bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of Goose- and Duck-Specific DNA Markers To Determine Sources of
Escherichia coli
in Waterways
Authors: Hamilton Matthew J. , Yan Tao , Sadowsky Michael J. 
Published: June 2006

ABSTRACT

The contamination of waterways with fecal material is a persistent threat to public health. Identification of the sources of fecal contamination is a vital component for abatement strategies and for determination of total maximum daily loads. While phenotypic and genotypic techniques have been used to determine potential sources of fecal bacteria in surface waters, most methods require construction of large known-source libraries, and they often fail to adequately differentiate among environmental isolates originating from different animal sources. In this study, we used pooled genomic tester and driver DNAs in suppression subtractive hybridizations to enrich for host source-specific DNA markers for
Escherichia coli
originating from locally isolated geese. Seven markers were identified. When used as probes in colony hybridization studies, the combined marker DNAs identified 76% of the goose isolates tested and cross-hybridized, on average, with 5% of the human
E. coli
strains and with less than 10% of the strains obtained from other animal hosts. In addition, the combined probes identified 73% of the duck isolates examined, suggesting that they may be useful for determining the contribution of waterfowl to fecal contamination. However, the hybridization probes reacted mainly with
E. coli
isolates obtained from geese in the upper midwestern United States, indicating that there is regional specificity of the markers identified. Coupled with high-throughput, automated macro- and microarray screening, these markers may provide a quantitative, cost-effective, and accurate library-independent method for determining the sources of genetically diverse
E. coli
strains for use in source-tracking studies. However, future efforts to generate DNA markers specific for
E. coli
must include isolates obtained from geographically diverse animal hosts.
A Constitutively Expressed, Truncated
umuDC
Operon Regulates the
recA
-Dependent DNA Damage Induction of a Gene in
Acinetobacter baylyi
Strain ADP1
Authors: Hare Janelle M. , Perkins Sara N. , Gregg-Jolly Leslie A. 
Published: June 2006

ABSTRACT

In response to environmentally caused DNA damage, SOS genes are up-regulated due to RecA-mediated relief of LexA repression. In
Escherichia coli
, the SOS
umuDC
operon is required for DNA damage checkpoint functions and for replicating damaged DNA in the error-prone process called SOS mutagenesis. In the model soil bacterium
Acinetobacter baylyi
strain ADP1, however, the content, regulation, and function of the
umuDC
operon are unusual. The
umuC
gene is incomplete, and a remnant of an ISEhe3-like transposase has replaced the middle 57% of the
umuC
coding region. The
umuD
open reading frame is intact, but it is 1.5 times the size of other
umuD
genes and has an extra 5′ region that lacks homology to known
umuD
genes. Analysis of a
umuD
::
lacZ
fusion showed that
umuD
was expressed at very high levels in both the absence and presence of mitomycin C and that this expression was not affected in a
recA
-deficient background. The
umuD
mutation did not affect the growth rate or survival after UV-induced DNA damage. However, the UmuD-like protein found in ADP1 (UmuDAb) was required for induction of an adjacent DNA damage-inducible gene,
ddrR
. The
umuD
mutation specifically reduced the DNA damage induction of the RecA-dependent DNA damage-inducible
ddrR
locus by 83% (from 12.9-fold to 2.3-fold induction), but it did not affect the 33.9-fold induction of
benA
, an unrelated benzoate degradation gene. These data suggest that the response of the ADP1
umuDC
operon to DNA damage is unusual and that UmuDAb specifically regulates the expression of at least one DNA damage-inducible gene.
Temporal Prevalence of Antimicrobial Resistance in
Campylobacter
spp. from Beef Cattle in Alberta Feedlots
Authors: Inglis G. D. , Morck D. W. , McAllister T. A. , Entz T. , Olson M. E. , Yanke L. J. , Read R. R. 
Published: June 2006

ABSTRACT

Antimicrobial resistance (AMR) was temporally assessed in campylobacters isolated from beef cattle (7,738 fecal samples from 2,622 animals) in four commercial feedlots in Alberta. All calves were administered chlortetracycline and oxytetracycline in feed, and a majority of the animals (93%) were injected with long-acting oxytetracycline upon arrival at the feedlot. Fecal samples from individual animals were collected upon arrival (i.e., entry sample), 69 days (standard deviation [SD] = 3 days) after arrival (i.e., interim sample), and 189 days (SD = 33 days) after arrival (i.e., exit sample) at the feedlot. In total, 1,586
Campylobacter
isolates consisting of
Campylobacter coli
(
n
= 154),
Campylobacter fetus
(
n
= 994),
Campylobacter jejuni
(
n
= 431),
Campylobacter hyointestinalis
(
n
= 4), and
Campylobacter lanienae
(
n
= 3) were recovered and characterized. The administration of antimicrobials did not decrease carriage rates of campylobacters, and minimal resistance (≤4%) to azithromycin, ciprofloxacin, enrofloxacin, gentamicin, and meropenem was observed. In contrast, substantive increases in the prevalence of isolates resistant to tetracycline and doxycycline (56 to 89%) for
C. coli
,
C. fetus
, and
C. jejuni
, as well as in the number of animals (7 to 42%) from which resistant isolates were recovered, were observed during the feedlot period. Increased resistance to erythromycin (total isolates and carriages rates) was also observed in isolates of
C. coli
over the three isolation times. The majority of
C. fetus
isolates recovered were resistant to nalidixic acid, but this was independent of when they were isolated. A relatively limited number of multidrug-resistant isolates were recovered and consisted primarily of
C. coli
resistant to tetracyclines and erythromycin (10% of isolates). Over the course of the feedlot period, considerable increases in antimicrobial resistance were observed in
C. coli
,
C. fetus
, and
C. jejuni
, but with the exception of erythromycin resistance in
C. coli
, the administration of antimicrobial agents to beef cattle was found to have a minimal impact on resistance to macrolides and fluoroquinolones, the two classes of antimicrobials used to treat campylobacteriosis in humans. However, the widespread use of antimicrobial agents in beef production and the possible horizontal transfer of mobile genetic elements with antimicrobial resistance determinants among
Campylobacter
and other bacterial taxa emphasize the need to monitor AMR development in bacteria from beef cattle.
Comparison of Mechanisms of Alkane Metabolism under Sulfate-Reducing Conditions among Two Bacterial Isolates and a Bacterial Consortium
Authors: Callaghan Amy V. , Gieg Lisa M. , Kropp Kevin G. , Suflita Joseph M. , Young Lily Y. 
Published: June 2006

ABSTRACT

Recent studies have demonstrated that fumarate addition and carboxylation are two possible mechanisms of anaerobic alkane degradation. In the present study, we surveyed metabolites formed during growth on hexadecane by the sulfate-reducing isolates AK-01 and Hxd3 and by a mixed sulfate-reducing consortium. The cultures were incubated with either protonated or fully deuterated hexadecane; the sulfate-reducing consortium was also incubated with [1,2-
13
C
2
]hexadecane. All cultures were extracted, silylated, and analyzed by gas chromatography-mass spectrometry. We detected a suite of metabolites that support a fumarate addition mechanism for hexadecane degradation by AK-01, including methylpentadecylsuccinic acid, 4-methyloctadecanoic acid, 4-methyloctadec-2,3-enoic acid, 2-methylhexadecanoic acid, and tetradecanoic acid. By using
d
34
-hexadecane, mass spectral evidence strongly supporting a carbon skeleton rearrangement of the first intermediate, methylpentadecylsuccinic acid, was demonstrated for AK-01. Evidence indicating hexadecane carboxylation was not found in AK-01 extracts but was observed in Hxd3 extracts. In the mixed sulfate-reducing culture, however, metabolites consistent with both fumarate addition and carboxylation mechanisms of hexadecane degradation were detected, which demonstrates that multiple alkane degradation pathways can occur simultaneously within distinct anaerobic communities. Collectively, these findings underscore that fumarate addition and carboxylation are important alkane degradation mechanisms that may be widespread among phylogenetically and/or physiologically distinct microorganisms.
Energetics and Surface Properties of
Pseudomonas putida
DOT-T1E in a Two-Phase Fermentation System with 1-Decanol as Second Phase
Authors: Neumann Grit , Cornelissen Sjef , van Breukelen Frank , Hunger Steffi , Lippold Holger , Loffhagen Norbert , Wick Lukas Y. , Heipieper Hermann J. 
Published: June 2006

ABSTRACT

The solvent-tolerant strain
Pseudomonas putida
DOT-T1E was grown in batch fermentations in a 5-liter bioreactor in the presence and absence of 10% (vol/vol) of the organic solvent 1-decanol. The growth behavior and cellular energetics, such as the cellular ATP content and the energy charge, as well as the cell surface hydrophobicity and charge, were measured in cells growing in the presence and absence of 1-decanol. Although the cells growing in the presence of 1-decanol showed an about 10% reduced growth rate and a 48% reduced growth yield, no significant differences were measured either in the ATP and potassium contents or in the energy charge, indicating that the cells adapted completely at the levels of membrane permeability and energetics. Although the bacteria needed additional energy for adaptation to the presence of the solvent, they were able to maintain or activate electron transport phosphorylation, allowing homeostasis of the ATP level and energy charge in the presence of the solvent, at the price of a reduced growth yield. On the other hand, significantly enhanced cell hydrophobicities and more negative cell surface charges were observed in cells grown in the presence of 1-decanol. Both reactions occurred within about 10 min after the addition of the solvent and were significantly different after killing of the cells with toxic concentrations of HgCl
2
. This adaptation of the surface properties of the bacterium to the presence of solvents seems to be very similar to previously observed reactions on the level of lipopolysaccharides, with which bacteria adapt to environmental stresses, such as heat shock, antibiotics, or low oxygen content. The results give clear physiological indications that the process with
P. putida
DOT-T1E as the biocatalyst and 1-decanol as the solvent is a stable system for two-phase biotransformations that will allow the production of fine chemicals in economically sound amounts.
Patterns of road traffic injuries in a vulnerable population in Hyderabad, India
Authors: Dandona R , Kumar G A , Raj T S , Dandona L 
Published: June 2006

Objective:To describe patterns of road traffic injuries (RTI) in a vulnerable population—pedestrians and users of motorized two-wheeled vehicles (MTVs)—in Hyderabad, India.Methods:4019 pedestrians and 4183 MTV drivers provided information on the most recent road traffic crash (RTC) irrespective of the level of injury in the last one year for 17 454 and 17 242 household members, respectively. Crashes in which any household member was involved as a pedestrian or MTV user were analysed.Results:Involvement in an RTC as a pedestrian or MTV user was reported for 1513 (4.4%, 95% CI 4.2 to 4.6%) people in the last one year. In these crashes, the person involved was an MTV user in 1264 (83.5%), aged 21–40 years in 973 (64.3%), and male in 1202 (79.4%). Six (0.4%) people died in RTCs and the cause was collision with a vehicle/person in 1133 (75%) crashes. Among the 1306 people who were injured and survived, 174 (13.3%) were treated as inpatients, 38 (2.9%) could not return fully to routine daily activities, 630 (48.2%) took leave from their regular occupation, and 13 (1%) lost their jobs following injury. Using a three month recall period, the annual incidence per 100 000 population of RTC as a pedestrian or MTV user was 2288 and of non-fatal RTI was 1931, and that of fatal RTI using one year recall period was 17.3 in this population.Conclusions:These findings on how RTI are caused, their type, and outcomes in pedestrians and MTV users can assist in identifying interventions to improve road safety for this vulnerable population in India, and can also be useful for monitoring the effectiveness of such interventions.
The association between changes in household firearm ownership and rates of suicide in the United States, 1981–2002
Authors: Miller M , Azrael D , Hepburn L , Hemenway D , Lippmann S J 
Published: June 2006

Objective:To explore whether recent declines in household firearm prevalence in the United States were associated with changes in rates of suicide for men, women, and children.Methods:This time series study compares changes in suicide rates to changes in household firearm prevalence, 1981–2002. Multivariate analyses adjust for age, unemployment, per capita alcohol consumption, and poverty. Regional fixed effects controlled for cross sectional, time invariant differences among the four census regions. Standard errors of parameter estimates are adjusted to account for serial autocorrelation of observations over time.Results:Over the 22 year study period household firearm ownership rates declined across all four regions. In multivariate analyses, each 10% decline in household firearm ownership was associated with significant declines in rates of firearm suicide, 4.2% (95% CI 2.3% to 6.1%) and overall suicide, 2.5% (95% CI 1.4% to 3.6%). Changes in non-firearm suicide were not associated with changes in firearm ownership. The magnitude of the association between changes in household firearm ownership and changes in rates of firearm and overall suicide was greatest for children: for each 10% decline in the percentage of households with firearms and children, the rate of firearm suicide among children 0–19 years of age dropped 8.3% (95% CI 6.1% to 10.5%) and the rate of overall suicide dropped 4.1% (2.3% to 5.9%).Conclusion:Changes in household firearm ownership over time are associated with significant changes in rates of suicide for men, women, and children. These findings suggest that reducing availability to firearms in the home may save lives, especially among youth.
Inequalities in hospital admission rates for unintentional poisoning in young children
Authors: Groom L , Kendrick D , Coupland C , Patel B , Hippisley-Cox J 
Published: June 2006

Objective:To determine the relationship between deprivation and hospital admission rates for unintentional poisoning, by poisoning agent in children aged 0–4 years.Design:Cross sectional study of routinely collected hospital admissions data.Setting:East Midlands, UK.Participants:1469 admissions due to unintentional poisoning over two years.Main outcome measure:Hospital admission rates for unintentional poisoning. Incidence rate ratios (IRRs) comparing hospital admission rates for poisoning in the most and least deprived electoral wards.Results:Children in the most deprived wards had admission rates for medicinal poisoning that were 2–3 times higher than those in the least deprived wards (IRR 2.49, 95% CI 1.87 to 3.30). Admission rates for non-medicinal poisoning were about twice as high in the most compared to the least deprived wards (IRR 1.77, 95% CI 1.19 to 2.64). Deprivation gradients were particularly steep for benzodiazepines (IRR 5.63, 95% CI 1.72 to 18.40), antidepressants (IRR 4.58, 95% CI 1.80 to 11.66), cough and cold remedies (IRR 3.93, 95% CI 1.67 to 9.24), and organic solvents (IRR 3.69, 95% CI 1.83 to 7.44).Conclusions:There are steep deprivation gradients for admissions to hospital for childhood poisoning, with particularly steep gradients for some psychotropic medicines. Interventions to reduce these inequalities should be directed towards areas of greater deprivation.
Genetic Risk for Ischemic and Hemorrhagic Stroke
Authors: Yamada Yoshiji , Metoki Norifumi , Yoshida Hidemi , Satoh Kei , Ichihara Sahoko , Kato Kimihiko , Kameyama Takashi , Yokoi Kiyoshi , Matsuo Hitoshi , Segawa Tomonori , Watanabe Sachiro , Nozawa Yoshinori 
Published: June 2006

Objective—We performed an association study to identify gene polymorphisms for assessing the genetic risk of ischemic or hemorrhagic stroke.Methods and Results—The study population comprised 3151 unrelated Japanese individuals: 1141 stroke patients (636 with atherothrombotic cerebral infarction, 282 with intracerebral hemorrhage, and 223 with subarachnoid hemorrhage) and 2010 controls. The genotypes for 202 polymorphisms of 152 genes were determined by suspension array technology. Multivariable logistic regression analysis with adjustment for conventional risk factors revealed that the –572G→C polymorphism of the interleukin-6 (IL-6) gene (IL6) was significantly (P<0.001) associated with both atherothrombotic cerebral infarction and intracerebral hemorrhage and that the –55C→T polymorphism of the uncoupling protein 3 gene (UCP3), the –863C→A polymorphism of the tumor necrosis factor (TNF) gene (TNF), and the G→A (Gly243Asp) polymorphism of the polycystic kidney disease 1–like gene (PKD1-like) were significantly associated with subarachnoid hemorrhage.Conclusions—IL6genotype may be useful in assessing the genetic risk for atherothrombotic cerebral infarction and intracerebral hemorrhage, and genotypes forUCP3,TNF, andPKD1-likemay be similarly beneficial in assessment of the risk for subarachnoid hemorrhage. Validation of our findings will require additional studies with independent subject panels.
Increased hematopoietic stem cell mobilization in aged mice
Authors: Xing Zhenlan , Ryan Marnie A. , Daria Deidre , Nattamai Kalpana J. , Van Zant Gary , Wang Lei , Zheng Yi , Geiger Hartmut 
Published: June 2006

AbstractHematopoietic stem and progenitor cells (HSPCs) are located in the bone marrow in close association with a highly organized 3-dimensional structure formed by stroma cells, referred to as the niche. Mobilization of HSPCs from bone marrow to peripheral blood in response to granulocyte colony-stimulating factor (G-CSF) requires de-adhesion of HSPCs from the niche. The influence of aging of HSPCs on cell-stroma interactions has not been determined in detail. Using a mouse model of G-CSF–induced mobilization, we demonstrated that the ability to mobilize hematopoietic stem cells is approximately 5-fold greater in aged mice. Competitive mobilization experiments confirmed that enhanced mobilization ability was intrinsic to the stem cell. Enhanced mobilization efficiency of primitive hematopoietic cells from aged mice correlated with reduced adhesion of hematopoietic progenitor cells to stroma and with elevated levels of GTP-bound Cdc42. These results might indicate that stroma–stem cell interactions are dynamic over a lifetime and result in physiologically relevant changes in the biology of primitive hematopoietic cells with age.
Reversible inhibition of the platelet procoagulant response through manipulation of the Gardos channel
Authors: Wolfs Jef L. , Wielders Simone J. , Comfurius Paul , Lindhout Theo , Giddings John C. , Zwaal Robert F. , Bevers Edouard M. 
Published: June 2006

AbstractThe platelet procoagulant response requires a sustained elevation of the intracellular Ca2+ concentration, [Ca2+]i, causing exposure of phosphatidylserine (PS) at the outer surface of the plasma membrane. An increased [Ca2+]i also activates Ca2+-dependent K+ channels. Here, we investigated the contribution of the efflux of K+ ions on the platelet procoagulant response in collagen-thrombin–activated platelets using selective K+ channel blockers. The Gardos channel blockers clotrimazol, charybdotoxin, and quinine caused a similar decrease in prothrombinase activity as well as in the number of PS-exposing platelets detected by fluorescence-conjugated annexin A5. Apamin and iberiotoxin, inhibitors of other K+ channels, were without effect. Only clotrimazol showed a significant inhibition of the collagen-plus-thrombin–induced intracellular calcium response. Clotrimazol and charybdotoxin did not inhibit aggregation and release under the conditions used. Inhibition by Gardos channel blockers was reversed by valinomycin, a selective K+ ionophore. The impaired procoagulant response of platelets from a patient with Scott syndrome was partially restored by pretreatment with valinomycin, suggesting a possible defect of the Gardos channel in this syndrome. Collectively, these results provide evidence for the involvement of efflux of K+ ions through Ca2+-activated K+ channels in the procoagulant response of platelets, opening potential strategies for therapeutic interventions.
Thymosin α1 activates dendritic cell tryptophan catabolism and establishes a regulatory environment for balance of inflammation and tolerance
Authors: Romani Luigina , Bistoni Francesco , Perruccio Katia , Montagnoli Claudia , Gaziano Roberta , Bozza Silvia , Bonifazi Pierluigi , Bistoni Giovanni , Rasi Guido , Velardi Andrea , Fallarino Francesca , Garaci Enrico , Puccetti Paolo 
Published: June 2006

Abstract
Thymosin α1 (Tα1), a naturally occurring thymic peptide, primes dendritic cells (DCs) for antifungal T-helper type 1 resistance through Toll-like receptor 9 (TLR9) signaling. As TLR9 signaling also activates the immuno-suppressive pathway of tryptophan catabolism via indoleamine 2,3-dioxygenase (IDO), we examined Tα1 for possible induction of DC-dependent regulatory effects. Tα1 affected T-helper cell priming and tolerance induction by human and murine DCs and induced IDO expression and function in the latter cells. IDO activation by Tα1 required TLR9 and type I interferon receptor signaling and resulted in interleukin-10 production and generation of regulatory T cells. In transfer experiments, functionally distinct subsets of differentiated DCs were required for priming and tolerance to a fungal pathogen or alloantigens. In contrast, Tα1-primed DCs fulfilled multiple requirements, including the induction of T-helper type 1 immunity within a regulatory environment. Thus, instructive immunotherapy with Tα1 targeting IDO-competent DCs could allow for a balanced control of inflammation and tolerance.
Computing Ka and Ks with a consideration of unequal transitional substitutions
Authors: Zhang Zhang , Li Jun , Yu Jun 
Published: June 2006

Abstract

Background
Approximate methods for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) among protein-coding sequences have adopted different mutation (substitution) models. In the past two decades, several methods have been proposed but they have not considered unequal transitional substitutions (between the two purines, A and G, or the two pyrimidines, T and C) that become apparent when sequences data to be compared are vast and significantly diverged.

Results
We propose a new method (MYN), a modified version of the Yang-Nielsen algorithm (YN), for evolutionary analysis of protein-coding sequences in general. MYN adopts the Tamura-Nei Model that considers the difference among rates of transitional and transversional substitutions as well as factors in codon frequency bias. We evaluate the performance of MYN by comparing to other methods, especially to YN, and to show that MYN has minimal deviations when parameters vary within normal ranges defined by empirical data.

Conclusion
Our comparative results deriving from consistency analysis, computer simulations and authentic datasets, indicate that ignoring unequal transitional rates may lead to serious biases and that MYN performs well in most of the tested cases. These results also suggest that acquisitions of reliable synonymous and nonsynonymous substitution rates primarily depend on less biased estimates of transition/transversion rate ratio.