bluuebunny/crossref_metadata_2025_split huggingface dataset:
Requirement of the Flagellar Protein Export Apparatus Component FliO for Optimal Expression of Flagellar Genes in Helicobacter pylori
Authors: Tsang Jennifer , Hoover Timothy R. 
Published: May 2014

ABSTRACT

Flagellar biogenesis in
Helicobacter pylori
involves the coordinated expression of flagellar genes with assembly of the flagellum. The
H. pylori
flagellar genes are organized into three regulons based on the sigma factor needed for their transcription (RpoD [σ
80
], RpoN [σ
54
], or FliA [σ
28
]). Transcription of RpoN-dependent genes is activated by a two-component system consisting of the sensor kinase FlgS and the response regulator FlgR. While the cellular cues sensed by the FlgS/FlgR two-component system remain to be elucidated, previous studies revealed that disrupting certain components of the flagellar export apparatus inhibited transcription of the RpoN regulon. FliO is the least conserved of the membrane-bound components of the export apparatus and has not been annotated for any of the
H. pylori
genomes sequenced to date. A PSI-BLAST analysis identified a potential
H. pylori
FliO protein which membrane topology algorithms predict to possess a large N-terminal periplasmic domain that is absent from FliO of
Escherichia coli
and
Salmonella
, the paradigms for flagellar structure/function studies. FliO was necessary for flagellar biogenesis as well as wild-type levels of motility and transcription of RpoN-dependent and FliA-dependent flagellar genes in
H. pylori
strain B128. FliO also appears to be required for wild-type levels of the export apparatus protein FlhA in the membrane. Interestingly, the periplasmic and cytoplasmic domains were somewhat dispensable for flagellar gene regulation and assembly, suggesting that these domains have relatively minor roles in flagellar synthesis.
Intracellular Concentrations of 65 Species of Transcription Factors with Known Regulatory Functions in Escherichia coli
Authors: Ishihama Akira , Kori Ayako , Koshio Etsuko , Yamada Kayoko , Maeda Hiroto , Shimada Tomohiro , Makinoshima Hideki , Iwata Akira , Fujita Nobuyuki 
Published: May 2014

ABSTRACT

The expression pattern of the
Escherichia coli
genome is controlled in part by regulating the utilization of a limited number of RNA polymerases among a total of its approximately 4,600 genes. The distribution pattern of RNA polymerase changes from modulation of two types of protein-protein interactions: the interaction of core RNA polymerase with seven species of the sigma subunit for differential promoter recognition and the interaction of RNA polymerase holoenzyme with about 300 different species of transcription factors (TFs) with regulatory functions. We have been involved in the systematic search for the target promoters recognized by each sigma factor and each TF using the newly developed Genomic SELEX system. In parallel, we developed the promoter-specific (PS)-TF screening system for identification of the whole set of TFs involved in regulation of each promoter. Understanding the regulation of genome transcription also requires knowing the intracellular concentrations of the sigma subunits and TFs under various growth conditions. This report describes the intracellular levels of 65 species of TF with known function in
E. coli
K-12 W3110 at various phases of cell growth and at various temperatures. The list of intracellular concentrations of the sigma factors and TFs provides a community resource for understanding the transcription regulation of
E. coli
under various stressful conditions in nature.
Physiological and Proteomic Analysis of Escherichia coli Iron-Limited Chemostat Growth
Authors: Folsom James Patrick , Parker Albert E. , Carlson Ross P. 
Published: May 2014

ABSTRACT

Iron bioavailability is a major limiter of bacterial growth in mammalian host tissue and thus represents an important area of study.
Escherichia coli
K-12 metabolism was studied at four levels of iron limitation in chemostats using physiological and proteomic analyses. The data documented an
E. coli
acclimation gradient where progressively more severe iron scarcity resulted in a larger percentage of substrate carbon being directed into an overflow metabolism accompanied by a decrease in biomass yield on glucose. Acetate was the primary secreted organic by-product for moderate levels of iron limitation, but as stress increased, the metabolism shifted to secrete primarily lactate (∼70% of catabolized glucose carbon). Proteomic analysis reinforced the physiological data and quantified relative increases in glycolysis enzyme abundance and decreases in tricarboxylic acid (TCA) cycle enzyme abundance with increasing iron limitation stress. The combined data indicated that
E. coli
responds to limiting iron by investing the scarce resource in essential enzymes, at the cost of catabolic efficiency (i.e., downregulating high-ATP-yielding pathways containing enzymes with large iron requirements, like the TCA cycle). Acclimation to iron-limited growth was contrasted experimentally with acclimation to glucose-limited growth to identify both general and nutrient-specific acclimation strategies. While the iron-limited cultures maximized biomass yields on iron and increased expression of iron acquisition strategies, the glucose-limited cultures maximized biomass yields on glucose and increased expression of carbon acquisition strategies. This study quantified ecologically competitive acclimations to nutrient limitations, yielding knowledge essential for understanding medically relevant bacterial responses to host and to developing intervention strategies.
Structural Features of the Pseudomonas fluorescens Biofilm Adhesin LapA Required for LapG-Dependent Cleavage, Biofilm Formation, and Cell Surface Localization
Authors: Boyd Chelsea D. , Smith T. Jarrod , El-Kirat-Chatel Sofiane , Newell Peter D. , Dufrêne Yves F. , O'Toole George A. 
Published: May 2014

ABSTRACT

The localization of the LapA protein to the cell surface is a key step required by
Pseudomonas fluorescens
Pf0-1 to irreversibly attach to a surface and form a biofilm. LapA is a member of a diverse family of predicted bacterial adhesins, and although lacking a high degree of sequence similarity, family members do share common predicted domains. Here, using mutational analysis, we determine the significance of each domain feature of LapA in relation to its export and localization to the cell surface and function in biofilm formation. Our previous work showed that the N terminus of LapA is required for cleavage by the periplasmic cysteine protease LapG and release of the adhesin from the cell surface under conditions unfavorable for biofilm formation. We define an additional critical region of the N terminus of LapA required for LapG proteolysis. Furthermore, our results suggest that the domains within the C terminus of LapA are not absolutely required for biofilm formation, export, or localization to the cell surface, with the exception of the type I secretion signal, which is required for LapA export and cell surface localization. In contrast, deletion of the central repetitive region of LapA, consisting of 37 repeats of 100 amino acids, results in an inability to form a biofilm. We also used single-molecule atomic force microscopy to further characterize the role of these domains in biofilm formation on hydrophobic and hydrophilic surfaces. These studies represent the first detailed analysis of the domains of the LapA family of biofilm adhesin proteins.
Nutrient-Regulated Proteolysis of MrpC Halts Expression of Genes Important for Commitment to Sporulation during Myxococcus xanthus Development
Authors: Rajagopalan Ramya , Kroos Lee 
Published: May 2014

ABSTRACT

Starved
Myxococcus xanthus
cells glide to aggregation centers and form fruiting bodies in which rod-shaped cells differentiate into ovoid spores. Commitment to development was investigated by adding nutrients at specific times after starvation and determining whether development halted or proceeded. At 24 h poststarvation, some rod-shaped cells were committed to subsequent shape change and to becoming sonication-resistant spores, but nutrients caused partial disaggregation of fruiting bodies. By 30 h poststarvation, 10-fold more cells were committed to becoming sonication-resistant spores, and compact fruiting bodies persisted after nutrient addition. During the critical period of commitment around 24 to 30 h poststarvation, the transcription factors MrpC and FruA cooperatively regulate genes important for sporulation. FruA responds to short-range C-signaling, which increases as cells form fruiting bodies. MrpC was found to be highly sensitive to nutrient-regulated proteolysis both before and during the critical period of commitment to sporulation. The rapid turnover of MrpC upon nutrient addition to developing cells halted expression of the
dev
operon, which is important for sporulation. Regulated proteolysis of MrpC appeared to involve ATP-independent metalloprotease activity and may provide a mechanism for monitoring whether starvation persists and halting commitment to sporulation if nutrients reappear.
Identification of Regulatory Elements That Control Expression of the
tbpBA
Operon in Neisseria gonorrhoeae
Authors: Vélez Acevedo Rosuany N. , Ronpirin Chalinee , Kandler Justin L. , Shafer William M. , Cornelissen Cynthia Nau 
Published: May 2014

ABSTRACT

Iron is an essential nutrient for survival and establishment of infection by
Neisseria gonorrhoeae
. The neisserial transferrin binding proteins (Tbps) comprise a bipartite system for iron acquisition from human transferrin. TbpA is the TonB-dependent transporter that accomplishes iron internalization. TbpB is a surface-exposed lipoprotein that makes the iron uptake process more efficient. Previous studies have shown that the genes encoding these proteins are arranged in a bicistronic operon, with the
tbpB
gene located upstream of
tbpA
and separated from it by an inverted repeat. The operon is under the control of the ferric uptake regulator (Fur); however, promoter elements necessary for regulated expression of the genes have not been experimentally defined. In this study, putative regulatory motifs were identified and confirmed by mutagenesis. Further examination of the sequence upstream of these promoter/operator motifs led to the identification of several novel repeats. We hypothesized that these repeats are involved in additional regulation of the operon. Insertional mutagenesis of regions upstream of the characterized promoter region resulted in decreased
tbpB
and
tbpA
transcript levels but increased protein levels for both TbpA and TbpB. Using RNA sequencing (RNA-Seq) technology, we determined that a long RNA was produced from the region upstream of
tbpB
. We localized the 5′ endpoint of this transcript to between the two upstream insertions by qualitative RT-PCR. We propose that expression of this upstream RNA leads to optimized expression of the gene products from within the
tbpBA
operon.
Control of Natural Transformation in Salivarius Streptococci through Specific Degradation of σ
X
by the MecA-ClpCP Protease Complex
Authors: Wahl Astrid , Servais Florence , Drucbert Anne-Sophie , Foulon Catherine , Fontaine Laetitia , Hols Pascal 
Published: May 2014

ABSTRACT

Competence for natural DNA transformation is a tightly controlled developmental process in streptococci. In mutans and salivarius species, the abundance of the central competence regulator σ
X
is regulated at two levels: transcriptional, by the ComRS signaling system via the σ
X
/ComX/SigX-inducing peptide (XIP), and posttranscriptional, by the adaptor protein MecA and its associated Clp ATPase, ClpC. In this study, we further investigated the mechanism and function of the MecA-ClpC control system in the salivarius species
Streptococcus thermophilus
. Using
in vitro
approaches, we showed that MecA specifically interacts with both σ
X
and ClpC, suggesting the formation of a ternary σ
X
-MecA-ClpC complex. Moreover, we demonstrated that MecA ultimately targets σ
X
for its degradation by the ClpCP protease in an ATP-dependent manner. We also identify a short sequence (18 amino acids) in the N-terminal domain of σ
X
as essential for the interaction with MecA and subsequent σ
X
degradation. Finally, increased transformability of a MecA-deficient strain in the presence of subinducing XIP concentrations suggests that the MecA-ClpCP proteolytic complex acts as an additional locking device to prevent competence under inappropriate conditions. A model of the interplay between ComRS and MecA-ClpCP in the control of σ
X
activity is proposed.
Psychometric properties of the Knee injury and Osteoarthritis Outcome Score for Children (KOOS-Child) in children with knee disorders
Authors: Örtqvist Maria , Iversen Maura D , Janarv Per-Mats , Broström Eva W , Roos Ewa M 
Published: May 2014

BackgroundThe Knee injury and Osteoarthritis Outcome Score (KOOS) is a self-administered valid and reliable questionnaire for adults with joint injury or degenerative disease. Recent data indicate a lack of comprehensibility when this is used with children. Thus, a preliminary KOOS-Child was developed. This study aims to evaluate psychometric properties of the final KOOS-Child when used in children with knee disorders.Methods115 children (boys/girls 51/64, 7–16 years) with knee disorders were recruited. All children (n=115) completed the KOOS-Child, the Child-Health Assessment Questionnaire (CHAQ) and the EQ-5D-Youth version (EQ-5D-Y) at baseline to evaluate construct validity. Two additional administrations (1–3 weeks and 3 months) were performed for analyses of reliability (internal consistency and test–retest; n=72) and responsiveness (n=91). An anchor-based approach was used to evaluate responsiveness and interpretability.ResultsAfter item reduction, the final KOOS-Child consists of 39 items divided into five subscales. No floor or ceiling effects (≤15%) were found. An exploratory factor analysis on subscale level demonstrated that items in all subscales except for Symptoms loaded on one factor (Eigenvalues 3.1–5.5, Symptom: 2 factors, Eigenvalue >1). Sufficient homogeneity was found for all subscales (Cronbach's α = 0.80–0.90) except for the Symptoms subscale (α = 0.59). Test–retest reliability was substantial to excellent for all subscales (Intraclass Correlation Coefficient 0.78–0.91, Smallest Detectable Change (SDC)ind14.6–22.6, SDCgroup1.7–2.7). Construct validity was confirmed, and greater effect sizes were seen in those reporting improved clinical status. Minimal important changes greater than the SDCs were found for patients reporting to be better and much better.ConclusionsThe final KOOS-Child demonstrates good psychometric properties and supports the use of the KOOS-Child when evaluating children with knee disorders.
Risk factors, testing and preventative strategies for non-contact injuries in professional football: current perceptions and practices of 44 teams from various premier leagues
Authors: McCall Alan , Carling Chris , Nedelec Mathieu , Davison Michael , Le Gall Franck , Berthoin Serge , Dupont Gregory 
Published: May 2014

PurposeLittle is known about injury prevention practices in professional football clubs. The purpose of this study was therefore to determine the current perceptions and practices of premier league football clubs internationally concerning risk factors, testing and preventative exercises for non-contact injuries.MethodsA survey was administered to 93 premier league football clubs internationally. The survey included four sections: (1) persons involved in the injury prevention programme: position, quantity, role, qualification; (2) perceptions regarding non-contact injury risk factors; (3) tests used to identify non-contact injury risk and (4) non-contact injury prevention exercises used, their perceived effectiveness and implementation strategies.Results44 surveys were successfully returned (47%). The position of physiotherapist was the most represented position in the injury prevention programme. The top five perceived risk factors in rank order were previous injury, fatigue, muscle imbalance, fitness and movement efficiency. The five most commonly used tests to identify injury risk (in rank order) were functional movement screen, questionnaire, isokinetic dynamometry, physical tests and flexibility. The top five exercises used by clubs were (also in rank order) eccentric exercise, balance/proprioception, hamstring eccentric, core stability and, sharing the fifth position, Nordic hamstring and gluteus activation.ConclusionsThe survey revealed the most common perceptions and practices of premier league football clubs internationally regarding risk factors, testing and preventative exercises. The findings can enable reduction of the gap between research and practice.
Objectively measured physical activity trajectories predict adolescent bone strength: Iowa Bone Development Study
Authors: Janz Kathleen F , Letuchy Elena M , Burns Trudy L , Eichenberger Gilmore Julie M , Torner James C , Levy Steven M 
Published: May 2014

BackgroundPhysical activity improves bone strength and reduces the risk for osteoporotic fractures. However, there are substantial gaps in our knowledge as to when, how and how much activity is optimal for bone health.PurposeIn this cohort study, we examined developmental trajectories of objectively measured physical activity from childhood to adolescence to discern if moderate-and-vigorous intensity physical activity (MVPA) predicts bone strength.MethodsStarting at age 5 and continuing at 8, 11, 13, 15 and 17 years, Iowa Bone Development Study participants (n=530) wore an accelerometer for 3–5 days. At age 17, we assessed dual X-ray energy absorptiometry outcomes of mass and estimated geometry (femoral neck cross-sectional area and section modulus). We also assessed geometric properties (bone stress index and polar moment of inertia) of the tibia using peripheral computer quantitative tomography. Latent class modelling was used to construct developmental trajectories of MVPA from childhood to late adolescence. General linear models were used to examine the trajectory groups as predictors of age 17 bone outcomes.ResultsGirls and boys who accumulated the most MVPA had greater bone mass and better geometry at 17 years when compared to less active peers. The proportion of participants achieving high levels of MVPA throughout childhood was very low (<6% in girls) and by late adolescence almost all girls were inactive.ConclusionsBone health benefits of physical activity are not being realised due to low levels of activity for most youth, especially in girls.
Increased utilisation of eye disorder-related ambulatory medical services prior to the diagnosis of Sjögren's syndrome in female patients: a longitudinal population-based study in Taiwan
Authors: Lu Ming-Chi , Fa Wen-Hsiung , Tsai Tzung-Yi , Koo Malcolm , Lai Ning-Sheng 
Published: May 2014

ObjectivesTo investigate the utilisation of eye disorder-related ambulatory medical services prior to the diagnosis of primary Sjögren's syndrome in female Taiwanese patients.DesignA nationwide, population-based case–control study.SettingTaiwan's National Health Insurance Research Database.ParticipantsA total of 347 patients with a diagnosis of primary Sjögren's syndrome from 2005 to 2010 and 1735 controls frequency matched on 10-year age interval and index year were identified from Taiwan's National Health Insurance Research Database. Diagnoses of eye disorder (International Classification of Diseases, Ninth Revision, clinical modification (ICD-9-CM) codes from 360 to 370) were retrospectively screened to 1997.Main outcome measureThe utilisation of eye disorder-related medical service over different intervals prior to diagnosis of Sjögren's syndrome between cases and controls were compared using generalised estimating equations with negative binomial distribution and log link function.ResultsA significantly higher proportion of patients with Sjögren's syndrome (7.5%) utilised eye disorder-related ambulatory medical services over an 8-year interval prior to the diagnosis of the disease compared with controls (4.8%). The annual frequency of utilisation of eye disorder-related ambulatory medical services increased significantly faster when closer to the index date in patients with Sjögren's syndrome compared with controls (interaction effect, p=0.010). Subgroup analyses indicated that the changes over time in the utilisation of services related to disorders of lacrimal system (interaction effect, p=0.019) and conjunctiva (interaction effect, p=0.066) were significantly greater in patients with Sjögren's syndrome compared with controls.ConclusionsAn increase in the utilisation of eye disorder-related ambulatory medical services was observed in patients with Sjögren's syndrome several years prior to the diagnosis of the disease. General practitioners and ophthalmologists can play an important role by including Sjögren's syndrome in the diagnostic evaluation of their patients afflicted with relevant symptoms.
Clinical outcomes and resource utilisation in Medicare patients with chronic liver disease: a historical cohort study
Authors: Younossi Zobair M , Zheng Li , Stepanova Maria , Venkatesan Chapy , Mishra Alita 
Published: May 2014

ObjectiveThe aim of this study is to assess recent trends in health resource utilisation and patient outcomes of Medicare beneficiaries with chronic liver disease (CLD).SettingLiver-related mortality is the 10th leading cause of death in the USA, and hepatitis C virus (HCV) and obesity-related non-alcoholic fatty liver disease are the major causes of CLD. As the US population ages and becomes more obese, the impact of CLD is expected to become more prominent for the Medicare population.ParticipantsThis is a retrospective cohort study of Medicare beneficiaries with a diagnosis of CLD based on inpatient (N=21 576; 14 977 unique patients) and outpatient (N=515 990; 244 196 patients) claims from 2005 to 2010.Primary and secondary outcome measuresThe study outcomes included hospital length of stay (LOS) and inpatient mortality as well as inpatient and outpatient inflation-adjusted payments.ResultsBetween 2005 and 2010, there was an annual decrease in LOS of 3.17% for CLD-related hospitalisations. Risk-adjusted in-hospital mortality decreased (OR 0.90, 95% CI 0.87 to 0.94), while short-term postdischarge mortality remained stable (1.00, 0.98 to 1.03). Inpatient per-claim payment increased from $11 769 in 2005 to $12 347 in 2010 (p=0.0006). Similarly, the average yearly payments for outpatient care increased from $366 to $404 (p<0.0001). This change in payment was observed together with a consistent decrease in the proportion of beneficiary-paid amount (25.4–20%, p<0.0001) as opposed to Medicare-paid amount (73.1–80%, p<0.0001). The major predictors of higher outpatient payments were younger age, Asian race or Hispanic ethnicity, living in California, and having more diagnoses and outpatient procedures per claim. The predictors of inpatient spending also included younger age, location and the number of inpatient procedures.ConclusionsLength of inpatient stay and inpatient mortality among Medicare beneficiaries with CLD decreased, while inpatient and outpatient spending increased.