bluuebunny/crossref_metadata_2025_split huggingface dataset:
VirB-Mediated Positive Feedback Control of the Virulence Gene Regulatory Cascade of Shigella flexneri
Authors: Kane Kelly A. , Dorman Charles J. 
Published: July 2012

ABSTRACT

Shigella flexneri
is a facultative intracellular pathogen that relies on a type III secretion system and its associated effector proteins to cause bacillary dysentery in humans. The genes that encode this virulence system are located on a 230-kbp plasmid and are transcribed in response to thermal, osmotic, and pH signals that are characteristic of the human lower gut. The virulence genes are organized within a regulatory cascade, and the nucleoid-associated protein H-NS represses each of the key promoters. Transcription derepression depends first on the VirF AraC-like transcription factor, a protein that antagonizes H-NS-mediated repression at the intermediate regulatory gene
virB
. The VirB protein in turn remodels the H-NS–DNA nucleoprotein complexes at the promoters of the genes encoding the type III secretion system and effector proteins, causing these genes to become derepressed. In this study, we show that the VirB protein also positively regulates the expression of its own gene (
virB
) via a
cis
-acting regulatory sequence. In addition, VirB positively regulates the gene coding for the VirF protein. This study reveals two hitherto uncharacterized feedback regulatory loops in the
S. flexneri
virulence cascade that provide a mechanism for the enhanced expression of the principal virulence regulatory genes.
Primer on Agar-Based Microbial Imaging Mass Spectrometry
Authors: Yang Jane Y. , Phelan Vanessa V. , Simkovsky Ryan , Watrous Jeramie D. , Trial Rachelle M. , Fleming Tinya C. , Wenter Roland , Moore Bradley S. , Golden Susan S. , Pogliano Kit , Dorrestein Pieter C. 
Published: July 2012

ABSTRACT
Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry (IMS) applied directly to microbes on agar-based medium captures global information about microbial molecules, allowing for direct correlation of chemotypes to phenotypes. This tool was developed to investigate metabolic exchange factors of intraspecies, interspecies, and polymicrobial interactions. Based on our experience of the thousands of images we have generated in the laboratory, we present five steps of microbial IMS: culturing, matrix application, dehydration of the sample, data acquisition, and data analysis/interpretation. We also address the common challenges encountered during sample preparation, matrix selection and application, and sample adherence to the MALDI target plate. With the practical guidelines described herein, microbial IMS use can be extended to bio-based agricultural, biofuel, diagnostic, and therapeutic discovery applications.
Characterization of the Organic Hydroperoxide Resistance System of Brucella abortus 2308
Authors: Caswell Clayton C. , Baumgartner John E. , Martin Daniel W. , Roop R. Martin 
Published: July 2012

ABSTRACTThe organic hydroperoxide resistance protein Ohr has been identified in numerous bacteria where it functions in the detoxification of organic hydroperoxides, and expression ofohris often regulated by a MarR-type regulator called OhrR. The genes annotated as BAB2_0350 and BAB2_0351 in theBrucella abortus2308 genome sequence are predicted to encode OhrR and Ohr orthologs, respectively. Using isogenicohrandohrRmutants andlacZpromoter fusions, it was determined that Ohr contributes to resistance to organic hydroperoxide, but not hydrogen peroxide, inB. abortus2308 and that OhrR represses the transcription of bothohrandohrRin this strain. Moreover, electrophoretic mobility shift assays and DNase I footprinting revealed that OhrR binds directly to a specific region in the intergenic region betweenohrandohrRthat shares extensive nucleotide sequence similarity with so-called “OhrR boxes” described in other bacteria. While Ohr plays a prominent role in protectingB. abortus2308 from organic hydroperoxide stress inin vitroassays, this protein is not required for the wild-type virulence of this strain in cultured murine macrophages or experimentally infected mice.
Cell Wall Amidase AmiC1 Is Required for Cellular Communication and Heterocyst Development in the Cyanobacterium Anabaena PCC 7120 but Not for Filament Integrity
Authors: Berendt Susanne , Lehner Josef , Zhang Yao Vincent , Rasse Tobias M. , Forchhammer Karl , Maldener Iris 
Published: July 2012

ABSTRACT

Filamentous cyanobacteria of the order
Nostocales
display typical properties of multicellular organisms. In response to nitrogen starvation, some vegetative cells differentiate into heterocysts, where fixation of N
2
takes place. Heterocysts provide a micro-oxic compartment to protect nitrogenase from the oxygen produced by the vegetative cells. Differentiation involves fundamental remodeling of the Gram-negative cell wall by deposition of a thick envelope and by formation of a neck-like structure at the contact site to the vegetative cells. Cell wall-hydrolyzing enzymes, like cell wall amidases, are involved in peptidoglycan maturation and turnover in unicellular bacteria. Recently, we showed that mutation of the amidase homologue
amiC2
gene in
Nostoc punctiforme
ATCC 29133 distorts filament morphology and function. Here, we present the functional characterization of two
amiC
paralogues from
Anabaena
sp. strain PCC 7120. The
amiC1
(
alr0092
) mutant was not able to differentiate heterocysts or to grow diazotrophically, whereas the
amiC2
(
alr0093
) mutant did not show an altered phenotype under standard growth conditions. In agreement, fluorescence recovery after photobleaching (FRAP) studies showed a lack of cell-cell communication only in the AmiC1 mutant. Green fluorescent protein (GFP)-tagged AmiC1 was able to complement the mutant phenotype to wild-type properties. The protein localized in the septal regions of newly dividing cells and at the neck region of differentiating heterocysts. Upon nitrogen step-down, no mature heterocysts were developed in spite of ongoing heterocyst-specific gene expression. These results show the dependence of heterocyst development on amidase function and highlight a pivotal but so far underestimated cellular process, the remodeling of peptidoglycan, for the biology of filamentous cyanobacteria.
Rethinking the Evolution of Single-Stranded RNA (ssRNA) Bacteriophages Based on Genomic Sequences and Characterizations of Two R-Plasmid-Dependent ssRNA Phages, C-1 and Hgal1
Authors: Kannoly Sherin , Shao Yongping , Wang Ing-Nang 
Published: July 2012

ABSTRACTWe have sequenced and characterized two R-plasmid-dependent single-stranded RNA bacteriophages (RPD ssRNA phages), C-1 and Hagl1. Phage C-1 requires a conjugative plasmid of the IncC group, while Hgal1 requires the IncH group. Both the adsorption rate constants and one-step growth curves are determined for both phages. We also empirically confirmed the lysis function of the predicted lysis genes. Genomic sequencing and phylogenetic analyses showed that both phages belong to theLevivirusgroup and are most closely related to another IncP-plasmid-dependent ssRNA phage, PRR1. Furthermore, our result strongly suggests that the stereotypical bauplans of genome organization found inLevivirusandAlloleviviruspredate phage specialization for conjugative plasmids, suggesting that the utilization of conjugative plasmids for cell attachment and entry comprises independent evolutionary events for these two main clades of ssRNA phages. Our result is also consistent with findings of a previous study, making theLevivirus-like genome organization ancestral and theAllolevivirus-like genome derived. To obtain a deeper insight into the evolution of ssRNA phages, more phages specializing for various conjugative plasmids and infecting different bacterial species would be needed.
The Small RNA RteR Inhibits Transfer of the Bacteroides Conjugative Transposon CTnDOT
Authors: Waters Jillian L. , Salyers Abigail A. 
Published: July 2012

ABSTRACT

CTnDOT is a 65-kb conjugative transposon present in
Bacteroides
spp. that confers resistance to erythromycin [
erm
(F)] and tetracycline [
tet
(Q)]. An interesting feature of CTnDOT is that both excision from the chromosome and transfer of CTnDOT are stimulated by exposure to tetracycline. However, when no tetracycline is present, transfer of CTnDOT is not detectable. Previous studies suggested that a region containing a small RNA, RteR, appeared to mediate repression of CTnDOT transfer; however, virtually nothing was known about RteR. We have demonstrated that RteR is a 90-nucleotide transcript that is not further processed. RteR inhibits conjugative transfer of CTnDOT by targeting the transfer region, a 13-kb operon that encodes the
tra
genes required to assemble the mating apparatus. We report here that RteR interacts with the region downstream of
traA
. Levels of the downstream
tra
mRNA are dramatically reduced when RteR is present. Further, RteR does not appear to decrease the half-life of the
tra
mRNA transcript, suggesting that RteR does not bind to the transcript to initiate RNase-dependent decay, similar to other
trans
-acting small RNAs. We predict that RteR may act to enhance termination of the
tra
operon within
traB
, which could account for the decreased abundance of the
tra
transcript downstream of
traA
and explain why the
tra
mRNA has the same half-life whether or not RteR is present. RteR is the only small RNA that has been characterized so far within the
Bacteroidetes
phylum.
The Primosomal Protein DnaD Inhibits Cooperative DNA Binding by the Replication Initiator DnaA in Bacillus subtilis
Authors: Bonilla Carla Y. , Grossman Alan D. 
Published: July 2012

ABSTRACTDnaA is an AAA+ ATPase and the conserved replication initiator in bacteria. Bacteria control the timing of replication initiation by regulating the activity of DnaA. DnaA binds to multiple sites in the origin of replication (oriC) and is required for recruitment of proteins needed to load the replicative helicase. DnaA also binds to other chromosomal regions and functions as a transcription factor at some of these sites.Bacillus subtilisDnaD is needed during replication initiation for assembly of the replicative helicase atoriCand during replication restart at stalled replication forks. DnaD associates with DnaA atoriCand at other chromosomal regions bound by DnaA. Using purified proteins, we found that DnaD inhibited the ability of DnaA to bind cooperatively to DNA and caused a decrease in the apparent dissociation constant. These effects of DnaD were independent of the ability of DnaA to bind or hydrolyze ATP. Other proteins known to regulateB. subtilisDnaA also affect DNA binding, whereas much of the regulation ofEscherichia coliDnaA affects nucleotide hydrolysis or exchange. We found that the rate of nucleotide exchange forB. subtilisDnaA was high and not affected by DnaD. The rapid exchange is similar to that ofStaphylococcus aureusDnaA and in contrast to the low exchange rate ofEscherichia coliDnaA. We suggest that organisms in which DnaA has a high rate of nucleotide exchange predominantly regulate the DNA binding activity of DnaA and that those with low rates of exchange regulate hydrolysis and exchange.
Characterization of a New GlnR Binding Box in the Promoter of
amtB
in Streptomyces coelicolor Inferred a PhoP/GlnR Competitive Binding Mechanism for Transcriptional Regulation of
amtB
Authors: Wang Ying , Cen Xu-Feng , Zhao Guo-Ping , Wang Jin 
Published: July 2012

ABSTRACT

The transcription of
amtB
in
Streptomyces coelicolor
has been proposed to be counter-regulated by GlnR (a global regulator for nitrogen metabolism) and PhoP (a global regulator for phosphate metabolism). However, the GlnR-protected region, which was deduced to be two 22-bp GlnR binding boxes (gTnAc-n6-GaAAc-n6-GtnAC-n6-GAAAc-n6, abbreviated as
a1-b1
and
a2-b2
), was separated from the PhoP-protected region in the promoter of
amtB
, leaving the mechanism for this regulation undefined. In this study, another 22-bp GlnR binding box, which consisted of
a3
-site-n6-
b3
-site (
a3-b3
) overlapping with the PhoP-binding sequences, was identified in the promoter region of
amtB
by a DNase I footprinting assay. An electrophoretic mobility shift assay (EMSA) using purified recombinant GlnR and the synthetic
amtB
promoter fragments with the three GlnR binding boxes individually mutated demonstrated that every box was involved in GlnR binding
in vitro
. Further
in vivo
assays using the
egfp
reporter gene fused to various kinds of mutated promoter regions of
amtB
demonstrated that all of the three GlnR binding boxes were required for GlnR-mediated activation of
amtB
transcription under the nitrogen-limited condition. The results of EMSA using the
amtB
promoter with mixtures of recombinant His-tagged GlnR and Trx-His-S-tagged PhoP inferred that PhoP might compete against GlnR from binding at the
a3-b3
site, attributable to the PhoP/GlnR counter-regulatory function subjected to further experimental proof.
Impact of a hospital-wide hand hygiene initiative on healthcare-associated infections: results of an interrupted time series
Authors: Kirkland Kathryn B , Homa Karen A , Lasky Rosalind A , Ptak Judy A , Taylor Eileen A , Splaine Mark E 
Published: July 2012

BackgroundEvidence that hand hygiene (HH) reduces healthcare-associated infections has been available for almost two centuries. Yet HH compliance among healthcare professionals continues to be low, and most efforts to improve it have failed.ObjectiveTo improve healthcare workers' HH, and reduce healthcare-associated infections.Design3-year interrupted time series with multiple sequential interventions and 1-year post-intervention follow-up.SettingTeaching hospital in rural New Hampshire.InterventionsIn five categories: (1) leadership/accountability; (2) measurement/feedback; (3) hand sanitiser availability; (4) education/training; and (5) marketing/communication.MeasurementMonthly changes in observed HH compliance (%) and rates of healthcare-associated infection (includingStaphylococcus aureusinfections,Clostridium difficileinfections and bloodstream infections) per 1000 inpatient days. The subset ofS aureusinfections attributable to the operating room served as a tracer condition. We used statistical process control charts to identify significant changes.ResultsHH compliance increased significantly from 41% to 87% (p<0.01) during the initiative, and improved further to 91% (p<0.01) the following year. Nurses achieved higher HH compliance (93%) than physicians (78%). There was a significant, sustained decline in the healthcare-associated infection rate from 4.8 to 3.3 (p<0.01) per 1000 inpatient days. The rate ofS aureusinfections attributable to the operating room rose, while the rate of otherS aureusinfections fell.ConclusionsOur initiative was associated with a large and significant hospital-wide improvement in HH which was sustained through the following year and a significant, sustained reduction in the incidence of healthcare-associated infection. The observed increased incidence of the tracer condition supports the assertion that HH improvement contributed to infection reduction. Persistent variation in HH performance among different groups requires further study.
Diagnostic errors in the intensive care unit: a systematic review of autopsy studies
Authors: Winters Bradford , Custer Jason , Galvagno Samuel M , Colantuoni Elizabeth , Kapoor Shruti G , Lee HeeWon , Goode Victoria , Robinson Karen , Nakhasi Atul , Pronovost Peter , Newman-Toker David 
Published: July 2012

ContextMisdiagnoses may be an underappreciated cause of preventable morbidity and mortality in the intensive care unit (ICU). Their prevalence, nature, and impact remain largely unknown.ObjectivesTo determine whether potentially fatal ICU misdiagnoses would be more common than in the general inpatient population (∼5%), and would involve more infections or vascular events.Data sourcesSystematic review of studies identified by electronic (MEDLINE, etc.) and manual searches (references in eligible articles) without language restriction (1966 through 2011).Study selection and data abstractionObservational studies examining autopsy-confirmed diagnostic errors in the adult ICU were included. Studies analysing misdiagnosis of one specific disease were excluded. Study results (autopsy rate, misdiagnosis prevalence, Goldman error class, diseases misdiagnosed) were abstracted and descriptive statistics calculated. We modelled the prevalence of Class I (potentially lethal) misdiagnoses as a non-linear function of the autopsy rate.ResultsOf 276 screened abstracts, 31 studies describing 5863 autopsies (median rate 43%) were analysed. The prevalence of misdiagnoses ranged from 5.5%–100% with 28% of autopsies reporting at least one misdiagnosis and 8% identifying a Class I diagnostic error. The projected prevalence of Class I misdiagnoses for a hypothetical autopsy rate of 100% was 6.3% (95% CI 4.0% to 7.5%). Vascular events and infections were the leading lethal misdiagnoses (41% each). The most common individual Class I misdiagnoses were PE, MI, pneumonia, and aspergillosis.ConclusionsOur data suggest that as many as 40 500 adult patients in an ICU in USA may die with an ICU misdiagnoses annually. Despite this, diagnostic errors receive relatively little attention and research funding. Future studies should seek to prospectively measure the prevalence and impact of diagnostic errors and potential strategies to reduce them.
Removal of doctors from practice for professional misconduct in Australia and New Zealand
Authors: Elkin Katie , Spittal Matthew J , Elkin David , Studdert David M 
Published: July 2012

ObjectiveTo examine how disciplinary tribunals assess different forms of misconduct in deciding whether to remove doctors from practice for professional misconduct.Design and settingMultivariable regression analysis of 485 cases in which tribunals found doctors guilty of professional misconduct. The cases came from four Australian states (New South Wales, Victoria, Queensland and Western Australia) and New Zealand and were decided over a 10-year period (1 January 2000 – 30 September 2009).Main outcome measuresType of misconduct, the tribunal's explanation for why the misconduct occurred, and the disciplinary measure imposed.Results43% of the cases resulted in removal of the offending doctor from practice, 37% in restrictions on practice and 19% in non-restrictive sanctions. The odds of removal were very high in cases involving sexual relationships with patients (OR 22.59; 95% CI 10.18 to 50.14) and moderately high in cases involving inappropriate sexual conduct (not in the context of a relationship), commission of criminal offences, and forms of inappropriate conduct unrelated to patients. Cases in which the misconduct was judged to be due to willful wrongdoing (OR 17.14; 95% CI 8.62 to 34.09), incompetence (OR 6.02; 95% CI 2.87 to 12.63) and issues in the doctor's personal life (OR 4.17; 95% CI 2.07 to 8.41) also had higher odds removal from practice.ConclusionTribunals in Australia and New Zealand tend to remove doctors from practice for behaviours indicative of character flaws and lack of insight, rather than behaviours exhibiting errors in care delivery, poor clinical judgement or lack of knowledge. The generalisability of these findings to regulatory regimes for health practitioners in other countries should be tested.
Improving outcome in severe trauma: what's new in ABC? Imaging, bleeding and brain injury
Authors: Harris Tim , Davenport Ross , Hurst Tom , Hunt Paul , Fotheringham Tim , Jones Jonathan 
Published: July 2012

Abstract
Appropriate imaging is critical in the initial assessment of patients with severe trauma. Plain radiographs remain integral to the primary survey. Focused ultrasonography is useful for identifying intraperitoneal fluid likely to represent haemorrhage in patients who are shocked and also has a role in identifying intrathoracic pathology. Modern scanners permit a greater role for CT, being more rapid and exposing the patient to less ionising radiation. ‘Whole body’ (head to pelvis) CT scanning has been shown to identify injuries missed by ‘traditional’ focused assessment and may be associated with an improved outcome. CT identifies more spinal injuries than plain radiographs, is the gold standard for diagnosing blunt aortic injury and facilitates non-operative management of solid organ injury and other bleeding. Coagulopathy occurs early in trauma as a direct result of injury and hypoperfusion. Damage control resuscitation with blood components is associated with an improved outcome in patients with trauma with massive haemorrhage. Packed cells and fresh frozen plasma should be used in a 1:1 to 1:2 ratio. Bedside measures of coagulopathy may prove useful. Adjuvant early treatment with tranexamic acid is of benefit in reducing blood loss and reducing mortality. Limited ‘damage control surgery’ with early optimisation of physiology augmented by interventional radiology to control haemorrhage is preferable to early definitive care. Limiting haemorrhage by correction of anticoagulation and minimising secondary brain injury through optimal supportive care is critical to improving outcome in neurotrauma.
Comparative outcomes of total hip and knee arthroplasty: a prospective cohort study
Authors: Hamilton David , Henderson G Robin , Gaston Paul , MacDonald Deborah , Howie Colin , Simpson A Hamish R W 
Published: July 2012

Abstract

Purpose
The comparative outcome of primary hip and knee arthroplasty is not well understood. This study aimed to investigate the outcome and satisfaction of these procedures and determine predictive models for 1 year patient outcome with a view to informing surgical management and patient expectations.

Study design
Prospective cohort study of all primary hip and knee arthroplasty procedures performed at the Royal Infirmary of Edinburgh between January 2006 and November 2008. General health (SF-12) and joint specific function (Oxford Score) was assessed pre-operatively and at 6 and 12 months post-operatively. Patient satisfaction was assessed at 12 months.

Results
1410 total hip arthroplasty (THA) and 1244 total knee arthroplasty (TKA) procedures were assessed. Oxford Score improved by 4.9 points more in THA patients than in TKA patients. SF-12 physical scores were on average 2.7 points greater in the THA patients at one year. Satisfaction was also greater (91%) following THA compared with TKA (81%). Regression modelling was not able to predict individual patient outcome; however, mean pre-operative Oxford Scores were found to be strong predictors of mean post-operative Oxford Scores for each procedure. Age, gender and pre-operative general health scores did not influence these models.

Conclusions
Both THA and TKA confer substantial improvement in patient outcome; however, greater joint specific, general health and satisfaction scores are reported following THA. This difference is physical in nature. Regression models are presented that can be applied to predict mean hip/knee arthroplasty outcome based on preoperative values.