bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors Associated withSalmonellaPresence in Environmental Samples and Bulk Tank Milk from US Dairies
Authors: Ruzante J. M. , Lombard J. E. , Wagner B. , Fossler C. P. , Karns J. S. , Van Kessel J. A. S. , Gardner I. A. 
Published: May 2010

SummaryThe objective of this study was to evaluate herd characteristics and management practices associated with presence ofSalmonellain the farm environment and in bulk tank milk (BTM) in US dairy herds. Herd management data, environmental culture, BTM and in‐line milk filter polymerase chain reaction results forSalmonellafrom 260 US dairy herds surveyed during the National Animal Health Monitoring System Dairy 2007 study were analysed. Herd characteristics and management practices were screened by univariate analysis, and selected variables were used to construct a logistic regression model to identify factors associated with the presence ofSalmonellain environmental samples. To identify factors associated with the occurrence ofSalmonellain BTM and milk filters,a prioriselected variables that were related to milking procedures were analysed univariately and a logistic regression model was constructed. The presence ofSalmonellain the farm environment was associated with location of the operation in the East (OR = 4.8; CI: 1.9–11.6), not using a broadcast manure spreader (OR = 3.2; CI: 1.4–7.5), use of bovine somatotropin (BST) (OR = 2.7; CI: 1.5–5.0) and use of anionic salts (OR = 2.2; CI: 1.2–3.9). In the final multivariable model, herds with fewer than 100 cows were at decreased odds (OR = 0.3; CI: 0.1–0.7) of being culture positive forSalmonellaas were herds with between 100 and 499 cows (OR = 0.4; CI: 0.2–0.8) compared with herds having 500 or more cows. The presence of culture‐positive environmental samples and herd size were significantly associated withSalmonellaBTM contamination. The herd‐level factors identified in this study were in agreement with prior studies but also identified other potential factors that can be targeted inSalmonellacontrol programmes.
Structural and Functional Characterization of Diffusible Signal Factor Family Quorum-Sensing Signals Produced by Members of the
Burkholderia cepacia
Complex
Authors: Deng Yinyue , Wu Ji'en , Eberl Leo , Zhang Lian-Hui 
Published: May 2010

ABSTRACT

Previous work has shown that
Burkholderia cenocepacia
produces the diffusible signal factor (DSF) family signal
cis
-2-dodecenoic acid (C
12
:Δ
2
, also known as BDSF), which is involved in the regulation of virulence. In this study, we determined whether C
12
:Δ
2
production is conserved in other members of the
Burkholderia cepacia
complex (Bcc) by using a combination of high-performance liquid chromatography, mass spectrometry, and bioassays. Our results show that five Bcc species are capable of producing C
12
:Δ
2
as a sole DSF family signal, while four species produce not only C
12
:Δ
2
but also a new DSF family signal, which was identified as
cis
,
cis
-11-methyldodeca-2,5-dienoic acid (11-Me-C
12
:Δ
2,5
). In addition, we demonstrate that the quorum-sensing signal
cis
-11-methyl-2-dodecenoic acid (11-Me-C
12
:Δ
2
), which was originally identified in
Xanthomonas campestris
supernatants, is produced by
Burkholderia multivorans
. It is shown that, similar to 11-Me-C
12
:Δ
2
and C
12
:Δ
2
, the newly identified molecule 11-Me-C
12
:Δ
2,5
is a potent signal in the regulation of biofilm formation, the production of virulence factors, and the morphological transition of
Candida albicans
. These data provide evidence that DSF family molecules are highly conserved bacterial cell-cell communication signals that play key roles in the ecology of the organisms that produce them.
Engineering of
Clostridium phytofermentans
Endoglucanase Cel5A for Improved Thermostability
Authors: Liu Wenjin , Zhang Xiao-Zhou , Zhang Zuoming , Zhang Y.-H. Percival 
Published: May 2010

ABSTRACT

A family 5 glycoside hydrolase from
Clostridium phytofermentans
was cloned and engineered through a cellulase cell surface display system in
Escherichia coli
. The presence of cell surface anchoring, a cellulose binding module, or a His tag greatly influenced the activities of wild-type and mutant enzymes on soluble and solid cellulosic substrates, suggesting the high complexity of cellulase engineering. The best mutant had 92%, 36%, and 46% longer half-lives at 60°C on carboxymethyl cellulose, regenerated amorphous cellulose, and Avicel, respectively.
Acinetobacter baylyi
Starvation-Induced Genes Identified through Incubation in Long-Term Stationary Phase
Authors: Lostroh C. Phoebe , Voyles Bruce A. 
Published: May 2010

ABSTRACT

Acinetobacter
species encounter cycles of feast and famine in nature. We show that populations of
A
cinetobacter
baylyi
strain ADP1 remain dynamic for 6 weeks in batch culture. We created a library of
lacZ
reporters inserted into SalI sites in the genome and then isolated 30 genes with
lacZ
insertions whose expression was induced by starvation during long-term stationary phase compared with their expression during exponential growth. The genes encode metabolic, gene expression, DNA maintenance, envelope, and conserved hypothetical proteins.
Neisseria gonorrhoeae
FA1090 Carries Genes Encoding Two Classes of Vsr Endonucleases
Authors: Kwiatek Agnieszka , Łuczkiewicz Maciej , Bandyra Katarzyna , Stein Daniel C. , Piekarowicz Andrzej 
Published: May 2010

ABSTRACT

A very short patch repair system prevents mutations resulting from deamination of 5-methylcytosine to thymine. The Vsr endonuclease is the key enzyme of this system, providing sequence specificity. We identified two genes encoding Vsr endonucleases V.NgoAXIII and V.NgoAXIV from
Neisseria gonorrhoeae
FA1090 based on DNA sequence similarity to genes encoding Vsr endonucleases from other bacteria. After expression of the gonococcal genes in
Escherichia coli
, the proteins were biochemically characterized and the endonucleolytic activities and specificities of V.NgoAXIII and V.NgoAXIV were determined. V.NgoAXIII was found to be multispecific and to recognize T:G mismatches in every nucleotide context tested, whereas V.NgoAXIV recognized T:G mismatches in the following sequences: GTGG, CTGG, GTGC, ATGC, and CTGC. Alanine mutagenesis of conserved residues showed that Asp50 and His68 of V.NgoAXIII and Asp51 and His69 of V.NgoAXIV are essential for hydrolytic activity. Glu25, His64, and Asp97 of V.NgoAXIV and Glu24, Asp63, and Asp97 of V.NgoAXIII are important but not crucial for the activity of V.NgoAXIII and V.NgoAXIV. However, Glu24 and Asp63 are also important for the specificity of V.NgoAXIII. On the basis of our results concerning features of Vsr endonucleases expressed by
N. gonorrhoeae
FA1090, we postulate that at least two types of Vsr endonucleases can be distinguished.
Changes in DnaA-Dependent Gene Expression Contribute to the Transcriptional and Developmental Response ofBacillus subtilisto Manganese Limitation in Luria-Bertani Medium
Authors: Hoover Sharon E. , Xu Weihong , Xiao Wenzhong , Burkholder William F. 
Published: May 2010

ABSTRACTThe SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such asBacillus subtilisalso respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing the transcription of genes in the DnaA regulon. We report here that simply growingB. subtilisin LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA inBacillus subtilisencodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB medium but not in LB medium supplemented with manganese, and the induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress.
Imaging OmpR Binding to Native Chromosomal Loci in
Escherichia coli
Authors: Libby Elizabeth A. , Ekici Seda , Goulian Mark 
Published: May 2010

ABSTRACT

Previously, an unexplained subcellular localization was reported for a functional fluorescent protein fusion to the response regulator OmpR in
Escherichia coli
. The pronounced regions of increased fluorescence, or foci, are dependent on OmpR phosphorylation and do not occupy fixed, easily identifiable positions, such as the poles or mid-cell. Here we show that the foci are due to OmpR-YFP (yellow fluorescent protein) fusion binding to specific sites in the chromosome. To identify positions of foci and quantify their fluorescence intensity, we used a simple system to tag virtually any chromosomal location with arrays of
lacO
or
tetO
. The brightest foci colocalize with the OmpR-regulated gene
ompF
, which is strongly expressed under our growth conditions. When we increased OmpR-YFP phosphorylation by stimulating the EnvZ/OmpR system with procaine, we observed a small increase in OmpR-YFP fluorescence at
ompF
and a significant increase at the OmpR-regulated gene
ompC
. This supports a model of hierarchical binding of OmpR to the
ompF
and
ompC
promoters. Our results explain the inhomogeneous distribution of OmpR-YFP fluorescence in cells and further demonstrate that for a transcription factor expressed at wild-type levels, binding to native sites in the chromosome can be imaged and quantified by fluorescence microscopy.
CTnDOT Integrase Interactions with Attachment Site DNA and Control of Directionality of the Recombination Reaction
Authors: Wood Margaret M. , DiChiara Jeanne M. , Yoneji Sumiko , Gardner Jeffrey F. 
Published: May 2010

ABSTRACT

IntDOT is a tyrosine recombinase encoded by the conjugative transposon CTnDOT. The core binding (CB) and catalytic (CAT) domains of IntDOT interact with core-type sites adjacent to the regions of strand exchange, while the N-terminal arm binding (N) domain interacts with arm-type sites distal to the core. Previous footprinting experiments identified five arm-type sites, but how the arm-type sites participate in the integration and excision of CTnDOT was not known.
In vitro
integration assays with substrates containing arm-type site mutants demonstrated that
attDOT
sequences containing mutations in the L1 arm-type site or in the R1 and R2 or R1 and R2′ arm-type sites were dramatically defective in integration. Substrates containing mutations in the L1 and R1 arm-type sites showed a 10- to 20-fold decrease in detectable
in vitro
excision, but introduction of multiple arm-type site mutations in
attR
did not have an effect on the excision frequency. A sixth arm-type site, the R1′ site, was also identified and shown to be required for integration and important for efficient excision. These results suggest that intramolecular IntDOT interactions are required for integration, while the actions of accessory factors are more important for excision. Gel shift assays performed in the presence of core- and arm-type site DNAs showed that IntDOT affinity for the
attDOT
core was enhanced when IntDOT was simultaneously bound to arm-type site DNA.
Moduli and Characteristics of Monotonicity in Some Banach Lattices
Authors: Foralewski Paweł , Hudzik Henryk , Kaczmarek Radosław , Krbec Miroslav 
Published: May 2010

AbstractFirst the characteristic of monotonicity of any Banach lattice "Equation missing" is expressed in terms of the left limit of the modulus of monotonicity of "Equation missing" at the point "Equation missing". It is also shown that for Köthe spaces the classical characteristic of monotonicity is the same as the characteristic of monotonicity corresponding to another modulus of monotonicity "Equation missing". The characteristic of monotonicity of Orlicz function spaces and Orlicz sequence spaces equipped with the Luxemburg norm are calculated. In the first case the characteristic is expressed in terms of the generating Orlicz function only, but in the sequence case the formula is not so direct. Three examples show why in the sequence case so direct formula is rather impossible. Some other auxiliary and complemented results are also presented. By the results of Betiuk-Pilarska and Prus (2008) which establish that Banach lattices "Equation missing" with "Equation missing" and weak orthogonality property have the weak fixed point property, our results are related to the fixed point theory (Kirk and Sims (2001)).
Hey2 acts upstream of Notch in hematopoietic stem cell specification in zebrafish embryos
Authors: Rowlinson Jonathan M. , Gering Martin 
Published: May 2010

AbstractHematopoietic stem cells (HSCs) are essential for homeostasis and injury-induced regeneration of the vertebrate blood system. Although HSC transplantations constitute the most common type of stem cell therapy applied in the clinic, we know relatively little about the molecular programming of HSCs during vertebrate embryogenesis. In vertebrate embryos, HSCs form in close association with the ventral wall of the dorsal aorta. We have shown previously that in zebrafish, HSC formation depends on the presence of a signaling cascade that involves Hedgehog, vascular endothelial growth factor, and Notch signaling. Here, we reveal that Hey2, a hairy/enhancer-of-split–related basic helix-loop-helix transcription factor often believed to act downstream of Notch, is also required for HSC formation. In dorsal aorta progenitors, Hey2 expression is induced downstream of cloche and the transcription factor Scl/Tal1, and is maintained by Hedgehog and vascular endothelial growth factor signaling. Whereas knockdown of Hey2 expression results in a loss of Notch receptor expression in dorsal aorta angioblasts, activation of Notch signaling in hey2 morphants rescues HSC formation in zebrafish embryos. These results establish an essential role for Hey2 upstream of Notch in HSC formation.
Induction of neuro-protective/regenerative genes in stem cells infiltrating post-ischemic brain tissue
Authors: Yilmaz Gokhan , Alexander J Steven , Erkuran Yilmaz Cigdem , Granger D Neil 
Published: May 2010

AbstractBackground-Although the therapeutic potential of bone marrow-derived stromal stem cells (BMSC) has been demonstrated in different experimental models of ischemic stroke, it remains unclear how stem cells (SC) induce neuroprotection following stroke. In this study, we describe a novel method for isolating BMSC that infiltrate postischemic brain tissue and use this method to identify the genes that are persistently activated or depressed in BMSC that infiltrate brain tissue following ischemic stroke.Methods-Ischemic strokes were induced in C57BL/6 mice by middle cerebral artery occlusion for 1 h, followed by reperfusion. BMSC were isolated from H-2 Kb-tsA58 (immortomouse™) mice, and were administered (i.v.) 24 h after reperfusion. At the peak of therapeutic improvement (14 days after the ischemic insult), infarcted brain tissue was isolated, and the BMSC were isolated by culturing at 33°C. Microarray analysis and RT-PCR were performed to compare differential gene expression between naïve and infiltrating BMSC populations.Results-Z-scoring revealed dramatic differences in the expression of extracellular genes between naïve and infiltrating BMSC. Pair-wise analysis detected 80 extracellular factor genes that were up-regulated (≥ 2 fold,P< 0.05, Benjamini-Hochberg correction) between naïve and infiltrated BMSC. Although several anticipated neuroregenerative, nerve guidance and angiogenic factor (e.g., bFGF, bone morphogenetic protein, angiopoietins, neural growth factor) genes exhibited an increased expression, a remarkable induction of genes for nerve guidance survival (e.g., cytokine receptor-like factor 1, glypican 1, Dickkopf homolog 2, osteopontin) was also noted.Conclusions-BMSC infiltrating the post-ischemic brain exhibit persistent epigenetic changes in gene expression for numerous extracellular genes, compared to their naïve counterparts. These genes are relevant to the neuroprotection, regeneration and angiogenesis previously described following stem cell therapy in animal models of ischemic stroke.
Efficacy of atypicalv.typical antipsychotics in the treatment of early psychosis: meta-analysis
Authors: Crossley Nicolas A. , Constante Miguel , McGuire Philip , Power Paddy 
Published: May 2010

BackgroundThere is an ongoing debate about the use of atypical antipsychotics as a first-line treatment for first-episode psychosis.AimsTo examine the evidence base for this recommendation.MethodMeta-analyses of randomised controlled trials in the early phase of psychosis, looking at long-term discontinuation rates, short-term symptom changes, weight gain and extrapyramidal side-effects. Trials were identified using a combination of electronic (Cochrane Central, EMBASE, MEDLINE and PsycINFO) and manual searches.ResultsFifteen randomised controlled trials with a total of 2522 participants were included. No significant differences between atypical and typical drugs were found for discontinuation rates (odds ratio (OR) = 0.7, 95% CI 0.4 to 1.2) or effect on symptoms (standardised mean difference (SMD) = –0.1, 95% CI –0.2 to 0.02). Participants on atypical antipsychotics gained 2.1 kg (95% CI 0.1 to 4.1) more weight than those on typicals, whereas those on typicals experienced more extrapyramidal side-effects (SMD = –0.4, 95% CI –0.5 to –0.2).ConclusionsThere was no evidence for differences in efficacy between atypical and typical antipsychotics, but there was a clear difference in the side-effect profile.
Effect of electroconvulsive therapy on brain 5-HT2receptors in major depression
Authors: Yatham Lakshmi N. , Liddle Peter F. , Lam Raymond W. , Zis Athanasios P. , Stoessl A. Jon , Sossi Vesna , Adam Michael J. , Ruth Thomas J. 
Published: May 2010

BackgroundBrain serotonin2(5-hydroxytryptamine2; 5-HT2) receptors were considered potential targets for therapeutic efficacy of electroconvulsive therapy (ECT), but pre-clinical studies showed that electroconvulsive shock up-regulates 5-HT2receptors in contrast to antidepressant medications, which down-regulate brain 5-HT2receptors. Positron emission tomography (PET) studies in individuals with depression confirmed that antidepressant medications reduce brain 5-HT2receptors, but the effects of ECT on these receptors in individuals with depression are unknown.AimsTo determine if a course of ECT alters brain 5-HT2receptors in individuals with depression and whether such changes correlate with improvement in symptoms.MethodFifteen people with major depression, refractory to antidepressant therapy and referred for a course of ECT, had an [18F]setoperone scan during baseline drug-free washout period and another after a course of ECT. We assessed changes in brain 5-HT2receptors with ECT and their relationship to therapeutic outcome.ResultsWidespread reduction in brain 5-HT2receptors was observed in all cortical areas with changes slightly more prominent in the right hemisphere. There was a trend for correlation between reduction in brain 5-HT2receptors in right parahippocampal gyrus, right lingual gyrus and right medial frontal gyrus, and improvement in depressive symptoms.ConclusionsUnlike in rodents, and similar to antidepressants, ECT reduces brain 5-HT2receptors in individuals with depression. The ability of ECT to further down-regulate brain 5-HT2receptors in antidepressant non-responsive individuals may explain its efficacy in those people with antidepressant refractory depression.
Cohort-specific risk of suicide for different mental disorders in China
Authors: Tong Yongsheng , Phillips Michael R. 
Published: May 2010

BackgroundThe effect of gender, age, and urban versus rural residence on suicide risk among people with different mental disorders is unknown.AimsTo estimate cohort-specific risk of suicide among people with different types of mental disorders using data from China's National Psychological Autopsy Study.MethodLogistic regression models estimated adjusted odd ratios (OR) in 895 suicides and 701 injury deaths.ResultsThe adjusted risk of suicide for mood disorders was highest (OR = 44.2) followed by that for other mental disorders (OR = 10.7), anxiety disorders (OR = 10.2), psychotic disorders (OR = 7.4), substance use disorders (2.7) and organic mental disorders (OR = 1.2). Risk of suicide among urban residents with any mental disorder was more than double that of rural residents (OR = 15.5v.7.6,P= 0.008).ConclusionsThe suicide risk associated with mental illness varies by type of illness and by demographic cohort. Lower risk of suicide among rural residents with mental disorders highlights the importance of non-mental health approaches to the prevention and management of suicidal behaviour in rural areas of low- and middle-income countries.
Combined catecholamine and indoleamine depletion following response to ECT
Authors: Cassidy Frederick , Weiner Richard D. , Cooper Thomas B. , Carroll Bernard J. 
Published: May 2010

SummaryThe mechanism of action of electroconvulsive therapy (ECT) in treating major depression is unknown. We studied two candidate mechanisms through inhibiting simultaneously the synthesis of noradrenaline and serotonin in patients immediately after successful treatment with ECT using a randomised, placebo-controlled, double-blind crossover design. There were no significant changes in depression scores under any experimental conditions, or between the amine-depleted and placebo groups despite reductions of 61% in serum homovanillic acid, 47% in 3-methoxy-4-hydroxyenylethyleneglycol, and 89% in serum tryptophan. Catecholamine and serotonin availability may not be necessary for maintaining the initial antidepressant response to ECT.
Family carers' distress and abusive behaviour: longitudinal study
Authors: Cooper Claudia , Blanchard Martin , Selwood Amber , Walker Zuzana , Livingston Gill 
Published: May 2010

BackgroundA third of family carers of people with dementia report abusive behaviour towards the person for whom they are caring. This is the first longitudinal study to investigate such behaviour.AimsTo test our hypotheses that carers' reports of abusive behaviour would increase over time, and that change in abuse scores would be predicted by change in anxiety and depression scores.MethodIn total, 131 (71.6%) of the family/friend dementia carers consecutively recruited from new referrals to Essex and London community mental health teams who were interviewed at baseline, completed the revised Modified Conflict Tactics Scale to measure abuse 1 year later.ResultsSixty-three (48.1%) of the carers reported any abusive behaviour at baseline compared with 81 (61.8%) a year later (χ2 = 6.9, P = 0.009). An increase in abuse scores was predicted by an increase in anxiety and depressive symptoms (respectively ß = 0.32, t = 3.9, P<0.001 and ß = 0.24, t = 2.9, P = 0.005), and by less domiciliary care at baseline (ß = –0.18, t =–2.2, P = 0.031).ConclusionsMost abusive behaviour reported by carers at baseline persisted or worsened in the following year, despite contact with specialist services. We suggest that trials of psychological interventions shown to reduce anxiety and depression in the carers of people with dementia are needed to determine whether they also reduce elder abuse, and can be delivered cost-effectively within the National Health Service (NHS).