bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contributions of Sinorhizobium meliloti Transcriptional Regulator DksA to Bacterial Growth and Efficient Symbiosis with Medicago sativa
Authors: Wippel Kathrin , Long Sharon R. 
Published: February 2016

ABSTRACT

The stringent response, mediated by the (p)ppGpp synthetase RelA and the RNA polymerase-binding protein DksA, is triggered by limiting nutrient conditions. For some bacteria, it is involved in regulation of virulence. We investigated the role of two DksA-like proteins from the Gram-negative nitrogen-fixing symbiont
Sinorhizobium meliloti
in free-living culture and in interaction with its host plant
Medicago sativa
. The two paralogs, encoded by the genes
SMc00469
and
SMc00049
, differ in the constitution of two major domains required for function in canonical DksA: the DXXDXA motif at the tip of a coiled-coil domain and a zinc finger domain. Using mutant analyses of single, double, and triple deletions for
SMc00469
(designated
dksA
),
SMc00049
, and
relA
, we found that the Δ
dksA
mutant but not the Δ
SMc00049
mutant showed impaired growth on minimal medium, reduced nodulation on the host plant, and lower nitrogen fixation activity in early nodules, while its
nod
gene expression was normal. The Δ
relA
mutant showed severe pleiotropic phenotypes under all conditions tested. Only
S. meliloti
dksA
complemented the metabolic defects of an
Escherichia coli dksA
mutant. Modifications of the DXXDXA motif in SMc00049 failed to establish DksA function. Our results imply a role for transcriptional regulator DksA in the
S. meliloti-M. sativa
symbiosis.

IMPORTANCE
The stringent response is a bacterial transcription regulation process triggered upon nutritional stress.
Sinorhizobium meliloti
, a soil bacterium establishing agriculturally important root nodule symbioses with legume plants, undergoes constant molecular adjustment during host interaction. Analyzing the components of the stringent response in this alphaproteobacterium helps understand molecular control regarding the development of plant interaction. Using mutant analyses, we describe how the lack of DksA influences symbiosis with
Medicago sativa
and show that a second paralogous
S. meliloti
protein cannot substitute for this missing function. This work contributes to the field by showing the similarities and differences of
S. meliloti
DksA-like proteins to orthologs from other species, adding information to the diversity of the stringent response regulatory system.
Formate Metabolism in Shewanella oneidensis Generates Proton Motive Force and Prevents Growth without an Electron Acceptor
Authors: Kane Aunica L. , Brutinel Evan D. , Joo Heena , Maysonet Rebecca , VanDrisse Chelsey M. , Kotloski Nicholas J. , Gralnick Jeffrey A. 
Published: February 2016

ABSTRACTShewanella oneidensisstrain MR-1 is a facultative anaerobe that thrives in redox-stratified environments due to its ability to utilize a wide array of terminal electron acceptors. Conversely, the electron donors utilized byS. oneidensisare more limited and include products of primary fermentation such as lactate, pyruvate, formate, and hydrogen. Lactate, pyruvate, and hydrogen metabolisms inS. oneidensishave been described previously, but little is known about the role of formate oxidation in the ecophysiology of these bacteria. Formate is produced byS. oneidensisthrough pyruvate formate lyase during anaerobic growth on carbon sources that enter metabolism at or above the level of pyruvate, and the genome contains three gene clusters predicted to encode three complete formate dehydrogenase complexes. To determine the contribution of each complex to formate metabolism, strains lacking one, two, or all three annotated formate dehydrogenase gene clusters were generated and examined for growth rates and yields on a variety of carbon sources. Here, we report that formate oxidation contributes to both the growth rate and yield ofS. oneidensisthrough the generation of proton motive force. Exogenous formate also greatly accelerated growth onN-acetylglucosamine, a carbon source normally utilized very slowly byS. oneidensisunder anaerobic conditions. Surprisingly, deletion of all three formate dehydrogenase gene clusters enabled growth ofS. oneidensisusing pyruvate in the absence of a terminal electron acceptor, a mode of growth never before observed in these bacteria. Our results demonstrate that formate oxidation is a fundamental strategy under anaerobic conditions for energy conservation inS. oneidensis.IMPORTANCEShewanellaspecies have garnered interest in biotechnology applications for their ability to respire extracellular terminal electron acceptors, such as insoluble iron oxides and electrodes. While much effort has gone into studying the proteins for extracellular electron transport, how electrons generated through the oxidation of organic carbon sources enter this pathway remains understudied. Here, we quantify the role of formate oxidation in the anaerobic physiology ofShewanella oneidensis. Formate oxidation contributes to both the growth rate and yield on a variety of carbon sources through the generation of proton motive force. Advances in our understanding of the anaerobic metabolism ofS. oneidensisare important for our ability to utilize and engineer this organism for applications in bioenergy, biocatalysis, and bioremediation.
Mycobacterium tuberculosis Transcription Machinery: Ready To Respond to Host Attacks
Authors: Flentie Kelly , Garner Ashley L. , Stallings Christina L. 
Published: February 2016

ABSTRACT

Regulating responses to stress is critical for all bacteria, whether they are environmental, commensal, or pathogenic species. For pathogenic bacteria, successful colonization and survival in the host are dependent on adaptation to diverse conditions imposed by the host tissue architecture and the immune response. Once the bacterium senses a hostile environment, it must enact a change in physiology that contributes to the organism's survival strategy. Inappropriate responses have consequences; hence, the execution of the appropriate response is essential for survival of the bacterium in its niche. Stress responses are most often regulated at the level of gene expression and, more specifically, transcription. This minireview focuses on mechanisms of regulating transcription initiation that are required by
Mycobacterium tuberculosis
to respond to the arsenal of defenses imposed by the host during infection. In particular, we highlight how certain features of
M. tuberculosis
physiology allow this pathogen to respond swiftly and effectively to host defenses. By enacting highly integrated and coordinated gene expression changes in response to stress,
M. tuberculosis
is prepared for battle against the host defense and able to persist within the human population.
Functional Dissection of the CroRS Two-Component System Required for Resistance to Cell Wall Stressors in Enterococcus faecalis
Authors: Kellogg Stephanie L. , Kristich Christopher J. 
Published: February 2016

ABSTRACT

Bacteria use two-component signal transduction systems (TCSs) to sense and respond to environmental changes via a conserved phosphorelay between a sensor histidine kinase and its cognate response regulator. The opportunistic pathogen
Enterococcus faecalis
utilizes a TCS comprised of the histidine kinase CroS and the response regulator CroR to mediate resistance to cell wall stresses such as cephalosporin antibiotics, but the molecular details by which CroRS promotes cephalosporin resistance have not been elucidated. Here, we analyzed mutants of
E. faecalis
carrying substitutions in CroR and CroS to demonstrate that phosphorylated CroR drives resistance to cephalosporins, and that CroS exhibits kinase and phosphatase activities to control the level of CroR phosphorylation
in vivo
. Deletion of
croS
in various lineages of
E. faecalis
revealed a CroS-independent mechanism for CroR phosphorylation and led to the identification of a noncognate histidine kinase capable of influencing CroR (encoded by
OG1RF_12162
; here called
cisS
). Further analysis of this TCS network revealed that both systems respond to cell wall stress.

IMPORTANCE
TCSs allow bacteria to sense and respond to many different environmental conditions. The opportunistic pathogen
Enterococcus faecalis
utilizes the CroRS TCS to mediate resistance to cell wall stresses, including clinically relevant antibiotics such as cephalosporins and glycopeptides. In this study, we use genetic and biochemical means to investigate the relationship between CroRS signaling and cephalosporin resistance in
E. faecalis
cells. Through this, we uncovered a signaling network formed between the CroRS TCS and a previously uncharacterized TCS that also responds to cell wall stress. This study provides mechanistic insights into CroRS signaling and cephalosporin resistance in
E. faecalis
.
Bacterial Cysteine-Inducible Cysteine Resistance Systems
Authors: Takumi Kazuhiro , Nonaka Gen 
Published: February 2016

ABSTRACT

Cysteine donates sulfur to macromolecules and occurs naturally in many proteins. Because low concentrations of cysteine are cytotoxic, its intracellular concentration is stringently controlled. In bacteria, cysteine biosynthesis is regulated by feedback inhibition of the activities of serine acetyltransferase (SAT) and 3-phosphoglycerate dehydrogenase (3-PGDH) and is also regulated at the transcriptional level by inducing the cysteine regulon using the master regulator CysB. Here, we describe two novel cysteine-inducible systems that regulate the cysteine resistance of
Pantoea ananatis
, a member of the family
Enterobacteriaceae
that shows great potential for producing substances useful for biotechnological, medical, and industrial purposes. One locus, designated
ccdA
(formerly PAJ_0331), encodes a novel cysteine-inducible cysteine desulfhydrase (CD) that degrades cysteine, and its expression is controlled by the transcriptional regulator encoded by
ccdR
(formerly PAJ_0332 or
ybaO
), located just upstream of
ccdA
. The other locus, designated
cefA
(formerly PAJ_3026), encodes a novel cysteine-inducible cysteine efflux pump that is controlled by the transcriptional regulator
cefR
(formerly PAJ_3027), located just upstream of
cefA
. To our knowledge, this is the first example where the expression of CD and an efflux pump is regulated in response to cysteine and is directly involved in imparting resistance to excess levels of cysteine. We propose that
ccdA
and
cefA
function as safety valves that maintain homeostasis when the intra- or extracellular cysteine concentration fluctuates. Our findings contribute important insights into optimizing the production of cysteine and related biomaterials by
P. ananatis
.

IMPORTANCE
Because of its toxicity, the bacterial intracellular cysteine level is stringently regulated at biosynthesis. This work describes the identification and characterization of two novel cysteine-inducible systems that regulate, through degradation and efflux, the cysteine resistance of
Pantoea ananatis
, a member of the family
Enterobacteriaceae
that shows great potential for producing substances useful for industrial purposes. We propose that this novel mechanism for sensing and regulating cysteine levels is a safety valve enabling adaptation to sudden changes in intra- or extracellular cysteine levels in bacteria. Our findings provide important insights into optimizing the production of cysteine and related biomaterials by
P. ananatis
and also a deep understanding of sulfur/cysteine metabolism and regulation in this plant pathogen and related bacteria.
Fit to WHO weight standard of European infants over time
Authors: Levin Daniel , Marryat Louise , Cole Tim J , McColl John , Harjunmaa Ulla , Ashorn Per , Wright Charlotte 
Published: February 2016

ObjectivesThe 2006 WHO growth charts were created to provide an international standard for optimal growth, based on healthy, breastfed populations, but it has been suggested that Northern European children fit them poorly. This study uses infant weight data spanning 50 years to determine how well-nourished preschool children from different eras fit the WHO standard, and discuss the implications of deviations.DesignFour longitudinal datasets from the UK and one from Finland were used comprising over 8000 children born between1959 and 2003. Weights from birth to 2 years were converted to age–sex-adjusted Z scores using the WHO standard and summarised using Generalized Additive Models for Location, Scale and Shape.ResultsWeights showed a variable fit to the WHO standard. Mean weights for all cohorts were above the WHO median at birth, but dipped by up to 0.5 SD to a nadir at 8 weeks before rising again. Birth weights increased in successive cohorts and the initial dip became slightly shallower. By age 1 year, cohorts were up to 0.75 SD above the WHO median, but there was no consistent pattern by era.ConclusionsThe WHO standard shows an acceptable, but variable fit for Northern European infants. While birth weights increased over time, there was, unexpectedly, no consistent variation by cohort beyond this initial period. Discrepancies in weight from the standard may reflect differences in measurement protocol and trends in infant feeding practice.
Sports injuries and illnesses during the 2015 Winter European Youth Olympic Festival
Authors: Ruedl G , Schnitzer M , Kirschner W , Spiegel R , Platzgummer H , Kopp M , Burtscher M , Pocecco E 
Published: February 2016

BackgroundThe prevention of injury and illness remains an important issue among young elite athletes. Systematic surveillance of injuries and illnesses during multi-sport events might provide a valuable basis to develop preventive measures, focusing especially on adequate information for youth athletes.AimTo analyse the frequencies and characteristics of injuries and illnesses during the 2015 Winter European Youth Olympic Festival (W-EYOF).MethodsAll National Olympic Committees were asked to report daily the occurrence or non-occurrence of newly sustained injuries and illnesses on a standardised reporting form.ResultsAmong the 899 registered athletes (37% female) with a mean age of 17.1±0.8 years, a total of 38 injuries and 34 illnesses during the 5 competition days of the W-EYOF were reported, resulting in an incidence of 42.3 injuries and 37.8 illnesses per 1000 athletes, respectively. Injury frequency was highest in snowboard cross (11%), Nordic combined (9%), alpine skiing (6%), and ice hockey (6%), taking into account the respective number of registered athletes. In snowboard cross, females showed a significant higher injury frequency compared to males (22% vs 4%, p=0.033). The lower back (16%), the pelvis (13%), the knee (11%), and the face (11%) were the most common injury locations. About 58% of injuries occurred in competition and about 42% in training. In total, 42% of injuries resulted in an absence of training or competition. The prevalence of illness was highest in figure skating (10%) and Nordic combined (9%), and the respiratory system was affected most often (53%).ConclusionsFour per cent of the athletes suffered from an injury and 4% from illnesses during the 2015 W-EYOF, which is about twofold lower compared to the first Winter Youth Olympic Games in 2012.
Using kernel density estimation to understand the influence of neighbourhood destinations on BMI
Authors: King Tania L , Bentley Rebecca J , Thornton Lukar E , Kavanagh Anne M 
Published: February 2016

ObjectivesLittle is known about how the distribution of destinations in the local neighbourhood is related to body mass index (BMI). Kernel density estimation (KDE) is a spatial analysis technique that accounts for the location of features relative to each other. Using KDE, this study investigated whether individuals living near destinations (shops and service facilities) that are more intensely distributed rather than dispersed, have lower BMIs.Study design and settingA cross-sectional study of 2349 residents of 50 urban areas in metropolitan Melbourne, Australia.MethodsDestinations were geocoded, and kernel density estimates of destination intensity were created using kernels of 400, 800 and 1200 m. Using multilevel linear regression, the association between destination intensity (classified in quintiles Q1(least)–Q5(most)) and BMI was estimated in models that adjusted for the following confounders: age, sex, country of birth, education, dominant household occupation, household type, disability/injury and area disadvantage. Separate models included a physical activity variable.ResultsFor kernels of 800 and 1200 m, there was an inverse relationship between BMI and more intensely distributed destinations (compared to areas with least destination intensity). Effects were significant at 1200 m: Q4, β −0.86, 95% CI −1.58 to −0.13, p=0.022; Q5, β −1.03 95% CI −1.65 to −0.41, p=0.001. Inclusion of physical activity in the models attenuated effects, although effects remained marginally significant for Q5 at 1200 m: β −0.77 95% CI −1.52, −0.02, p=0.045.ConclusionsThis study conducted within urban Melbourne, Australia, found that participants living in areas of greater destination intensity within 1200 m of home had lower BMIs. Effects were partly explained by physical activity. The results suggest that increasing the intensity of destination distribution could reduce BMI levels by encouraging higher levels of physical activity.
SCALS: a fourth-generation study of assisted living technologies in their organisational, social, political and policy context
Authors: Greenhalgh Trisha , Shaw Sara , Wherton Joe , Hughes Gemma , Lynch Jenni , A'Court Christine , Hinder Sue , Fahy Nick , Byrne Emma , Finlayson Alexander , Sorell Tom , Procter Rob , Stones Rob 
Published: February 2016

IntroductionResearch to date into assisted living technologies broadly consists of 3 generations: technical design, experimental trials and qualitative studies of the patient experience. We describe a fourth-generation paradigm: studies of assisted living technologies in their organisational, social, political and policy context. Fourth-generation studies are necessarily organic and emergent; they view technology as part of a dynamic, networked and potentially unstable system. They use co-design methods to generate and stabilise local solutions, taking account of context.Methods and analysisSCALS (Studies in Co-creating Assisted Living Solutions) consists (currently) of 5 organisational case studies, each an English health or social care organisation striving to introduce technology-supported services to support independent living in people with health and/or social care needs. Treating these cases as complex systems, we seek to explore interdependencies, emergence and conflict. We employ a co-design approach informed by the principles of action research to help participating organisations establish, refine and evaluate their service. To that end, we are conducting in-depth ethnographic studies of people's experience of assisted living technologies (micro level), embedded in evolving organisational case studies that use interviews, ethnography and document analysis (meso level), and exploring the wider national and international context for assisted living technologies and policy (macro level). Data will be analysed using a sociotechnical framework developed from structuration theory.Ethics and disseminationResearch ethics approval for the first 4 case studies has been granted. An important outcome will be lessons learned from individual co-design case studies. We will document the studies’ credibility and rigour, and assess the transferability of findings to other settings while also recognising unique aspects of the contexts in which they were generated. Academic outputs will include a cross-case analysis and progress in theory and method of fourth-generation assisted living technology research. We will produce practical guidance for organisations, policymakers, designers and service users.
HIV counselling and testing practices for children seen in an urban emergency department of a tertiary referral hospital in Dar es Salaam, Tanzania: a retrospective cross-sectional study
Authors: Sawe Hendry R , Mfinanga Juma A , Ringo Faith H , Mwafongo Victor , Reynolds Teri A , Runyon Michael S 
Published: February 2016

ObjectivesTo describe the HIV counselling and testing practices for children presenting to an emergency department (ED) in a low-income country.SettingThe ED of a large east African national referral hospital.ParticipantsThis retrospective review of all paediatric (<18 years old) ED visits in 2012 enrolled patients who had an HIV test ordered and excluded those without testing. Files were available for 5540/5774 (96%) eligible patients and 1632 (30%) were tested for HIV, median age 1.3 years (IQR 9 months to 4 years), 58% <18 months old and 61% male.Primary and secondary outcome measuresThe primary outcome measure was documentation of pretest and post-test counselling, or deferral of counselling, for children tested for HIV in the ED. Secondary measures included the overall rate of HIV testing, rate of counselling documented in the inpatient record when deferred in the ED, rate of counselling documented when testing was initiated by the inpatient service, rate of counselling documented by test result (positive vs negative) and the rate of referral to follow-up HIV care among patients testing positive.ResultsOf 418 patients tested in the ED, counselling, or deferral of counselling, was documented for 70 (17%). When deferred to the ward, subsequent counselling was documented for 15/42 (36%). Counselling was documented in 33% of patients testing positive versus 1.1% patients testing negative (OR 43 (95% CI 23 to 83). Of 199 patients who tested positive and survived to hospital discharge, 76 (38%) were referred for follow-up at the HIV clinic on discharge.ConclusionsPhysicians documented the provision, or deferral, of counselling for <20% of children tested for HIV in the ED. Counselling was much more likely to be documented when the test result was positive. Less than 40% of those testing positive were referred for follow-up care.