bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of Regulatory Interactions among Global Regulators GlxR, SugR, and RamA in Expression of
ramA
in Corynebacterium glutamicum
Authors: Toyoda Koichi , Teramoto Haruhiko , Gunji Wataru , Inui Masayuki , Yukawa Hideaki 
Published: February 2013

ABSTRACT

The central carbon metabolism genes in
Corynebacterium glutamicum
are under the control of a transcriptional regulatory network composed of several global regulators. It is known that the promoter region of
ramA
, encoding one of these regulators, interacts with its gene product, RamA, as well as with the two other regulators, GlxR and SugR,
in vitro
and/or
in vivo
. Although RamA has been confirmed to repress its own expression, the roles of GlxR and SugR in
ramA
expression have remained unclear. In this study, we examined the effects of GlxR binding site inactivation on expression of the
ramA
promoter-
lacZ
fusion in the genetic background of single and double deletion mutants of
sugR
and
ramA
. In the wild-type background, the
ramA
promoter activity was reduced to undetectable levels by the introduction of mutations into the GlxR binding site but increased by
sugR
deletion, indicating that GlxR and SugR function as the transcriptional activator and repressor, respectively. The marked repression of
ramA
promoter activity by the GlxR binding site mutations was largely compensated for by deletions of
sugR
and/or
ramA
. Furthermore,
ramA
promoter activity in the
ramA
-
sugR
double mutant was comparable to that in the
ramA
mutant but was significantly higher than that in the
sugR
mutant. Taken together, it is likely that the level of
ramA
expression is dynamically balanced by GlxR-dependent activation and repression by RamA along with SugR in response to perturbation of extracellular and/or intracellular conditions. These findings add multiple regulatory loops to the transcriptional regulatory network model in
C. glutamicum
.
RNA Type III Secretion Signals That Require Hfq
Authors: Niemann George S. , Brown Roslyn N. , Mushamiri Ivy T. , Nguyen Nhu T. , Taiwo Rukayat , Stufkens Afke , Smith Richard D. , Adkins Joshua N. , McDermott Jason E. , Heffron Fred 
Published: February 2013

ABSTRACT

Salmonella
virulence is largely mediated by two type III secretion systems (T3SS) that deliver effector proteins from the bacterium to a host cell; however, the secretion signal is poorly defined. Effector N termini are thought to contain the signal, but they lack homology, possess no identifiable motif, and adopt intrinsically disordered structures. Alternative studies suggest that RNA-encoded signals may also be recognized and that they can be located in the 5′ untranslated leader sequence. We began our study by establishing the minimum sequence required for reporter translocation. Untranslated leader sequences predicted from 42 different
Salmonella
effector proteins were fused to the adenylate cyclase reporter (CyaA′), and each of them was tested for protein injection into J774 macrophages. RNA sequences derived from five effectors,
gtgA
,
cigR
,
gogB
,
sseL
, and
steD
, were sufficient for CyaA′ translocation into host cells. To determine the mechanism of signal recognition, we identified proteins that bound specifically to the
gtgA
RNA. One of the unique proteins identified was Hfq. Hfq had no effect upon the translocation of full-length CigR and SteD, but injection of intact GtgA, GogB, and SseL was abolished in an
hfq
mutant, confirming the importance of Hfq. Our results demonstrated that the
Salmonella
pathogenicity island 2 (SPI-2) T3SS assembled into a functional apparatus independently of Hfq. Since particular effectors required Hfq for translocation, Hfq-RNA complexes may participate in signal recognition.
A Genomic Signature and the Identification of New Sporulation Genes
Authors: Abecasis Ana B. , Serrano Mónica , Alves Renato , Quintais Leonor , Pereira-Leal José B. , Henriques Adriano O. 
Published: February 2013

ABSTRACTBacterial endospores are the most resistant cell type known to humans, as they are able to withstand extremes of temperature, pressure, chemical injury, and time. They are also of interest because the endospore is the infective particle in a variety of human and livestock diseases. Endosporulation is characterized by the morphogenesis of an endospore within a mother cell. Based on the genes known to be involved in endosporulation in the model organismBacillus subtilis, a conserved core of about 100 genes was derived, representing the minimal machinery for endosporulation. The core was used to define a genomic signature of about 50 genes that are able to distinguish endospore-forming organisms, based on complete genome sequences, and we show this 50-gene signature is robust against phylogenetic proximity and other artifacts. This signature includes previously uncharacterized genes that we can now show are important for sporulation inB. subtilisand/or are under developmental control, thus further validating this genomic signature. We also predict that a series of polyextremophylic organisms, as well as several gut bacteria, are able to form endospores, and we identified 3 new loci essential for sporulation inB. subtilis:ytaF,ylmC, andylzA. In all, the results support the view that endosporulation likely evolved once, at the base of theFirmicutesphylum, and is unrelated to other bacterial cell differentiation programs and that this involved the evolution of new genes and functions, as well as the cooption of ancestral, housekeeping functions.
Sialic Acid Catabolism in Staphylococcus aureus
Authors: Olson Michael E. , King Jessica M. , Yahr Timothy L. , Horswill Alexander R. 
Published: February 2013

ABSTRACT

Staphylococcus aureus
is a ubiquitous bacterial pathogen that is the causative agent of numerous acute and chronic infections.
S. aureus
colonizes the anterior nares of a significant portion of the healthy adult population, but the mechanisms of colonization remain incompletely defined. Sialic acid (
N
-acetylneuraminic acid [Neu5Ac]) is a bioavailable carbon and nitrogen source that is abundant on mucosal surfaces and in secretions in the commensal environment. Our findings demonstrate that Neu5Ac can serve as an
S. aureus
carbon source, and we have identified a previously uncharacterized chromosomal locus (
nan
) that is required for Neu5Ac utilization. Molecular characterization of the
nan
locus indicates that it contains five genes, organized into four transcripts, and the genes were renamed
nanE
,
nanR
,
nanK
,
nanA
, and
nanT
. Initial studies with gene deletions indicate that
nanT
, predicted to encode the Neu5Ac transporter, and
nanA
and
nanE
, predicted to encode catabolic enzymes, are essential for growth on Neu5Ac. Furthermore, a
nanE
deletion mutant exhibits a growth inhibition phenotype in the presence of Neu5Ac. Transcriptional fusions and Northern blot analyses indicate that NanR represses the expression of both the
nanAT
and
nanE
transcripts, which can be relieved with Neu5Ac. Electrophoretic mobility studies demonstrate that NanR binds to the
nanAT
and
nanE
promoter regions, and the Neu5Ac catabolic intermediate
N
-acetylmannosamine-6-phosphate (ManNAc-6P) relieves NanR promoter binding. Taken together, these data indicate that the
nan
gene cluster is essential for Neu5Ac utilization and may perform an important function for
S. aureus
survival in the host.
The role of hip abductor and external rotator muscle strength in the development of exertional medial tibial pain: a prospective study
Authors: Verrelst Ruth , Willems Tine Marieke , Clercq Dirk De , Roosen Philip , Goossens Lennert , Witvrouw Erik 
Published: February 2013

ObjectiveTo prospectively identify proximal risk factors contributing to the development of exertional medial tibial pain (EMTP).MethodsData were prospectively collected on healthy female students in physical education, who were freshmen in 2010–2011 and 2011–2012. 95 female students, aged 18.15±0.84, were tested at the beginning of their first academic year. Testing included isokinetic hip strength measurements of the abductors, adductors, internal rotators and external rotators. The follow-up of the individulas was assessed using a weekly online questionnaire and a 3-monthly retrospective control questionnaire. EMTP was diagnosed by an experienced MD (Doctor of Medicine). Cox regression analysis was used to identify the potential risk factors for the development of EMTP.Results21 individuals were diagnosed with EMTP during follow-up. The results of this study identified that decreased hip abductor concentric strength is a predictive parameter for the development of EMTP in females. More specifically, total work (p=0.010) and average power (p=0.045) for concentric abduction strength were found to be significant predictors for this lower leg overuse injury.ConclusionsHip abductor weakness is a significant predictor for EMTP in women. Preventive screening methods for EMTP should therefore include this proximal contributing factor.
Comparison of routine prenatal iron prophylaxis and screening and treatment for anaemia: pregnancy results and preliminary birth results from a pragmatic randomised controlled trial (PROFEG) in Maputo, Mozambique
Authors: Parkkali Saara , Abacassamo Fatima , Nwaru Bright Ibeabughichi , Salomé Graca , Augusto Orvalho , Regushevskaya Elena , Dgedge Martinho , Sousa Cesar , Cliff Julie , Chilundo Baltazar , Hemminki Elina 
Published: February 2013

ObjectiveTo present the pregnancy results and interim birth results of a pragmatic randomised controlled trial comparing routine iron prophylaxis with screening and treatment for anaemia during pregnancy in a setting of endemic malaria and HIV.DesignA pragmatic randomised controlled trial.SettingTwo health centres (1° de Maio and Machava) in Maputo, Mozambique, a setting of endemic malaria and high prevalence of HIV.ParticipantsPregnant women (≥18-year-olds; non-high-risk pregnancy, n=4326) attending prenatal care consultation at the two health centres were recruited to the trial.InterventionsThe women were randomly allocated to either Routine iron (n=2184; 60 mg ferrous sulfate plus 400 μg of folic acid daily throughout pregnancy) or Selective iron (n=2142; screening and treatment for anaemia and daily intake of 1 mg of folic acid).Outcome measuresThe primary outcomes were preterm delivery (delivery <37 weeks of gestation) and low birth weight (<2500 g). The secondary outcomes were symptoms suggestive of malaria and self-reported malaria during pregnancy; birth length; caesarean section; maternal and child health status after delivery.ResultsThe number of follow-up visits was similar in the two groups. Between the first and fifth visits, the two groups were similar regarding the occurrence of fever, headache, cold/chills, nausea/vomiting and body aches. There was a suggestion of increased incidence of self-reported malaria during pregnancy (OR 1.37, 95% CI 0.98 to1.92) in the Routine iron group. Birth data were available for 1109 (51%) in the Routine iron group and for 1149 (54%) in the Selective iron group. The birth outcomes were relatively similar in the two groups. However, there was a suggestion (statistically non-significant) of poorer outcomes in the Routine iron group with regard to long hospital stay after birth (relative risk (RR) 1.43, 95% CI 0.97 to 1.26; risk difference (RD) 0.02, 95% CI −0.00 to 0.03) and unavailability of delivery data (RR 1.06, 95% CI 1.00 to 1.13; RD 0.03, 95% CI −0.01 to 0.07).ConclusionsThese interim results suggest that routine iron prophylaxis during pregnancy did not confer advantage over screening and treatment for anaemia regarding maternal and child health. Complete data on birth outcomes are being collected for firmer conclusions.Trial registrationThe trial is registered at ClinicalTrials.gov, numberNCT00488579(June 2007). The first women were randomised to the trial proper April 2007–March 2008. The pilot was November 2006–March 2008. The 3-month lag was due to technical difficulties in completing trial registration.
Dietary patterns and colorectal cancer recurrence and survival: a cohort study
Authors: Zhu Yun , Wu Hao , Wang Peizhong Peter , Savas Sevtap , Woodrow Jennifer , Wish Tyler , Jin Rong , Green Roger , Woods Michael , Roebothan Barbara , Buehler Sharon , Dicks Elizabeth , Mclaughlin John R , Campbell Peter T , Parfrey Patrick S 
Published: February 2013

ObjectiveTo examine the association between dietary patterns and colorectal cancer (CRC) survival.DesignCohort study.SettingA familial CRC registry in Newfoundland.Participants529 newly diagnosed CRC patients from Newfoundland. They were recruited from 1999 to 2003 and followed up until April 2010.Outcome measureParticipants reported their dietary intake using a food frequency questionnaire. Dietary patterns were identified with factor analysis. Multivariable Cox proportional hazards models were employed to estimate HR and 95% CI for association of dietary patterns with CRC recurrence and death from all causes, after controlling for covariates.ResultsDisease-free survival (DFS) among CRC patients was significantly worsened among patients with a high processed meat dietary pattern (the highest vs the lowest quartile HR 1.82, 95% CI 1.07 to 3.09). No associations were observed with the prudent vegetable or the high-sugar patterns and DFS. The association between the processed meat pattern and DFS was restricted to patients diagnosed with colon cancer (the highest vs the lowest quartile: HR 2.29, 95% CI 1.19 to 4.40) whereas the relationship between overall survival (OS) and this pattern was observed among patients with colon cancer only (the highest vs the lowest quartile: HR 2.13, 95% CI 1.03 to 4.43). Potential effect modification was noted for sex (p value for interaction 0.04, HR 3.85 for women and 1.22 for men).ConclusionsThe processed meat dietary pattern prior to diagnosis is associated with higher risk of tumour recurrence, metastasis and death among patients with CRC.
The relative incidence of fracture non-union in the Scottish population (5.17 million): a 5-year epidemiological study
Authors: Mills Leanora Anne , Simpson A Hamish R W 
Published: February 2013

ObjectivesIn the UK there are approximately 850 000 new fractures seen each year. Rates of non-union of 5–10% of fractures have been suggested, the cost to the National Health Service of treating non-union has been reported to range between £7000 and £79 000 per person yet there are little actual data available. The objective of this epidemiological study therefore is for the first time to report the rates of fracture non-union.DesignA cross-sectional epidemiological study.SettingThe population of Scotland.ParticipantsAll patient admissions to hospital in Scotland are coded according to diagnosis. These data are collected by (and were obtained from) Information Services Department Scotland. Those who have been coded for a bone non-union between 2005 and 2010 were included in the study. No patients were excluded. Population data were obtained from the Registrar General for Scotland.Outcome measureThe number of fracture non-unions per 100 000 population of Scotland according to age, sex and anatomical distribution of non-union.Results4895 non-unions were treated as inpatients in Scotland between 2005 and 2010, averaging 979 per year, with an overall incidence of 18.94 per 100 000 population per annum. The distribution according to gender was 57% male and 43% female. The overall peak incidence according to age was between 30 and 40 years. The mean population of Scotland between 2005 and 2010 was 5 169 140 people.ConclusionFracture non-union in the population as a whole remains low at less than 20 per 100 000 population and peaks in the fourth decade of life. Further research is required to determine the risk of non-union per fracture according to age/sex/anatomical distribution..
Methods to improve recruitment to randomised controlled trials: Cochrane systematic review and meta-analysis
Authors: Treweek Shaun , Lockhart Pauline , Pitkethly Marie , Cook Jonathan A , Kjeldstrøm Monica , Johansen Marit , Taskila Taina K , Sullivan Frank M , Wilson Sue , Jackson Catherine , Jones Ritu , Mitchell Elizabeth D 
Published: February 2013

This review is an abridged version of a Cochrane Review previously published in the Cochrane Database of Systematic Reviews 2010, Issue 4, Art. No.: MR000013 DOI: 10.1002/14651858.MR000013.pub5 (seewww.thecochranelibrary.comfor information). Cochrane Reviews are regularly updated as new evidence emerges and in response to feedback, and Cochrane Database of Systematic Reviews should be consulted for the most recent version of the review.ObjectiveTo identify interventions designed to improve recruitment to randomised controlled trials, and to quantify their effect on trial participation.DesignSystematic review.Data sourcesThe Cochrane Methodology Review Group Specialised Register in the Cochrane Library, MEDLINE, EMBASE, ERIC, Science Citation Index, Social Sciences Citation Index, C2-SPECTR, the National Research Register and PubMed. Most searches were undertaken up to 2010; no language restrictions were applied.Study selectionRandomised and quasi-randomised controlled trials, including those recruiting to hypothetical studies. Studies on retention strategies, examining ways to increase questionnaire response or evaluating the use of incentives for clinicians were excluded. The study population included any potential trial participant (eg, patient, clinician and member of the public), or individual or group of individuals responsible for trial recruitment (eg, clinicians, researchers and recruitment sites). Two authors independently screened identified studies for eligibility.Results45 trials with over 43 000 participants were included. Some interventions were effective in increasing recruitment: telephone reminders to non-respondents (risk ratio (RR) 1.66, 95% CI 1.03 to 2.46; two studies, 1058 participants), use of opt-out rather than opt-in procedures for contacting potential participants (RR 1.39, 95% CI 1.06 to 1.84; one study, 152 participants) and open designs where participants know which treatment they are receiving in the trial (RR 1.22, 95% CI 1.09 to 1.36; two studies, 4833 participants). However, the effect of many other strategies is less clear, including the use of video to provide trial information and interventions aimed at recruiters.ConclusionsThere are promising strategies for increasing recruitment to trials, but some methods, such as open-trial designs and opt-out strategies, must be considered carefully as their use may also present methodological or ethical challenges. Questions remain as to the applicability of results originating from hypothetical trials, including those relating to the use of monetary incentives, and there is a clear knowledge gap with regard to effective strategies aimed at recruiters.
Economic evaluation of Australian acute care accreditation (ACCREDIT-CBA (Acute)): study protocol for a mixed-method research project
Authors: Mumford Virginia , Greenfield David , Hinchcliff Reece , Moldovan Max , Forde Kevin , Westbrook Johanna I , Braithwaite Jeffrey 
Published: February 2013

IntroductionThe Accreditation Collaborative for the Conduct of Research, Evaluation and Designated Investigations through Teamwork—Cost–Benefit Analysis (ACCREDIT-CBA (Acute)) study is designed to determine and make explicit the costs and benefits of Australian acute care accreditation and to determine the effectiveness of acute care accreditation in improving patient safety and quality of care. The cost–benefit analysis framework will be provided in the form of an interactive model for industry partners, health regulators and policy makers, accreditation agencies and acute care service providers.Methods and designThe study will use a mixed-method approach to identify, quantify and monetise the costs and benefits of accreditation. Surveys, expert panels, focus groups, interviews and primary and secondary data analysis will be used in cross-sectional and case study designs.Ethics and disseminationThe University of New South Wales Human Research Ethics Committee has approved this project (approval number HREC 10274). The results of the study will be reported via peer-reviewed publications, conferences and seminar resentations and will form part of a doctoral thesis.
Deriving the East Riding Elbow Rule (ER2): a maximally sensitive decision tool for elbow injury
Authors: Arundel David , Williams Paul , Townend Will 
Published: February 2013

ObjectiveTo derive a maximally sensitive decision rule for clinical practice to rule out the need for x-ray examination after elbow injury in adults and children.MethodsEmergency department patients with acute elbow injury were recruited. Practitioners used their usual judgement to assess whether x-ray examination was required. Radiographs were reported on by radiologists blind to clinical assessment. Patients not x-rayed were followed-up at 7 days by telephone interview, and those with ongoing pain were recalled for assessment. Recursive partitioning was used to derive a maximally sensitive decision tool. Inter-rater variability for significant discriminators was subsequently evaluated by a cohort of 20 emergency department clinicians.Results492 patients were recruited (May 2006–November 2008): 50.4% were male; 26.8% were children; 444 (90.2%) had an x-ray; 167 (37.6%) showed abnormality. A follow-up telephone interview was conducted with 28; none were recalled. Thirteen could not be contacted, none of whom returned within 3 months. Sixteen patients with fractures were able to fully extend their elbow. The sensitivity of elbow extension alone was 84% (95% CI 77% to 88%), with specificity of 54% (95% CI 53% to 58%). A 100% sensitive (95% CI 97% to 100%) decision rule for adults (n=348) was derived based on (1) inability to fully extend the elbow, (2) tenderness over radial head, olecranon or medial epicondyle, and (3) presence of bruising (specificity 24% (95% CI 19% to 30%)). A similar rule for children could not be derived.ConclusionsA simple and highly sensitive clinical decision rule for adult elbow fracture was derived in our cohort. A validation study in a second population is now required. At present, we are unable to recommend a rule-out strategy for elbow injuries in children.
Presence of Clostridium botulinum and botulinum toxin in milk and udder tissue of dairy cows with suspected botulism
Authors: Böhnel H. , Gessler F. 
Published: February 2013

Clostridium botulinum is an anaerobic spore‐forming bacterium prevalent in the environment, and causes botulism in man and animals via toxins. Dairy cattle may be contaminated or infected by feed, water or other environmental factors. Milk may also carry the pathogen. Hence, milk and udder samples need to be tested. The number of clinical cases of bovine botulism in Germany has been increasing since the mid‐1990s. Besides routine samples, additional 99 milk samples from 37 farms, and 51 udder samples from 51 farms from sick animals presumably affected by botulism were tested microbiologically by the mouse bioassay. Milk from three farms (8.1 per cent) contained botulinum toxin, and from two (5.4 per cent) bacterial states of C botulinum. Ten udder samples (19.6 per cent) contained toxin, and 7 (13.7 per cent) bacterial forms, including one case where both toxin and bacteria were found. The findings are discussed. Positive milk samples containing botulinum toxin or bacteria raise concern of food safety for the human consumer. Pathological udder samples may show either infection prior to, or contamination after death.