bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Heterogeneity of the UpaH Autotransporter Protein from Uropathogenic Escherichia coli
Authors: Allsopp Luke P. , Beloin Christophe , Moriel Danilo Gomes , Totsika Makrina , Ghigo Jean-Marc , Schembri Mark A. 
Published: August 2012

ABSTRACT

Uropathogenic
Escherichia coli
(UPEC) is responsible for the majority of urinary tract infections (UTI). To cause a UTI, UPEC must adhere to the epithelial cells of the urinary tract and overcome the shear flow forces of urine. This function is mediated primarily by fimbrial adhesins, which mediate specific attachment to host cell receptors. Another group of adhesins that contributes to UPEC-mediated UTI is autotransporter (AT) proteins. AT proteins possess a range of virulence properties, such as adherence, aggregation, invasion, and biofilm formation. One recently characterized AT protein of UPEC is UpaH, a large adhesin-involved-in-diffuse-adherence (AIDA-I)-type AT protein that contributes to biofilm formation and bladder colonization. In this study we characterized a series of naturally occurring variants of UpaH. We demonstrate that extensive sequence variation exists within the passenger-encoding domain of UpaH variants from different UPEC strains. This sequence variation is associated with functional heterogeneity with respect to the ability of UpaH to mediate biofilm formation. In contrast, all of the UpaH variants examined retained a conserved ability to mediate binding to extracellular matrix (ECM) proteins. Bioinformatic analysis of the UpaH passenger domain identified a conserved region (UpaH
CR
) and a hydrophobic region (UpaH
HR
). Deletion of these domains reduced biofilm formation but not the binding to ECM proteins. Despite variation in the
upaH
sequence, the transcription of
upaH
was repressed by a conserved mechanism involving the global regulator H-NS, and mutation of the
hns
gene relieved this repression. Overall, our findings shed new light on the regulation and functions of the UpaH AT protein.
Analysis of the Effects of a
gerP
Mutation on the Germination of Spores of Bacillus subtilis
Authors: Butzin Xuan Yi , Troiano Anthony J. , Coleman William H. , Griffiths Keren K. , Doona Christopher J. , Feeherry Florence E. , Wang Guiwen , Li Yong-qing , Setlow Peter 
Published: August 2012

ABSTRACT

As previously reported,
gerP Bacillus subtilis
spores were defective in nutrient germination triggered via various germinant receptors (GRs), and the defect was eliminated by severe spore coat defects. The
gerP
spores' GR-dependent germination had a longer lag time between addition of germinants and initiation of rapid release of spores' dipicolinic acid (DPA), but times for release of >90% of DPA from individual spores were identical for wild-type and
gerP
spores. The
gerP
spores were also defective in GR-independent germination by DPA with its associated Ca
2+
divalent cation (CaDPA) but germinated better than wild-type spores with the GR-independent germinant dodecylamine. The
gerP
spores exhibited no increased sensitivity to hypochlorite, suggesting that these spores have no significant coat defect. Overexpression of GRs in
gerP
spores did lead to faster germination via the overexpressed GR, but this was still slower than germination of comparable
gerP
+
spores. Unlike wild-type spores, for which maximal nutrient germinant concentrations were between 500 μM and 2 mM for
l
-alanine and ≤10 mM for
l
-valine, rates of
gerP
spore germination increased up to between 200 mM and 1 M
l
-alanine and 100 mM
l
-valine, and at 1 M
l
-alanine, the rates of germination of wild-type and
gerP
spores with or without all alanine racemases were almost identical. A high pressure of 150 MPa that triggers spore germination by activating GRs also triggered germination of wild-type and
gerP
spores identically. All these results support the suggestion that GerP proteins facilitate access of nutrient germinants to their cognate GRs in spores' inner membrane.
Functional Analysis of the Genes Encoding Diaminopropionate Ammonia Lyase in Escherichia coli and Salmonella enterica Serovar Typhimurium
Authors: Kalyani J. N. , Ramachandra Nagaraju , Kachroo Aashiq H. , Mahadevan S. , Savithri H. S. 
Published: August 2012

ABSTRACT

Diaminopropionate ammonia lyase (DAPAL) is a pyridoxal-5′phosphate (PLP)-dependent enzyme that catalyzes the conversion of diaminopropionate (DAP) to pyruvate and ammonia and plays an important role in cell metabolism. We have investigated the role of the
ygeX
gene of
Escherichia coli
K-12 and its ortholog,
STM1002
, in
Salmonella enterica
serovar Typhimurium LT2, presumed to encode DAPAL, in the growth kinetics of the bacteria. While
Salmonella
Typhimurium LT2 could grow on
dl-
DAP as a sole carbon source, the wild-type
E. coli
K-12 strain exhibited only marginal growth on
dl-DAP
, suggesting that DAPAL is functional in
S.
Typhimurium
.
The expression of
ygeX
in
E. coli
was low as detected by reverse transcriptase PCR (RT-PCR), consistent with the poor growth of
E. coli
on
dl-
DAP. Strains of
S.
Typhimurium and
E. coli
with
STM1002
and
ygeX
, respectively, deleted showed loss of growth on
dl-DAP
, confirming that
STM1002
(
ygeX
) is the locus encoding DAPAL. Interestingly, the presence of
dl-
DAP caused a growth inhibition of the wild-type
E. coli
strain as well as the knockout strains of
S.
Typhimurium and
E. coli
in minimal glucose/glycerol medium. Inhibition by
dl-
DAP was rescued by transforming the strains with plasmids containing the
STM1002
(
ygeX
) gene encoding DAPAL or supplementing the medium with Casamino Acids. Growth restoration studies using media lacking specific amino acid supplements suggested that growth inhibition by
dl-
DAP in the absence of DAPAL is associated with auxotrophy related to the inhibition of the enzymes involved in the biosynthetic pathways of pyruvate and aspartate and the amino acids derived from them.
Genomic Basis of a Polyagglutinating Isolate of Neisseria meningitidis
Authors: Rishishwar Lavanya , Katz Lee S. , Sharma Nitya V. , Rowe Lori , Frace Michael , Dolan Thomas Jennifer , Harcourt Brian H. , Mayer Leonard W. , Jordan I. King 
Published: August 2012

ABSTRACT

Containment strategies for outbreaks of invasive
Neisseria meningitidis
disease are informed by serogroup assays that characterize the polysaccharide capsule. We sought to uncover the genomic basis of conflicting serogroup assay results for an isolate (M16917) from a patient with acute meningococcal disease. To this end, we characterized the complete genome sequence of the M16917 isolate and performed a variety of comparative sequence analyses against
N. meningitidis
reference genome sequences of known serogroups. Multilocus sequence typing and whole-genome sequence comparison revealed that M16917 is a member of the ST-11 sequence group, which is most often associated with serogroup C. However, sequence similarity comparisons and phylogenetic analysis showed that the serogroup diagnostic capsule polymerase gene (
synD
) of M16917 belongs to serogroup B. These results suggest that a capsule-switching event occurred based on homologous recombination at or around the capsule locus of M16917. Detailed analysis of this locus uncovered the locations of recombination breakpoints in the M16917 genome sequence, which led to the introduction of an ∼2-kb serogroup B sequence cassette into the serogroup C genomic background. Since there is no currently available vaccine for serogroup B strains of
N. meningitidis
, this kind capsule-switching event could have public health relevance as a vaccine escape mutant.
Meningoencephalitis with Subdural Empyema Caused by Toxigenic Clostridium perfringens Type A
Authors: Hugelshofer Michael , Achermann Yvonne , Kovari Helen , Dent Wolfgang , Hombach Michael , Bloemberg Guido 
Published: August 2012

ABSTRACT

We report a clinical case of meningoencephalitis with subdural empyema in an immunocompromised farmer caused by toxigenic
Clostridium perfringens
type A, which was identified by 16S RNA gene analysis of cerebrospinal fluid and subdural empyema. In immunocompromised patients,
C. perfringens
should be considered a potential pathogen of sepsis.
Ampicillin Susceptibility Can Predict
In Vitro
Susceptibility of Penicillin-Resistant, Ampicillin-Susceptible Enterococcus faecalis Isolates to Amoxicillin but Not to Imipenem and Piperacillin
Authors: Conceição Natália , de Oliveira Cristina da Cunha Hueb Barata , da Silva Lucas Emanuel Pinheiro , de Souza Laís Rezende Cardoso , de Oliveira Adriana Gonçalves 
Published: August 2012

ABSTRACT

Our findings demonstrated that the results obtained for ampicillin may accurately predict the
in vitro
susceptibility to amoxicillin but not to imipenem and piperacillin among isolates of
Enterococcus faecalis
resistant to penicillin but susceptible to ampicillin, which have emerged recently, in contrast to penicillin- and ampicillin-susceptible isolates.
Peptide Interactions Stabilize and Restructure Human Papillomavirus Type 16 E6 To Interact with p53
Authors: Ansari Tina , Brimer Nicole , Vande Pol Scott B. 
Published: August 2012

ABSTRACT

Human papillomavirus type 16 (HPV-16) E6 (16E6) binds the E3 ubiquitin ligase E6AP and p53, thereby targeting degradation of p53 (M. Scheffner, B. A. Werness, J. M. Huibregtse, A. J. Levine, and P. M. Howley, Cell 63:1129–1136, 1990). Here we show that minimal 16E6-binding LXXLL peptides reshape 16E6 to confer p53 interaction and stabilize 16E6
in vivo
but that degradation of p53 by 16E6 requires E6AP expression. These experiments establish a general mechanism for how papillomavirus E6 binding to LXXLL peptides reshapes E6 to then act as an adapter molecule.
A Three-Helix Junction Is the Interface between Two Functional Domains of Prohead RNA in ϕ29 DNA Packaging
Authors: Zhao Wei , Saha Mitul , Ke Ailong , Morais Marc C. , Jardine Paul J. , Grimes Shelley 
Published: August 2012

ABSTRACT

The double-stranded-DNA bacteriophages employ powerful molecular motors to translocate genomic DNA into preformed capsids during the packaging step in phage assembly.
Bacillus subtilis
bacteriophage ϕ29 has an oligomeric prohead RNA (pRNA) that is an essential component of its packaging motor. The crystal structure of the pRNA-prohead binding domain suggested that a three-helix junction constitutes both a flexible region and part of a rigid RNA superhelix. Here we define the functional role of the three-helix junction in motor assembly and DNA packaging. Deletion mutagenesis showed that a U-rich region comprising two sides of the junction plays a role in the stable assembly of pRNA to the prohead. The retention of at least two bulged residues in this region was essential for pRNA binding and thereby subsequent DNA packaging. Additional deletions resulted in the loss of the ability of pRNA to multimerize in solution, consistent with the hypothesis that this region provides the flexibility required for pRNA oligomerization and prohead binding. The third side of the junction is part of a large RNA superhelix that spans the motor. The insertion of bases into this feature resulted in a loss of DNA packaging and an impairment of initiation complex assembly. Additionally, cryo-electron microscopy (cryoEM) analysis of third-side insertion mutants showed an increased flexibility of the helix that binds the ATPase, suggesting that the rigidity of the RNA superhelix is necessary for efficient motor assembly and function. These results highlight the critical role of the three-way junction in bridging the prohead binding and ATPase assembly functions of pRNA.
The Cytoplasmic Tail Domain of Influenza B Virus Hemagglutinin Is Important for Its Incorporation into Virions but Is Not Essential for Virus Replication in Cell Culture in the Presence of Compensatory Mutations
Authors: Imai Masaki , Watanabe Shinji , Kawaoka Yoshihiro 
Published: August 2012

ABSTRACT

Influenza B virus hemagglutinin (BHA) contains a predicted cytoplasmic tail of 10 amino acids that are highly conserved among influenza B viruses. To understand the role of this cytoplasmic tail in infectious virus production, we used reverse genetics to generate a recombinant influenza B virus lacking the BHA cytoplasmic tail domain. The resulting virus, designated BHATail
−
, had a titer approximately 5 log units lower than that of wild-type virus but grew normally when BHA was supplemented in
trans
by BHA-expressing cells. Although the levels of BHA cell surface expression were indistinguishable between truncated and wild-type BHA, the BHATail
−
virus produced particles containing dramatically less BHA. Moreover, removal of the cytoplasmic tail abrogated the association of BHA with Triton X-100-insoluble lipid rafts. Interestingly, long-term culture of a virus lacking the BHA cytoplasmic tail in Madin-Darby canine kidney (MDCK) cells yielded a mutant with infectivities somewhat similar to that of wild-type virus. Sequencing revealed that the mutant virus retained the original cytoplasmic tail deletion but acquired additional mutations in its BHA, neuraminidase (NA), and M1 proteins. Viral growth kinetic analysis showed that replication of BHA cytoplasmic tailless viruses could be improved by compensatory mutations in the NA and M1 proteins. These findings indicate that the cytoplasmic tail domain of BHA is important for efficient incorporation of BHA into virions and tight lipid raft association. They also demonstrate that the domain is not absolutely required for virus viability in cell culture in the presence of compensatory mutations.
Factors influencing infant sleep position: decisions do not differ by SES in African-American families
Authors: Robida David , Moon Rachel Y 
Published: August 2012

ObjectiveTo investigate factors influencing African-American parents’ knowledge, attitudes and practice regarding infant sleep position and determine if these differ by socioeconomic status (SES).MethodsA cross-sectional sample of 412 parents with infants ≤6 months of age participated in a validated survey of knowledge, attitudes and practice.ResultsThere was no significant difference in attitudes or practice, and knowledge was similar regarding infant sleep position between African-American parents of higher and lower SES. The healthcare provider recommendation of exclusive supine sleep position use was associated with increased knowledge, overall decreased use of the side position (5.0% vs 16.8%, p<0.01) and increased occasional use of the supine position in the lower SES group (81.6% vs 68.6%, p=0.03). It was not associated with increased positive parental attitudes about the supine sleep position in either group. Neither a senior caregiver living in the home nor observation of hospital personnel placing infants in a non-supine position was associated with differences in sleep position practices in either group.ConclusionsSleep position practices in African-American families do not differ by SES. Improved attitudes toward positioning and increased use of supine positioning may result if healthcare providers address common concerns and misconceptions about sleep position.
Low injury rate strongly correlates with team success in Qatari professional football
Authors: Eirale Cristiano , Tol J L , Farooq Abdulaziz , Smiley Faten , Chalabi Hakim 
Published: August 2012

BackgroundAlthough the incidence of football injuries should relate to team success there is little empirical evidence.ObjectiveWe investigated the relationship between injury incidence and team success in Qatar first-division football clubs.MethodsUsing a prospective cohort study design, we captured exposure and injuries in Qatar male elite football for a season. Club performance was measured by total league points, ranking, goal scored, goals conceded and number of matches won, drawn or lost.ResultsLower injury incidence was strongly correlated with team ranking position (r=0.929, p=0.003), more games won (r=0.883, p=0.008), more goals scored (r=0.893, p=0.007), greater goal difference (r=0.821, p=0.003) and total points (r=0.929, p=0.003).ConclusionsLower incidence rate was strongly correlated with team success. Prevention of injuries may contribute to team success.
Upper limb injury in rugby union football: results of a cohort study
Authors: Usman Juliana , McIntosh Andrew Stuart 
Published: August 2012

BackgroundThere have been few in-depth studies of upper limb injury epidemiology in rugby union football, despite reports that they accounted for between 14% and 28% of all rugby injuries.ObjectiveTo report on upper limb injury incidence, injury severity and to identify the risk factors associated with upper limb injuries, for example, level of play, season (years) and playing position.DesignProspective cohort study across five rugby seasons from 2004 to 2008.SettingFormal rugby competitions—suburban, provincial and international.Participants1475 adult male rugby players in Colts, Grade and Elite competitions.Main outcome measurementsAn upper limb injury resulting in a missed game and its characteristics.ResultsA total of 61 598 athletic exposures (AE) and 606 upper limb injuries were recorded. About 66% of the injuries were to the shoulder. The overall upper limb injury incidence rate (IIR) was 9.84 injuries/1000 AE (95% CI 9.06 to 10.62). Statistically significant associations were found between upper limb injuries and level of play; and between shoulder injuries and playing position (p<0.05). No association was found between upper limb and shoulder injuries and study year. The overall upper limb IIR decreased as the level of play increased; 10.74 upper limb injuries/1000 AE (95% CI 9.93 to 11.56) in Colts to 6.07 upper limb injuries/1000 AE (95% CI 5.46 to 6.69) in Elite.ConclusionsThe upper limb IIR decreased as the level of play increased indicating that age, level of skill and playing experience may be risk factors for upper limb injury.
Do pregnant women follow exercise guidelines? Prevalence data among 3482 women, and prediction of low-back pain, pelvic girdle pain and depression
Authors: Gjestland Kristin , Bø Kari , Owe Katrine Mari , Eberhard-Gran Malin 
Published: August 2012

PurposeWe describe exercise level in mid-pregnancy, associated sociodemographic variables, and investigate the association between exercise in mid-pregnancy and subsequent low-back pain, pelvic girdle pain and depression at 32 weeks of pregnancy.Material and methodsThe study included 3482 pregnant women participating in the Akershus Birth Cohort study (response rate 80.5%). Data were collected by a questionnaire in pregnancy weeks 17–21, pregnancy week 32 and electronic birth journal. The results were analysed by logistic regression and are presented as crude (cOR) and adjusted OR (aOR) with 95% CI.ResultsOnly 14.6% of the respondents followed the current exercise prescription for exercise during pregnancy (≥3 times a week, >20 min at moderate intensity). One-third of the study sample exercised less than once a week at pregnancy weeks 17–21. Women exercising either 1–2 times or ≥3 times a week at mid-pregnancy were more often primiparous, higher-educated and had less often prepregnacy body mass index >30 kg/m2compared with women exercising less than once a week. Women who exercised ≥3 times a week were less likely to report pelvic girdle pain (aOR: 0.76, 95% CI 0.61 to 0.96), while women exercising 1–2 times a week were less likely to report low-back pain (aOR: 0.80, 95% CI 0.66 to 0.97) and depression (aOR: 0.66, 95% CI 0.48 to 0.91).ConclusionsFew Norwegian women follow current exercise prescriptions for exercise in mid-pregnancy. The results may indicate an association between exercising mid-pregnancy and lower prevalence of low-back pain, pelvic girdle pain and depression in late pregnancy.
ICAM-1K469E polymorphism is a genetic determinant for the clinical risk factors of T2D subjects with retinopathy in Indians: a population-based case–control study
Authors: Vinita Kumari , Sripriya Sarangapani , Prathiba Krishnamurthy , Vaitheeswaran Kulothungan , Sathyabaarathi Ravichandran , Rajesh Mahendran , Amali John , Umashankar Vetrivel , Kumaramanickavel Govindasamy , Pal Swakshyar Saumya , Raman Rajiv , Sharma Tarun 
Published: August 2012

ObjectiveElevated levels of intercellular adhesion molecule-1 (ICAM-1) are demonstrated in diabetes complications. The current study aims to understand association of K469E (rs5498) inICAM-1gene, in type 2 diabetic (T2D) subjects with retinopathy.DesignCase–control study.SettingSankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetic Study, an epidemiology study (on prevalence of diabetic retinopathy in T2D subjects (T2DR) from south India) and outpatient department of Sankara Nethralaya, a tertiary care hospital, in Chennai, India.ParticipantsA total of 356 T2D subjects of >15 years of diabetes duration, with (n=199) and without (n=157) retinopathy.MethodsThe rs5498 polymorphism was genotyped by direct sequencing. Multivariate analysis for various clinical covariates was done using SPSS V.14. Comparative assessment of structure stability, folding rate of the variants were assessed using bioinformatics tools like STRIDE, MuPro, ModellerV97, fold rate server, etc.ResultsThe AA genotype of rs5498 was seen at a higher frequency in the retinopathy group (p=0.012). The risk for diabetic retinopathy (DR) increased in the presence of AA genotype (OR=1.89–4.82) after the sequential addition of various clinical covariates. Multivariate logistic regression analysis showed 8.26 times high risk for developing DR in the AG genotype (p=0.003). Structural superimposition of ICAM-1 wild type (K469) and variant (E469) showed 0.943 Å of backbone root mean square deviation as calculated by PYMOL software. A difference in the fold rate time was also observed between the wild type (5.4/s) and variant (3.3/s).ConclusionsThis study shows that allele A of rs5498 inICAM-1is a putative risk predisposing allele for T2D retinopathy and its clinical covariates in Indian population. The folding rate of the protein decreases for the A allele implicating a potential effect on the structure and function of ICAM-1.
A randomised cross-over cohort study of exposure to emissions from a road tunnel ventilation stack
Authors: Cowie Christine T , Ezz Wafaa , Xuan Wei , Lilley William , Rose Nectarios , Rae Michael , Marks Guy B 
Published: August 2012

Background and objectiveRoad tunnels are increasingly important components of urban infrastructure. However, knowledge of their health impact on surrounding communities is limited. Our objective was to estimate the short-term respiratory health effects of exposure to emissions from a road tunnel ventilation stack.MethodsWe conducted a randomised cross-over cohort study in 36 volunteers who underwent three exposure scenarios in 2006 before the road tunnel opened, and in 2007 (n=27) and 2008 (n=20) after the tunnel opened. Exposure downwind of the stack was compared to upwind of the stack and to a distant heavily trafficked location adjacent to a main road. Spirometry, exhaled nitric oxide (eNO) and symptom scores were measured repeatedly during each 2 h exposure session.ResultsDownwind locations were associated with increased reports of ‘dry nose’ (score difference 0.36; 95% CI 0.09 to 0.63) compared with the control location (2006 vs 2007/2008), but not with impaired lung function, increased airway inflammation or other symptoms. The heavily trafficked location was associated with significantly increased eNO (ratio=1.09; 95% CI 1.04 to 1.14), eye (score difference 0.05; 95% CI 0.01 to 0.10) and chest (score difference 0.21; 95% CI 0.09 to 0.33) symptoms compared to the stack locations.ConclusionsThere was no consistent evidence of adverse respiratory effects from short-term exposures downwind of the tunnel ventilation stack, except for dry nose symptoms. However, the findings of increased airway inflammation and symptoms in subjects after only 2 h exposure at the heavily trafficked location, are suggestive of detrimental effects of short-term exposures to traffic-related air pollution.