bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia coli
O157:H7 Lacking the
qseBC
-Encoded Quorum-Sensing System Outcompetes the Parental Strain in Colonization of Cattle Intestines
Authors: Sharma V. K. , Casey T. A. 
Published: January 2014

ABSTRACT

The
qseBC
-encoded quorum-sensing system regulates the motility of
Escherichia coli
O157:H7 in response to bacterial autoinducer 3 (AI-3) and the mammalian stress hormones epinephrine (E) and norepinephrine (NE). The
qseC
gene encodes a sensory kinase that autophosphorylates in response to AI-3, E, or NE and subsequently phosphorylates its cognate response regulator QseB. In the absence of QseC, QseB downregulates bacterial motility and virulence in animal models. In this study, we found that 8- to 10-month-old calves orally inoculated with a mixture of
E. coli
O157:H7 and its isogenic
qseBC
mutant showed significantly higher fecal shedding of the
qseBC
mutant.
In vitro
analysis revealed similar growth profiles and motilities of the
qseBC
mutant and the parental strain in the presence or absence of NE. The magnitudes of the response to NE and expression of flagellar genes
flhD
and
fliC
were also similar for the
qseBC
mutant and the parental strain. The expression of
ler
(a positive regulator of the locus of enterocyte effacement [LEE]), the
ler
-regulated
espA
gene, and the
csgA
gene (encoding curli fimbriae) was increased in the
qseBC
mutant compared to the parental strain. On the other hand, growth, motility, and transcription of
flhD
,
fliC
,
ler
,
espA
, and
csgA
were significantly reduced in the
qseBC
mutant complemented with a plasmid-cloned copy of the
qseBC
genes. Thus,
in vitro
motility and gene expression data indicate that the near-parental level of motility, ability to respond to NE, and enhanced expression of LEE and curli genes might in part be responsible for increased colonization and fecal shedding of the
qseBC
mutant in calves.
Achromobacter denitrificans
Strain YD35 Pyruvate Dehydrogenase Controls NADH Production To Allow Tolerance to Extremely High Nitrite Levels
Authors: Doi Yuki , Shimizu Motoyuki , Fujita Tomoya , Nakamura Akira , Takizawa Noboru , Takaya Naoki 
Published: January 2014

ABSTRACT

We identified the extremely nitrite-tolerant bacterium
Achromobacter denitrificans
YD35 that can grow in complex medium containing 100 mM nitrite (NO
2
−
) under aerobic conditions. Nitrite induced global proteomic changes and upregulated tricarboxylate (TCA) cycle enzymes as well as antioxidant proteins in YD35. Transposon mutagenesis generated NO
2
−
-hypersensitive mutants of YD35 that had mutations at genes for aconitate hydratase and α-ketoglutarate dehydrogenase in the TCA cycle and a pyruvate dehydrogenase (Pdh) E1 component, indicating the importance of TCA cycle metabolism to NO
2
−
tolerance. A mutant in which the
pdh
gene cluster was disrupted (Δ
pdh
mutant) could not grow in the presence of 100 mM NO
2
−
. Nitrite decreased the cellular NADH/NAD
+
ratio and the cellular ATP level. These defects were more severe in the Δ
pdh
mutant, indicating that Pdh contributes to upregulating cellular NADH and ATP and NO
2
−
-tolerant growth. Exogenous acetate, which generates acetyl coenzyme A and then is metabolized by the TCA cycle, compensated for these defects caused by disruption of the
pdh
gene cluster and those caused by NO
2
−
. These findings demonstrate a link between NO
2
−
tolerance and pyruvate/acetate metabolism through the TCA cycle. The TCA cycle mechanism in YD35 enhances NADH production, and we consider that this contributes to a novel NO
2
−
-tolerating mechanism in this strain.
Identifying Beneficial Qualities of
Trichoderma parareesei
for Plants
Authors: Rubio M. Belén , Quijada Narciso M. , Pérez Esclaudys , Domínguez Sara , Monte Enrique , Hermosa Rosa 
Published: January 2014

ABSTRACT

Trichoderma parareesei
and
Trichoderma reesei
(teleomorph
Hypocrea jecorina
) produce cellulases and xylanases of industrial interest. Here, the anamorphic strain T6 (formerly
T. reesei
) has been identified as
T. parareesei
, showing biocontrol potential against fungal and oomycete phytopathogens and enhanced hyphal growth in the presence of tomato exudates or plant cell wall polymers in
in vitro
assays. A
Trichoderma
microarray was used to examine the transcriptomic changes in T6 at 20 h of interaction with tomato plants. Out of a total 34,138
Trichoderma
probe sets deposited on the microarray, 250 showed a significant change of at least 2-fold in expression in the presence of tomato plants, with most of them being downregulated.
T. parareesei
T6 exerted beneficial effects on tomato plants in terms of seedling lateral root development, and in adult plants it improved defense against
Botrytis cinerea
and growth promotion under salt stress. Time course expression patterns (0 to 6 days) observed for defense-related genes suggest that T6 was able to prime defense responses in the tomato plants against biotic and abiotic stresses. Such responses undulated, with a maximum upregulation of the jasmonic acid (JA)/ethylene (ET)-related
LOX1
and
EIN2
genes and the salt tolerance
SOS1
gene at 24 h and that of the salicylic acid (SA)-related
PR-1
gene at 48 h after T6 inoculation. Our study demonstrates that the
T. parareesei
T6-tomato interaction is beneficial to both partners.
Intestinal Microbiota and Species Diversity of
Campylobacter
and
Helicobacter
spp. in Migrating Shorebirds in Delaware Bay
Authors: Ryu Hodon , Grond Kirsten , Verheijen Bram , Elk Michael , Buehler Deborah M. , Santo Domingo Jorge W. 
Published: January 2014

ABSTRACT

Using 16S rRNA gene sequencing analysis, we examined the bacterial diversity and the presence of opportunistic bacterial pathogens (i.e.,
Campylobacter
and
Helicobacter
) in red knot (
Calidris canutus
;
n
= 40), ruddy turnstone (
Arenaria interpres
;
n
= 35), and semipalmated sandpiper (
Calidris pusilla
;
n
= 22) fecal samples collected during a migratory stopover in Delaware Bay. Additionally, we studied the occurrence of
Campylobacter
spp., enterococci, and waterfowl fecal source markers using quantitative PCR (qPCR) assays. Of 3,889 16S rRNA clone sequences analyzed, the bacterial community was mostly composed of
Bacilli
(63.5%),
Fusobacteria
(12.7%),
Epsilonproteobacteria
(6.5%), and
Clostridia
(5.8%). When epsilonproteobacterium-specific 23S rRNA gene clone libraries (i.e., 1,414 sequences) were analyzed, the sequences were identified as
Campylobacter
(82.3%) or
Helicobacter
(17.7%) spp. Specifically, 38.4%, 10.1%, and 26.0% of clone sequences were identified as
C. lari
(>99% sequence identity) in ruddy turnstone, red knot, and semipalmated sandpiper clone libraries, respectively. Other pathogenic species of
Campylobacter
, such as
C. jejuni
and
C. coli
, were not detected in excreta of any of the three bird species. Most
Helicobacter
-like sequences identified were closely related to
H. pametensis
(>99% sequence identity) and
H. anseris
(92% sequence identity). qPCR results showed that the occurrence and abundance of
Campylobacter
spp. was relatively high compared to those of fecal indicator bacteria, such as
Enterococcus
spp.,
E. faecalis
, and
Catellicoccus marimammalium
. Overall, the results provide insights into the complexity of the shorebird gut microbial community and suggest that these migratory birds are important reservoirs of pathogenic
Campylobacter
species.
Safety of the Surrogate Microorganism
Enterococcus faecium
NRRL B-2354 for Use in Thermal Process Validation
Authors: Kopit Lauren M. , Kim Eun Bae , Siezen Roland J. , Harris Linda J. , Marco Maria L. 
Published: January 2014

ABSTRACT

Enterococcus faecium
NRRL B-2354 is a surrogate microorganism used in place of pathogens for validation of thermal processing technologies and systems. We evaluated the safety of strain NRRL B-2354 based on its genomic and functional characteristics. The genome of
E. faecium
NRRL B-2354 was sequenced and found to comprise a 2,635,572-bp chromosome and a 214,319-bp megaplasmid. A total of 2,639 coding sequences were identified, including 45 genes unique to this strain. Hierarchical clustering of the NRRL B-2354 genome with 126 other
E. faecium
genomes as well as
pbp5
locus comparisons and multilocus sequence typing (MLST) showed that the genotype of this strain is most similar to commensal, or community-associated, strains of this species.
E. faecium
NRRL B-2354 lacks antibiotic resistance genes, and both NRRL B-2354 and its clonal relative ATCC 8459 are sensitive to clinically relevant antibiotics. This organism also lacks, or contains nonfunctional copies of, enterococcal virulence genes including
acm
,
cyl
, the
ebp
operon,
esp
,
gelE
,
hyl
, IS
16
, and associated phenotypes. It does contain
scm
,
sagA
,
efaA
, and
pilA
, although either these genes were not expressed or their roles in enterococcal virulence are not well understood. Compared with the clinical strains TX0082 and 1,231,502,
E. faecium
NRRL B-2354 was more resistant to acidic conditions (pH 2.4) and high temperatures (60°C) and was able to grow in 8% ethanol. These findings support the continued use of
E. faecium
NRRL B-2354 in thermal process validation of food products.
Gut Adhesive Bacillus subtilis Spores as a Platform for Mucosal Delivery of Antigens
Authors: Tavares Batista Milene , Souza Renata D. , Paccez Juliano D. , Luiz Wilson B. , Ferreira Ewerton L. , Cavalcante Rafael C. M. , Ferreira Rita C. C. , Ferreira Luís C. S. 
Published: January 2014

ABSTRACT

Bacillus subtilis
spores have been used as safe and heat-resistant antigen delivery vectors. Nonetheless, the oral administration of spores typically induces weak immune responses to the passenger antigens, which may be attributed to the fast transit through the gastrointestinal tract. To overcome this limitation, we have developed
B. subtilis
spores capable of binding to the gut epithelium by means of expressing bacterial adhesins on the spore surface. The resulting spores bound to
in vitro
intestinal cells, showed a longer transit through the mouse intestinal tract, and interacted with Peyer's patch cells. The adhesive spores increased the systemic and secreted antibody responses to the
Streptococcus mutans
P1 protein, used as a model antigen, following oral, intranasal, and sublingual administration. Additionally, P1-specific antibodies efficiently inhibited the adhesion of the oral pathogen
Streptococcus mutans
to abiotic surfaces. These results support the use of gut-colonizing
B. subtilis
spores as a new platform for the mucosal delivery of vaccine antigens.
SCO5745, a Bifunctional RNase J Ortholog, Affects Antibiotic Production in Streptomyces coelicolor
Authors: Bralley Patricia , Aseem Madiha , Jones George H. 
Published: January 2014

ABSTRACT

The bacterial RNases J are considered bifunctional RNases possessing both endo- and exonucleolytic activities. We have isolated an RNase J ortholog from
Streptomyces coelicolor
encoded by the gene
sco5745
. We overexpressed a decahistidine-tagged version of SCO5745 and purified the overexpressed protein by immobilized metal ion affinity chromatography. We demonstrated the presence of both 5′-to-3′ exonucleolytic and endonucleolytic activities on the
Bacillus subtilis
thrS
transcript. Exonucleoytic activity predominated with 5′ monophosphorylated
thrS
, while endonucleolytic activity predominated with 5′ triphosphorylated
thrS
. While
sco5745
is the only RNase J allele in
S. coelicolor
, the gene is not essential. Its disruption resulted in delayed production of the antibiotic actinorhodin, overproduction of undecylprodigiosin, and diminished production of the calcium-dependent antibiotic, in comparison with the parental strain.
Expanding the Universal Medication Schedule: a patient-centred approach
Authors: Bailey Stacy Cooper , Wolf Michael S , Lopez Andrea , Russell Allison , Chen Alice Hm , Schillinger Dean , Moy Glen , Sarkar Urmimala 
Published: January 2014

ObjectiveImproved drug labelling for chronic pill-form medications has been shown to promote patient comprehension, adherence and safety. We extended health literacy principles and included patients' perspectives to improve instructions for: (1) non-pill form, (2) short term, (3) ‘as needed,’ (4) tapered and (5) escalating dose medications.SettingParticipants were recruited via convenience sampling from primary care clinics in Chicago, Illinois and San Francisco, California, USA.Participants40 adult, English-speaking participants who reported taking at least one prescription drug in the past 12 months were enrolled in the study.Primary and secondary outcomesParticipant opinions, preferences and comprehension of standard and improved medication instructions were assessed during four iterative waves of discussion groups. Brief interviews preceding the discussion groups measured individuals’ literacy skills, sociodemographic and health characteristics.ResultsOn average, participants were 46 years old, took four medications and reported two chronic health conditions. Patients varied sociodemographically; 40% were men and 33% had limited literacy skills. Patients agreed on the need for simpler terminology and specificity in instructions. Discussions addressed optimal ways of presenting numeric information, indication and duration of use information to promote comprehension and safe medication use. Consensus was reached on how to improve most of the instructions.ConclusionsThrough this patient-centred approach, we developed a set of health literacy-informed instructions for more challenging medications. Findings can inform current drug labelling initiatives and promote safe and appropriate medication use.
Trends in time to invasive examination and treatment from 2001 to 2009 in patients admitted first time with non-ST elevation myocardial infarction or unstable angina in Denmark
Authors: Mårtensson Solvej , Gyrd-Hansen Dorte , Prescott Eva , Andersen Per Kragh , Zwisler Ann-Dorthe Olsen , Osler Merete 
Published: January 2014

ObjectiveTo investigate trends in time to invasive examination and treatment for patient with first time diagnosis of non-ST elevation myocardial infarction (NSTEMI) and unstable angina during the period from 2001 to 2009 in Denmark.DesignFrom 1 January 2001 to 31 December 2009 all first time hospitalisations with NSTEMI and unstable angina were identified in the National Patient Registry (n=65 909). Time from admission to initiation of coronary angiography (CAG), percutaneous coronary intervention (PCI) or coronary artery bypass graft (CABG) was calculated. We described the development in invasive examination and treatment probability (CAG, PCI and CABG at 3, 7, 10, 30 and 60 days) for the years 2001–2009, taking the competing risk of death into account using Aalen–Johansen estimators and a Fine-Gray model.SettingNationwide Danish cohort.ResultsThe proportion of patients receiving a CAG and PCI increased substantially over time while the proportion receiving a CABG decreased for both NSTEMI and unstable angina. For both NSTEMI and unstable angina, a significant increase in invasive examination and treatment probability at 3 days for CAG and PCI were seen especially from 2007 through to 2009. For NSTEMI, the CAG examination probability at 3 days leaped from 20% in 2007 to 32% in 2008 and 39% in 2009, and for PCI the same was true with a leap in treatment probability from 19% to 28% from 2008 to 2009.ConclusionsIn Denmark the use of CAG and PCI in treatment of NSTEMI and unstable angina has increased from 2001 to 2009, while the use of CABG has decreased. During the same period, there was a marked increase in invasive examination and treatment probability at 3 days, that is, more patients were treated faster which is in line with the political aim of reducing time to treatment.
Exploratory application of the Ages and Stages (ASQ) child development screening test in a low-income Peruvian shantytown population
Authors: Kyerematen Victoria , Hamb Averine , Oberhelman Richard A , Cabrera Lilia , Bernabe-Ortiz Antonio , Berry Susan J 
Published: January 2014

ObjectivesPublic health research on child health is increasingly focusing on the long-term impacts of infectious diseases, malnutrition and social deprivation on child development. The objectives of this exploratory study were to (1) implement the Ages and Stages Questionnaires (ASQ) in children aged 3 months to 5 years in a low-income Peruvian population and (2) to correlate outcomes of the ASQ with risk factors such as nutritional status, diarrhoea incidence and wealth index.SettingPrimary data collection was carried out in the Pampas de San Juan de Miraflores, a periurban low-income community in Lima, Peru.ParticipantsThe study population included 129 children selected through community census data, with a mean age of 22 months (SD 6.8) and with almost equal gender distribution (51% males).InterventionA Peruvian psychologist administered the age-appropriate (ASQ2 for participants enrolled in 2009, ASQ3 for participants enrolled in 2010). Results of the ASQ are reported separately for five scales, including Communication, Gross Motor, Fine Motor, Problem Solving and Personal-Social.Primary and secondary outcome measuresFor each scale, results are reported as normal or suspect, meaning that some milestone attainment was not evident and further evaluation is recommended.ResultsOverall, 50 of 129 children (38.7%) had suspect results for at least one of the five scales, with the highest rates of suspect results on the Communication (15.5%) and Problem Solving scales (13.9%). Higher rates of suspect outcomes were seen in older children, both overall (p=0.06) and on Problem Solving (p=0.009), and for some scales there were trends between suspect outcomes and wealth index or undernutrition.ConclusionsThe ASQ was successfully applied in a community-based study in a low-income Peruvian population, and with further validation, the ASQ may be an effective tool for identifying at-risk children in resource-poor areas of Latin America.
The PACT study protocol: a time series study investigating the impact, acceptability and cost of an integrated model for psychosocial screening, care and treatment of patients with urological and head and neck cancers
Authors: Girgis Afaf , Kelly Brian , Boyes Allison , Haas Marion , Viney Rosalie , Descallar Joseph , Candler Hayley , Bellamy Douglas , Proietto Anthony 
Published: January 2014

IntroductionWhile there is good evidence of the effectiveness of a variety of interventions and services to prevent and/or relieve distress experienced by people affected by cancer, much of this psychosocial morbidity is undetected and untreated, with consequent exacerbated suffering, decreased satisfaction with care, impaired adherence to treatment regimens and poorer morbidity and mortality outcomes. The objective of this study is to develop, implement and assess the impact, acceptability and cost of an integrated, patient-centred Psychosocial Assessment, Care and Treatment (PACT) model of care for patients with urological and head and neck cancers.Methods and analysisA time series research design will be used to test the PACT model of care, newly introduced in an Australian tertiary hospital. The primary outcome is system-level impact, assessed through audit of patients’ medical records and Medicare claims for follow-up care. The secondary outcomes are impact of the model on patients' experience and healthcare professionals’ (HCPs) knowledge and confidence, assessed via patient and HCP surveys at baseline and at follow-up. Acceptability of the intervention will be assessed through HCP interviews at follow-up, and cost will be assessed from Medicare and Pharmaceutical Benefits Scheme claims information and information logged pertaining to intervention activities (eg, time spent by the newly appointed psycho-oncology staff in direct patient contact, providing training sessions, engaging in case review) and their associated costs (eg, salaries, training materials and videoconferencing).Ethics and disseminationEthics approval was obtained from the Human Research Ethics Committees of Hunter New England Local Health District and the University of NSW.ResultsThe results will be widely disseminated to the funding body and through peer-reviewed publications, HCP and consumer publications, oncology conferences and meetings.Trial registrationThe study is registered with the Australian New Zealand Clinical Trials Registry with registration number ACTRN12613000916741.
CCL20 mediates lipopolysaccharide induced liver injury and is a potential driver of inflammation and fibrosis in alcoholic hepatitis
Authors: Affò Silvia , Morales-Ibanez Oriol , Rodrigo-Torres Daniel , Altamirano José , Blaya Delia , Dapito Dianne H , Millán Cristina , Coll Mar , Caviglia Jorge M , Arroyo Vicente , Caballería Juan , Schwabe Robert F , Ginès Pere , Bataller Ramón , Sancho-Bru Pau 
Published: January 2014

ObjectiveChemokines are known to play an important role in the pathophysiology of alcoholic hepatitis (AH), a form of acute-on-chronic liver injury frequently mediated by gut derived lipopolysaccharide (LPS). In our study, we hypothesise that chemokine CCL20, one of the most upregulated chemokines in patients with AH, is implicated in the pathogenesis of AH by mediating LPS induced liver injury.DesignCCL20 gene expression and serum levels and their correlation with disease severity were assessed in patients with AH. Cellular sources of CCL20 and its biological effects were evaluated in vitro and in vivo in chronic, acute and acute-on-chronic experimental models of carbon tetrachloride and LPS induced liver injury. RNA interference technology was used to knockdown CCL20 in vivo.ResultsCCL20 hepatic and serum levels were increased in patients with AH and correlated with the degree of fibrosis, portal hypertension, endotoxaemia, disease severity scores and short term mortality. Moreover, CCL20 expression was increased in animal models of liver injury and particularly under acute-on-chronic conditions. Macrophages and hepatic stellate cells (HSCs) were identified as the main CCL20 producing cell types. Silencing CCL20 in vivo reduced LPS induced aspartate aminotransferase and lactate dehydrogenase serum levels and hepatic proinflammatory and profibrogenic genes. CCL20 induced proinflammatory and profibrogenic effects in cultured primary HSCs.ConclusionsOur results suggest that CCL20 upregulation is strongly associated with LPS and may not only represent a new potential biomarker to predict outcome in patients with AH but also an important mediator linking hepatic inflammation, injury and fibrosis in AH.