bluuebunny/crossref_metadata_2025_split huggingface dataset:
The δ Subunit of RNA Polymerase Is Required for Rapid Changes in Gene Expression and Competitive Fitness of the Cell
Authors: Rabatinová Alžbeta , Šanderová Hana , Jirát Matějčková Jitka , Korelusová Jana , Sojka Luděk , Barvík Ivan , Papoušková Veronika , Sklenář Vladimír , Žídek Lukáš , Krásný Libor 
Published: March 2013

ABSTRACT

RNA polymerase (RNAP) is an extensively studied multisubunit enzyme required for transcription of DNA into RNA, yet the δ subunit of RNAP remains an enigmatic protein whose physiological roles have not been fully elucidated. Here, we identify a novel, so far unrecognized function of δ from
Bacillus subtilis
. We demonstrate that δ affects the regulation of RNAP by the concentration of the initiating nucleoside triphosphate ([iNTP]), an important mechanism crucial for rapid changes in gene expression in response to environmental changes. Consequently, we demonstrate that δ is essential for cell survival when facing a competing strain in a changing environment. Hence, although δ is not essential
per se
, it is vital for the cell's ability to rapidly adapt and survive in nature. Finally, we show that two other proteins, GreA and YdeB, previously implicated to affect regulation of RNAP by [iNTP] in other organisms, do not have this function in
B. subtilis
.
Competence for Natural Genetic Transformation in the Streptococcus bovis Group Streptococci S. infantarius and S. macedonicus
Authors: Morrison Donald A. , Guédon Eric , Renault Pierre 
Published: March 2013

ABSTRACT

Natural genetic transformation is common among many species of the genus
Streptococcus
, but it has never, or rarely, been reported for the
Streptococcus pyogenes
and
S. bovis
groups of species, even though many streptococcal competence genes and the competence regulators SigX, ComR, and ComS are well conserved in both groups. To explore the incidence of competence in the
S. bovis
group, 25 isolates of
S. infantarius
and
S. macedonicus
were surveyed by employing culture in chemically defined media devoid of peptide nutrients and treatment with synthetic candidate pheromone peptides predicted from the sequence of the gene
comS
. Approximately half of strains examined were transformable, many transforming at high rates comparable to those for the well-characterized streptococcal natural transformation systems. In
S. infantarius
, nanomolar amounts of the synthetic pheromone LTAWWGL induced robust but transient competence in high-density cultures, but mutation of the ComRS locus abolished transformation. We conclude that at least these two species of the
S. bovis
group retain a robust system of natural transformation regulated by a ComRS pheromone circuit and the alternative sigma factor SigX and infer that transformation is even more common among the streptococci than has been recognized. The tools presented here will facilitate targeted genetic manipulation in this group of streptococci.
Activity and Regulation of Various Forms of CwlJ, SleB, and YpeB Proteins in Degrading Cortex Peptidoglycan of Spores of Bacillus Species
In Vitro
and during Spore Germination
Authors: Li Yunfeng , Butzin Xuan Y. , Davis Andrew , Setlow Barbara , Korza George , Üstok Fatma Işik , Christie Graham , Setlow Peter , Hao Bing 
Published: March 2013

ABSTRACT

Germination of
Bacillus
spores requires degradation of a modified layer of peptidoglycan (PG) termed the spore cortex by two redundant cortex-lytic enzymes (CLEs), CwlJ and SleB, plus SleB's partner protein, YpeB. In this study,
in vitro
and
in vivo
analyses have been used to clarify the roles of individual SleB and YpeB domains in PG degradation. Purified mature
Bacillus cereus
SleB without its signal sequence (SleB
M
) and the SleB C-terminal catalytic domain (SleB
C
) efficiently triggered germination of decoated
Bacillus megaterium
and
Bacillus subtilis
spores lacking endogenous CLEs; previously, SleB's N-terminal domain (SleB
N
) was shown to bind PG but have no enzymatic activity. YpeB lacking its putative membrane anchoring sequence (YpeB
M
) or its N- and C-terminal domains (YpeB
N
and YpeB
C
) alone did not exhibit degradative activity, but YpeB
N
inhibited SleB
M
and SleB
C
activity
in vitro
. The severe germination defect of
B. subtilis
c
wlJ sleB
or
cwlJ sleB ypeB
spores was complemented by ectopic expression of full-length
sleB
[
sleB
(FL)] and
ypeB
[
ypeB
(FL)], but normal levels of SleB
FL
in spores required normal spore levels of YpeB
FL
and vice versa.
sleB
(FL) or
ypeB
(FL) alone,
sleB
(FL) plus
ypeB
(C) or
ypeB
(N), and
sleB
(C) or
sleB
(N) plus
ypeB
(FL) did not complement the cortex degradation defect in
cwlJ sleB ypeB
spores. In addition, ectopic expression of
sleB
(FL) or
cwlJ
(FL) with a Glu-to-Gln mutation in a predicted active-site residue failed to restore the germination of
cwlJ sleB
spores, supporting the role of this invariant glutamate as the key catalytic residue in SleB and CwlJ.
Maltose Uptake by the Novel ABC Transport System MusEFGK
2
I Causes Increased Expression of
ptsG
in Corynebacterium glutamicum
Authors: Henrich Alexander , Kuhlmann Nora , Eck Alexander W. , Krämer Reinhard , Seibold Gerd M. 
Published: March 2013

ABSTRACT

The Gram-positive
Corynebacterium glutamicum
efficiently metabolizes maltose by a pathway involving maltodextrin and glucose formation by 4-α-glucanotransferase, glucose phosphorylation by glucose kinases, and maltodextrin degradation via maltodextrin phosphorylase and α-phosphoglucomutase. However, maltose uptake in
C. glutamicum
has not been investigated. Interestingly, the presence of maltose in the medium causes increased expression of
ptsG
in
C. glutamicum
by an unknown mechanism, although the
ptsG
-encoded glucose-specific EII permease of the phosphotransferase system itself is not required for maltose utilization. We identified the maltose uptake system as an ABC transporter encoded by
musK
(
cg2708
; ATPase subunit),
musE
(
cg2705
; substrate binding protein),
musF
(
cg2704
; permease), and
musG
(
cg2703
; permease) by combination of data obtained from characterization of maltose uptake and reanalyses of transcriptome data. Deletion of the
mus
gene cluster in
C. glutamicum
Δ
mus
abolished maltose uptake and utilization. Northern blotting and reverse transcription-PCR experiments revealed that
musK
and
musE
are transcribed monocistronically, whereas
musF
and
musG
are part of an operon together with
cg2701
(
musI
), which encodes a membrane protein of unknown function with no homologies to characterized proteins. Characterization of growth and [
14
C]maltose uptake in the
musI
insertion strain
C. glutamicum
IM
cg2701
showed that
musI
encodes a novel essential component of the maltose ABC transporter of
C. glutamicum
. Finally,
ptsG
expression during cultivation on different carbon sources was analyzed in the maltose uptake-deficient strain
C. glutamicum
Δ
mus
. Indeed, maltose uptake by the novel ABC transport system MusEFGK
2
I is required for the positive effect of maltose on
ptsG
expression in
C. glutamicum
.
Relaxed Cleavage Specificity within the RelE Toxin Family
Authors: Goeders Nathalie , Drèze Pierre-Luc , Van Melderen Laurence 
Published: March 2013

ABSTRACT

Bacterial type II toxin-antitoxin systems are widespread in bacteria. Among them, the RelE toxin family is one of the most abundant. The RelE
K-12
toxin of
Escherichia coli
K-12 represents the paradigm for this family and has been extensively studied, both
in vivo
and
in vitro
. RelE
K-12
is an endoribonuclease that cleaves mRNAs that are translated by the ribosome machinery as these transcripts enter the A site. Earlier
in vivo
reports showed that RelE
K-12
cleaves preferentially in the 5′-end coding region of the transcripts in a codon-independent manner. To investigate whether the molecular activity as well as the cleavage pattern are conserved within the members of this toxin family, RelE-like sequences were selected in
Proteobacteria
,
Cyanobacteria
,
Actinobacteria
, and
Spirochaetes
and tested in
E. coli
. Our results show that these RelE-like sequences are part of toxin-antitoxin gene pairs, and that they inhibit translation in
E. coli
by cleaving transcripts that are being translated. Primer extension analyses show that these toxins exhibit specific cleavage patterns
in vivo
, both in terms of frequency and location of cleavage sites. We did not observe codon-dependent cleavage but rather a trend to cleave upstream purines and between the second and third positions of codons, except for the actinobacterial toxin. Our results suggest that RelE-like toxins have evolved to rapidly and efficiently shut down translation in a large spectrum of bacterial species, which correlates with the observation that toxin-antitoxin systems are spreading by horizontal gene transfer.
A Critical Role for the
cccA
Gene Product, Cytochrome
c
2
, in Diverting Electrons from Aerobic Respiration to Denitrification in Neisseria gonorrhoeae
Authors: Hopper Amanda C. , Li Ying , Cole Jeffrey A. 
Published: March 2013

ABSTRACT

Neisseria gonorrhoeae
is a microaerophile that, when oxygen availability is limited, supplements aerobic respiration with a truncated denitrification pathway, nitrite reduction to nitrous oxide. We demonstrate that the
cccA
gene of
Neisseria gonorrhoeae
strain F62 (accession number
NG0292
) is expressed, but the product, cytochrome
c
2
, accumulates to only low levels. Nevertheless, a
cccA
mutant reduced nitrite at about half the rate of the parent strain. We previously reported that cytochromes
c
4
and
c
5
transfer electrons to cytochrome oxidase
cbb
3
by two independent pathways and that the CcoP subunit of cytochrome oxidase
cbb
3
transfers electrons to nitrite. We show that mutants defective in either cytochrome
c
4
or
c
5
also reduce nitrite more slowly than the parent. By combining mutations in
cccA
(Δ
c
2
),
cycA
(Δ
c
4
),
cycB
(Δ
c
5
), and
ccoP
(
ccoP
-C368A), we demonstrate that cytochrome
c
2
is required for electron transfer from cytochrome
c
4
via the third heme group of CcoP to the nitrite reductase, AniA, and that cytochrome
c
5
transfers electrons to nitrite reductase by an independent pathway. We propose that cytochrome
c
2
forms a complex with cytochrome oxidase. If so, the redox state of cytochrome
c
2
might regulate electron transfer to nitrite or oxygen. However, our data are more consistent with a mechanism in which cytochrome
c
2
and the CcoQ subunit of cytochrome oxidase form alternative complexes that preferentially catalyze nitrite and oxygen reduction, respectively. Comparison with the much simpler electron transfer pathway for nitrite reduction in the meningococcus provides fascinating insights into niche adaptation within the pathogenic neisseriae.
The Effect of Electroacupuncture on Osteotomy Gap Healing in a Rat Fibula Model
Authors: Inoue Motohiro , Nakajima Miwa , Hojo Tatsuya , Itoi Megumi , Kitakoji Hiroshi 
Published: March 2013

Objective To examine the effect of electroacupuncture (EA) on osteotomy gap healing in a rat fibula model. Methods A total of 40 12-week-old male Wistar rats underwent unilateral open osteotomy of the fibula to create a 2 mm gap. The rats were randomly assigned to an EA group (n=20) and a control group (n=20). In the EA group, a cathodal electrode was connected to an acupuncture needle percutaneously at the surgery site, while another acupuncture needle inserted 15 mm proximal to the surgery site was used as an anodal electrode. EA was performed 5 days a week for 6 weeks. The control group received no treatment. Some rats were killed at 3 days and 1 week after surgery and the cut end of the distal part of the fibula was surgically removed and histologically assessed. Haematoxylin and eosin (H&E) staining was used to measure total cell count and immunohistochemical staining to assess the increase in the bone morphogenetic protein 2 (BMP-2)-positive cells. The healing process was also assessed weekly after surgery via x-ray examinations. Results At each time point, total cell count showed a marked increase in the EA group (p<0.05), while BMP-2 expression showed a tendency to increase in the EA group. Radiological examination showed a marked reduction in the distance between the cut ends of the fibula in the EA group. Conclusions There was a marked increase in cell count and expression of growth factor in the EA group. These results indicate direct current EA could be useful for promoting bone healing.
Injury patterns in Swedish elite athletics: annual incidence, injury types and risk factors
Authors: Jacobsson Jenny , Timpka Toomas , Kowalski Jan , Nilsson Sverker , Ekberg Joakim , Dahlström Örjan , Renström Per A 
Published: March 2013

ObjectiveTo estimate the incidence, type and severity of musculoskeletal injuries in youth and adult elite athletics athletes and to explore risk factors for sustaining injuries.DesignProspective cohort study conducted during a 52-week period.SettingMale and female youth and adult athletics athletes ranked in the top 10 in Sweden (n=292).Results199 (68%) athletes reported an injury during the study season. Ninety-six per cent of the reported injuries were non-traumatic (associated with overuse). Most injuries (51%) were severe, causing a period of absence from normal training exceeding 3 weeks. Log-rank tests revealed risk differences with regard to athlete category (p=0.046), recent previous injury (>3 weeks time-loss; p=0.039) and training load rank index (TLRI; p=0.019). Cox proportional hazards regression analyses showed that athletes in the third (HR 1.79; 95% CI 1.54 to 2.78) and fourth TLRI quartiles (HR 1.79; 95% CI 1.16 to 2.74) had almost a twofold increased risk of injury compared with their peers in the first quartile and interaction effects between athlete category and previous injury; youth male athletes with a previous serious injury had more than a fourfold increased risk of injury (HR=4.39; 95% CI 2.20 to 8.77) compared with youth females with no previous injury.ConclusionsThe injury incidence among both youth and adult elite athletics athletes is high. A training load index combing hours and intensity and a history of severe injury the previous year were predictors for injury. Further studies on measures to quantify training content and protocols for safe return to athletics are warranted.
Parent perceptions of children's hospital safety climate
Authors: Cox Elizabeth D , Carayon Pascale , Hansen Kristofer W , Rajamanickam Victoria P , Brown Roger L , Rathouz Paul J , DuBenske Lori L , Kelly Michelle M , Buel Linda A 
Published: March 2013

BackgroundBecause patients are at the frontline of care where safety climate is closely tied to safety events, understanding patient perceptions of safety climate is crucial. We sought to develop and evaluate a parent-reported version of the Agency for Healthcare Research and Quality Hospital Survey on Patient Safety Culture and to relate parent-reported responses to parental need to watch over their child's care to ensure mistakes are not made.MethodsParents (n=172) were surveyed about perceptions of hospital safety climate (14 items representing four domains—overall perceptions of safety, openness of staff and parent communication, and handoffs and transitions) and perceived need to watch over their child's care. Confirmatory factor analysis (CFA) was used to validate safety climate domain measures. Logistic regression was used to relate need to watch over care to safety climate domains.ResultsCFA indices suggested good model fit for safety climate domains. Thirty-nine per cent of parents agreed or strongly agreed they needed to watch over care. In adjusted models, need to watch over care was significantly related to overall perceptions of safety (OR 0.20, 95% CI 0.11 to 0.37) and to handoffs and transitions (0.25, 0.14 to 0.46), but not to openness of staff (0.67, 0.40 to 1.12) or parent (0.83, 0.48 to 1.45) communication.ConclusionsFindings suggest parents can provide valuable data on specific safety climate domains. Opportunities exist to improve our safety climate's impact on parent burden to watch over their child's care, such as targeting overall perceptions of safety as well as handoffs and transitions.
A prospective observational study of techniques to remove corneal foreign body in the emergency department
Authors: Quirke Michael , Mullarkey Caitriona , Askoorum Shakti , Coffey Norma , Binchy James 
Published: March 2013

IntroductionPatients with corneal foreign bodies (CFBs) often present to the emergency department (ED). However, removal techniques vary among emergency physicians (EPs). A prospective, single-blinded, observational study was performed to compare slit-lamp-aided (SLA) versus non-slit-lamp-aided (NSLA) CFB removal by EPs.MethodsFive EPs enrolled consecutive patients with a CFB over 3 months. One blinded EP reviewed patients after 3 days. The study end points were: change in visual acuity; visual analogue pain scale (VAS) score at 12 and 24 h; satisfaction rating; symptoms at follow-up; and rate of complications.Results54 patients were enrolled: 28 had SLA removal and 26 NSLA removal; 52 were male; 22 had undergone previous CFB removal; six were wearing eye protection at the time of injury. Forty-three patients were reviewed: 26 by attendance and 18 by telephone. There was no difference in any end points at review. However, patients in the SLA group had median VAS scores that were 1.5 cm lower after 24 h than patients in the NSLA group (p=0.43, 95% CI −2.0 to 1.0). One patient in the SLA group developed keratitis.ConclusionsWe show that patient satisfaction ratings, complications and visual acuity were similar for the two methods. There was a trend for increased pain in the NSLA group at 12 and 24 h. Slit-lamp biomicroscopy and the use of magnification to remove CFBs remains the gold standard of care, and more intensive training should be given to EPs at the departmental level, particularly in EDs that receive patients with eye injuries.
Vasohibin-1 is a new predictor of disease-free survival in operated patients with renal cell carcinoma
Authors: Kanomata Naoki , Sato Yasufumi , Miyaji Yoshiyuki , Nagai Atsushi , Moriya Takuya 
Published: March 2013

BackgroundVasohibin-1 (VASH1) is an endothelium-produced angiogenesis inhibitor. Renal cell carcinoma is highly vascularised, but the significance of endogenous VASH1 in renal cell carcinoma has not been defined.AimsTo identify VASH1 expression and its possible relationship with various clinicopathological factors and prognosis in renal cell carcinoma.MethodsA retrospective analysis of 122 tumours obtained from 118 consecutive patients with renal cell carcinoma was performed. The expression patterns of VASH1, CD31, vascular endothelial growth factor (VEGF) and VEGF receptor type 2 (VEGFR2) were examined immunohistochemically and their relationships with clinicopathological factors were analysed.ResultsMicrovessel density, VASH1 and VEGFR2 expression were significantly higher in clear cell carcinoma than in other subtypes. The VEGF expression pattern differed significantly between clear cell carcinoma and other histological subtypes. VASH1, pT factor and TNM stage were significantly associated with disease-free survival (p=0.030, p = 0.0012 and p = 0.0018, respectively). Cox models of multivariable disease-free survival analyses indicated that VASH1 and stage are independent prognostic factors (p=0.019 and p = 0.024).ConclusionsVASH1 expression may be useful for estimating the prognosis of renal cell carcinoma. Further studies of the role of VASH1 in renal cell carcinoma involving larger sample sizes are warranted.
Common mental disorders and mortality in the West of Scotland Twenty-07 Study: comparing the General Health Questionnaire and the Hospital Anxiety and Depression Scale
Authors: Hannah Mary Kathleen , Batty G David , Benzeval Michaela 
Published: March 2013

BackgroundWhile various measures of common mental disorders (CMD) have been found to be associated with mortality, a comparison of how different measures predict mortality may improve our understanding of the association. This paper compares how the Hospital Anxiety and Depression Scale (HADS) and the 30-item General Health Questionnaire (GHQ-30) predict all cause and cause-specific mortality.MethodsData on 2547 men and women from two cohorts, aged approximately 39 and 55 years, from the West of Scotland Twenty-07 Study who were followed up for mortality over an average of 18.9 (SD 5.0) years. Scores were calculated for HADS depression (HADS-D), HADS Anxiety (HADS-A) and GHQ-30. Cox Proportional Hazards Models were used to determine how each CMD measure predicted mortality.ResultsAfter adjusting for serious physical illness, smoking, social class, alcohol, obesity, pulse rate and living alone, HRs (95% CI) per SD increase in score for all-cause mortality were: 1.15 (1.07 to 1.25) for HADS-D; 1.13 (1.04 to 1.23) for GHQ-30 and 1.05 (0.96 to 1.14) for HADS-A. After the same adjustments, cardiovascular disease mortality was also related to HADS-D (HR 1.24 (1.07 to 1.43)), to GHQ-30 (HR 1.24 (1.11 to 1.40)) and to HADS-A (HR 1.15 (1.01 to 1.32)); respiratory mortality to GHQ-30 (HR 1.33 (1.13 to 1.55)) and mortality from other causes, excluding injuries, to HADS-D (HR 1.28 (1.05 to 1.55)).ConclusionsThere were associations between CMD and both all-cause and cause-specific mortality which were broadly similar for GHQ-30 and HADS-D and were still present after adjustment for important confounders and mediators.
Time to First Cigarette and 4-(Methylnitrosamino)-1-(3-Pyridyl)-1-Butanol (NNAL) Levels in Adult Smokers; National Health and Nutrition Examination Survey (NHANES), 2007–2010
Authors: Branstetter Steven A. , Muscat Joshua E. 
Published: March 2013

Abstract
Background: The time to first cigarette (TTFC) is a good indicator of several dimensions of nicotine dependence. An early TTFC is also associated with increased lung and oral cancer risk. Our objective was to determine the relationship between TTFC and exposure to tobacco smoke carcinogens.
Methods: We conducted a cross-sectional analysis of a nationally representative subsample of smoking adults that had urinary samples analyzed for tobacco biomarkers. The study included 1,945 participants from the 2007–2008 and 2009–2010 National Health and Nutrition and Examination Survey. The main outcome measure was creatinine-adjusted urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) levels.
Results: The cigarette-per-day adjusted levels of NNAL were twice as high in participants who smoked within 5 minutes after waking than in participants who refrained from smoking for at least 1 hour (0.58 vs. 0.28 ng/mL, P &lt; 0.001). In multivariate linear models, a shorter TTFC was significantly associated with increasing NNAL levels, after adjusting for cigarettes smoked per day (or cotinine), secondhand smoke exposure, age, sex, race/ethnicity, and other potential confounders.
Conclusions: These data show that in a nationally representative sample, there is a dose-dependent relationship between earlier smoking in the day and higher biologic exposure to a tobacco smoke carcinogen.
Impact: Our study provides further evidence that highlights the relationship between TTFC, nicotine dependence, and cancer risk. Cancer Epidemiol Biomarkers Prev; 22(4); 615–22. ©2013 AACR.