseudomonas aeruginosa
. Paradoxically, pathogenic strains are often susceptible to antibiotics, but the infection cannot be eradicated with antimicrobial therapy. We find that in a majority of patients with airway infections, late isolates of
P. aeruginosa
produce increased levels of drug-tolerant persister cells. The genomes of a clonal pair of early/late isolates from a single patient have been previously sequenced, and the late isolate (obtained at age 96 months) showed a 100-fold increase in persister levels. The 96-month isolate carries a large number of mutations, including a mutation in
mutS
that confers a hypermutator phenotype. There is also a mutation in the
mexZ
repressor controlling the expression of the MexXY-OprM multidrug pump, which results in a moderate increase in the ofloxacin, carbenicillin, and tobramycin MICs. Knocking out the
mexXY
locus restored the resistance to that of the parent strain but did not affect the high levels of persisters formed by the 96-month isolate. This suggests that the late isolate is a high-persister (
hip
) mutant. Increased persister formation was observed in exponential phase, stationary phase, and biofilm populations of the 96-month isolate. Analysis of late isolates from 14 additional patients indicated that 10 of them are
hip
mutants. Most of these
hip
mutants did not have higher drug resistance. Increased persister formation appears to be their sole mechanism for surviving chemotherapy. Taken together, these findings suggest a link between persisters and recalcitrance of CF infection and identify an overlooked culprit—high-persister mutants producing elevated levels of drug-tolerant cells. Persisters may play a similarly critical role in the recalcitrance of other chronic infections.
A prospective evaluation of air quality and workers' health in broiler and layer operations
Authors: Senthilselvan Ambikaipakan , Beach Jeremy , Feddes John , Cherry Nicola , Wenger Irene
Published: October 2010

Objectives

In developed countries, poultry are raised in totally confined buildings in which workers are exposed to indoor airborne contaminants. A prospective study was conducted to investigate the relationship between workers' respiratory health and airborne contaminants during the life cycle of broiler and layer flocks.

Methods

Seventeen layer and 16 broiler operations were chosen within a 200 km radius of Edmonton. An attempt was made to visit each broiler operation twice during the winter and summer seasons in the early and later periods of the 6-week production cycle and visit each layer operation three times during the early, middle and later periods of the 40-week production cycle.

Results

In broiler operations, respirable particle counts, total dust and endotoxin concentrations, and ammonia levels increased with flock age, while mean endotoxin load (EU/mg) decreased in the winter and summer seasons. Increases in dust and endotoxin concentrations in the winter season were not statistically significance. Mean endotoxin concentration increased and mean dust concentration and ammonia level decreased with flock age in layer operations, although not all these changes were statistically significant. Mean across-shift decrements in FEV1and FVC increased with flock age among workers from layer operations. Endotoxin concentration was significantly associated with across-shift changes in FEV1among workers in layer operations.

Conclusion

In our study, changes in lung function appear more closely associated with changes in endotoxin than other contaminants. Changes in indoor environmental conditions occurring in poultry barns which are dependent on the flock age may affect workers' health in poultry operations.
The risk of hospitalisation for infectious pneumonia in mineral dust exposed industries: Table 1
Authors: Koh Dong-Hee , Moon Ki-Tae , Kim Jeong-Youn , Choe Seong-Weon
Published: October 2010

Objectives

The purpose of the study was to elucidate the relationship between industries characterised by mineral dust exposure and infectious pneumonia.

Methods

The authors applied a retrospective record linkage design and used the nationwide specific health examination database and identified industries where mineral dust exposure occurs and a control group composed of workers who had been exposed to noise-only during a 2000–2004 period. The database was matched with National Health Insurance claim records to identify pneumonia admissions from 2000 to 2005. The indirectly standardised admission ratios (SARs) for pneumonia admissions were estimated by comparing mineral dust exposed industry workers with noise-only exposed workers.

Results

The authors found significantly elevated SARs in both men (1.54, 95% CI 1.13 to 2.05) and women (3.23, 95% CI 1.40 to 6.37) working in the cement, lime, plaster and plaster products industries, and only in men working in the cast-metals industry (foundry) (1.64, 95% CI 1.25 to 2.11).

Conclusions

These results support the association between mineral dust exposure, as well as metal fumes, and infectious pneumonia.
Hand-arm vibration syndrome among a group of construction workers in Malaysia
Authors: Su Ting Anselm , Hoe Victor Chee Wai , Masilamani Retneswari , Awang Mahmud Awang Bulgiba
Published: October 2010

Objectives

To determine the extent of hand transmitted vibration exposure problems, particularly hand-arm vibration syndrome (HAVS), among construction workers in Malaysia.

Methods

A cross-sectional study was conducted on a construction site in Kuala Lumpur, Malaysia. 243 workers were recruited. Questionnaire interviews and hand examinations were administered to 194 respondents. Vibration magnitudes for concrete breakers, drills and grinders were measured using a 3-axis accelerometer. Clinical outcomes were compared and analysed according to vibration exposure status.

Results

Vibration total values for concrete breakers, impact drills and grinders were 10.02 ms−2, 7.72 ms−2and 5.29 ms−2, respectively. The mean 8 h time-weighted hand transmitted vibration exposure, A(8), among subjects on current and previous construction sites was 7.52 (SD 2.68) ms−2and 9.21 (SD 2.48) ms−2, respectively. Finger tingling, finger numbness, musculoskeletal problems of the neck, finger coldness, abnormal Phalen's test and abnormal light touch sensation were significantly more common in the high vibration exposure group (n=139) than the low–moderate vibration exposure group (n=54). Mean total lifetime vibration dose among exposed subjects was 15.2 (SD 3.2) m2h3s−4(ln scale). HAVS prevalence was 18% and the prevalence ratio of stage 1 and higher disease in the high vibration exposure group versus the low–moderate vibration exposure group was 4.86 (95% CI 1.19 to 19.80).

Conclusions

Hand transmitted vibration is a recognisable problem in tropical countries including Malaysia. The current study has identified clinical symptoms and signs suggesting HAVS among construction workers exposed to hand transmitted vibration in a warm environment.
Prospective study of incident injuries among southeastern United States commercial fishermen
Authors: Kucera Kristen L , Loomis Dana , Lipscomb Hester , Marshall Stephen W
Published: October 2010

Objective

The purpose of this study was to describe occupational exposures and the incidence of non-fatal injuries among a group of southeastern US small-scale fishermen.

Methods

Participants (n=219) were enrolled in a prospective cohort study and followed from August 1999 to May 2002. Demographic information was obtained at baseline, and weekly and biweekly telephone interviews elicited information on number of days worked, fishery, fishing gear used, maintenance work, glove use and any work-related injury events. Incidence rate ratios (IRR) and 95% CIs were calculated with Poisson regression for each factor and multivariate models controlled for potential confounders.

Results

Over a third of participants (81/217) reported 125 injury events over 46 153 work-days for rate of 2.74 per 1000 work-days (95% CI 2.19 to 3.41). The majority of injuries were penetrating wounds to the hand, thumb and finger (35%) or back sprains and strains (8%); most required no medical care or time off work (67%). Injury rates were similar for on and off the water work (1.9 per 1000 work-days). Injury rates differed by fishery, water location and month. Factors associated with an increased injury rate included working on someone else's boat and maintenance work. Glove use was protective.

Conclusion

Similar injury characteristics were observed in small-scale fishing as compared to large-scale. For small-scale fishermen, off and on the water work locations, and particularly maintenance work, were important predictors of injury. Despite the protective association for glove use, penetrating wounds to the hand, thumb and finger were common.
Differences in blood pressure and vascular responses associated with ambient fine particulate matter exposures measured at the personal versus community level
Authors: Brook Robert D , Bard Robert L , Burnett Richard T , Shin Hwashin H , Vette Alan , Croghan Carry , Phillips Michael , Rodes Charles , Thornburg Jonathan , Williams Ron
Published: October 2010

Background

Higher ambient fine particulate matter (PM2.5) levels can be associated with increased blood pressure and vascular dysfunction.

Objectives

To determine the differential effects on blood pressure and vascular function of daily changes in community ambient- versus personal-level PM2.5measurements.

Methods

Cardiovascular outcomes included vascular tone and function and blood pressure measured in 65 non-smoking subjects. PM2.5exposure metrics included 24 h integrated personal- (by vest monitors) and community-based ambient levels measured for up to 5 consecutive days (357 observations). Associations between community- and personal-level PM2.5exposures with alterations in cardiovascular outcomes were assessed by linear mixed models.

Results

Mean daily personal and community measures of PM2.5were 21.9±24.8 and 15.4±7.5 μg/m3, respectively. Community PM2.5levels were not associated with cardiovascular outcomes. However, a 10 μg/m3increase in total personal-level PM2.5exposure (TPE) was associated with systolic blood pressure elevation (+1.41 mm Hg; lag day 1, p<0.001) and trends towards vasoconstriction in subsets of individuals (0.08 mm; lag day 2 among subjects with low secondhand smoke exposure, p=0.07). TPE and secondhand smoke were associated with elevated systolic blood pressure on lag day 1. Flow-mediated dilatation was not associated with any exposure.

Conclusions

Exposure to higher personal-level PM2.5during routine daily activity measured with low-bias and minimally-confounded personal monitors was associated with modest increases in systolic blood pressure and trends towards arterial vasoconstriction. Comparable elevations in community PM2.5levels were not related to these outcomes, suggesting that specific components within personal and background ambient PM2.5may elicit differing cardiovascular responses.
Associations of occupation, job control and job demands with intima-media thickness: The Multi-Ethnic Study of Atherosclerosis (MESA)
Authors: Fujishiro Kaori , Diez Roux Ana V , Landsbergis Paul , Baron Sherry , Barr R Graham , Kaufman Joel D , Polak Joseph F , Stukovsky Karen Hinckley
Published: October 2010

Objectives

Occupation has been linked to cardiovascular disease (CVD) incidence and mortality, but few studies have investigated occupation in relation to early atherosclerotic disease. This study examined associations between various occupational characteristics and carotid artery intima-media thickness (IMT) in a multi-ethnic sample.

Methods

The Multi-Ethnic Study of Atherosclerosis (MESA) recruited 6814 adults aged 45–84 years and free of clinical CVD (response rate 60%, 51% female). Questionnaire data were used to determine occupational group (managerial/professional, sales/office, service, blue-collar), psychosocial job characteristics (ie, job demands, job control) and other sociodemographic information.

Results

Common carotid artery (CCA)-IMT was greater for blue-collar jobs than for management/professional jobs (mean difference=0.012 mm, p=0.049) after adjustment for age, sex, race, place of birth (US or foreign born) and CVD risk factors. Compared to management/professional jobs, internal carotid artery (ICA)-IMT was greater for sales/office, service and blue-collar jobs (mean difference=0.071 mm, p<0.001; 0.057 mm, p=0.009; and 0.110 mm, p<0.001, respectively) after adjustment for age, sex, race and place of birth. The difference between blue-collar jobs and management/professional jobs remained significant after additional adjustment for CVD risk factors, income and education (mean difference=0.048 mm, p=0.045). Higher levels of control at work were associated with thinner CCA-IMT (mean difference=−0.009 mm, p=0.016, adjusted for age, sex, race and place of birth) but not with ICA-IMT. Job demands had no significant association with IMT.

Conclusions

Blue-collar jobs and low levels of job control were associated with the development of subclinical atherosclerosis.
A prospective study of floor surface, shoes, floor cleaning and slipping in US limited-service restaurant workers
Authors: Verma Santosh K , Chang Wen Ruey , Courtney Theodore K , Lombardi David A , Huang Yueng-Hsiang , Brennan Melanye J , Mittleman Murray A , Ware James H , Perry Melissa J
Published: October 2010

Objectives

Slips and falls are a leading cause of injury at work. Few studies, however, have systematically examined risk factors of slipping outside the laboratory environment. This study examined the association between floor surface characteristics, slip-resistant shoes, floor cleaning frequency and the risk of slipping in limited-service restaurant workers.

Methods

475 workers from 36 limited-service restaurants from three major chains in six states in the USA were recruited to participate in a prospective cohort study of workplace slipping. Kitchen floor surface roughness and coefficient of friction (COF) were measured in eight working areas and then averaged within each restaurant. The use of slip-resistant shoes was determined by examining the participant's shoes and noting the presence of a ‘slip-resistant’ marking on the sole. Restaurant managers reported the frequency of daily kitchen floor cleaning. Participants reported their slip experience and work hours weekly for up to 12 weeks. The survey materials were made available in three languages: English, Spanish and Portuguese. The associations between rate of slipping and risk factors were assessed using a multivariable negative binomial generalised estimating equation model.

Results

The mean of individual slipping rate varied among the restaurants from 0.02 to 2.49 slips per 40 work hours. After adjusting for age, gender, BMI, education, primary language, job tenure and restaurant chain, the use of slip-resistant shoes was associated with a 54% reduction in the reported rate of slipping (95% CI 37% to 64%), and the rate of slipping decreased by 21% (95% CI 5% to 34%) for each 0.1 increase in the mean kitchen COF. Increasing floor cleaning frequency was significantly associated with a decreasing rate of slipping when considered in isolation but not after statistical adjustment for other factors.

Conclusion

These results provide support for the use of slip-resistant shoes and measures to increase COF as preventive interventions to reduce slips, falls and injuries.
Occupational kidney disease among Chinese herbalists exposed to herbs containing aristolochic acids
Authors: Yang Hsiao-Yu , Wang Jung-Der , Lo Tsai-Chang , Chen Pau-Chung
Published: October 2010

Objective

Many Chinese herbs contain aristolochic acids (ALAs) which are nephrotoxic and carcinogenic. The objective of this study was to identify whether exposure to herbs containing ALAs increased the risk of kidney disease among Chinese herbalists.

Methods

A nested case–control study was carried out on 6538 Chinese herbalists registered between 1985 and 1998. All incident cases of chronic renal failure reported to the Database of Catastrophic Illness of the National Health Insurance Bureau between 1995 and 2000 were defined as the case group. Up to four controls without renal failure were randomly matched to each case by sex and year of birth. A structured questionnaire survey was administered between November and December 2002. The Mantel–Haenszel method and conditional logistic regression were used to estimate the risks.

Results

40 cases and 98 matched controls were included in the final analysis. After adjusting for age, frequent analgesic use, and habitual consumption of alcohol, fermented or smoked food, we found manufacturing and selling Chinese herbal medicine (OR 3.43, 95% CI 1.16 to 10.19), processing, selling or dispensing herbal medicines containing Fangji (OR 4.17, 95% CI 1.36 to 12.81), living in the workplace (OR 3.14, 95% CI 1.11 to 8.84) and a history of taking of herbal medicines containing Fangji (frequently or occasionally) (OR 5.42, 95% CI 1.18 to 24.96) were significantly associated with renal failure.

Conclusion

Occupational exposure to and consumption of herbs containing ALAs increases the risk of renal failure in Chinese herbalists.
Tropical liver fluke‐induced stress in experimentally infected and immunised buffaloes
Authors: Edith R. , Thilagar M. B. , Godara R. , Sharma R. L.
Published: October 2010

Disease‐related stress associated with Fasciola gigantica infection was investigated in 16 male, yearling Murrah buffaloes. The animals were randomly assigned to one of four groups. Animals in groups 1 and 2 were vaccinated subcutaneously with 4.8 mg of excretory‐secretory antigen (group 1) or 1300 μg infection‐specific antigen (group 2), in three doses. Subsequently, all the animals in groups 1, 2 and 3 were infected orally with 800 viable F gigantica metacercariae (bubaline origin) on week 6 of the experiment. The animals in group 4 served as healthy controls. The clinical progress of the disease with respect to the adrenocortical response to infection was assessed periodically. The infected animals in group 3 developed characteristic signs of the disease and had the highest in situ fluke population (mean [se] 331.8 [19.5]). One of the four animals in group 3 died on day 110 postinfection (PI). Animals that had been immunised before infection (groups 1 and 2) acquired adequate levels of immunity, were comparatively healthier and had significantly lower (P<0.05) fluke populations (mean [se] 194.3 [11.8] in group 1 and 164.5 [9.2] in group 2). Throughout the course of the disease, the group 3 animals had significantly higher cortisol levels than those in groups 1 and 2 (P<0.01) from week 4 PI onward. Although animals in the immunised groups (groups 1 and 2) had increased hormone levels, they were not significantly different from those in the control animals in group 4. Cortisol levels were higher during the early prepatency phase (weeks 1 to 6 PI) than during the late prepatency and/or patency phases of the disease. Cortisol levels in the healthy control animals in group 4 remained within the normal range.
Guarding the welfare of farm animals
Authors: Wathes Christopher
Published: October 2010

Who should be the guardian of farm animal welfare? Christopher Wathes, chairman of the Farm Animal Welfare Council, argues that guardianship is a duty of Government, acting on behalf of British citizens.