bluuebunny/crossref_metadata_2025_split huggingface dataset:
In VivoRecognition of thefecA3Target Promoter byHelicobacter pyloriNikR
Authors: Romagnoli Simona , Agriesti Francesca , Scarlato Vincenzo 
Published: January 2011

ABSTRACTInHelicobacter pylori, the transcriptional regulatorHpNikR represses transcription of thefecA3gene by binding to two adjacent operators spanning a region of almost 80 nucleotides along thefecA3promoter in a nickel-dependent manner. By employing hydroxyl radical footprinting, we mapped the protected nucleotides within each operator. Three short sequences rich in A and T nucleotides were identified within each operator, comprising just 24 bases for both operators, with 4 or 5 protected bases interspaced by 4 to 7 free nucleotides, with no center of symmetry. Base substitutions at any site strongly reduced the affinity ofHpNikR for the operators and also affected the stability of the DNA-protein complex, when the promoter-regulator interaction was analyzedin vitro. The effect of these substitutions was remarkably different when transcription of the mutant promoters was analyzedin vivo. Base changes introduced at the farthest subsites impaired theHpNikR-dependent repression, with the mutations closer to +1 completely abolishing the repression, the more distal one still allowing almost 50% of transcription, and the mutations in the middle being ineffective. The data presented here show thatHpNikR may first select its targets by identifying sequences within the previously defined consensus and subsequently establish base-specific contacts to firmly bind DNA. In particular,HpNikR seems to interact in an asymmetric mode with thefecA3target to repress its transcription.
Activators of the Glutamate-Dependent Acid Resistance System Alleviate Deleterious Effects of YidC Depletion inEscherichia coli
Authors: Yu Zhong , Bekker Martijn , Tramonti Angela , Cook Gregory M. , van Ulsen Peter , Scheffers Dirk-Jan , de Mattos Joost Teixeira , De Biase Daniela , Luirink Joen 
Published: January 2011

ABSTRACTThe function of the essential inner membrane protein (IMP) YidC inEscherichia colihas been studied for a limited number of model IMPs and primarily using targeted approaches. These studies suggested that YidC acts at the level of insertion, folding, and quality control of IMPs, both in the context of the Sec translocon and as a separate entity. To further our understanding of YidC's role in IMP biogenesis, we screened a random overexpression library for factors that rescued the growth of cells upon YidC depletion. We found that the overexpression of the GadX and GadY regulators of the glutamate-dependent acid resistance system complemented the growth defect of YidC-depleted cells. Evidence is presented that GadXY overexpression counteracts the deleterious effects of YidC depletion on at least two fronts. First, GadXY prepares the cells for the decrease in respiratory capacity upon the depletion of YidC. Most likely, GadXY-regulated processes reduce the drop in proton-motive force that impairs the fitness of YidC-depleted cells. Second, in GadXY-overproducing cells increased levels of the general chaperone GroEL cofractionate with the inner membranes, which may help to keep newly synthesized inner membrane proteins in an insertion-competent state when YidC levels are limiting.
The Integrity of the Periplasmic Domain of the VirA Sensor Kinase Is Critical for Optimal Coordination of the Virulence Signal Response inAgrobacterium tumefaciens
Authors: Nair Gauri R. , Lai Xiaoqin , Wise Arlene A. , Rhee Benjamin Wonjae , Jacobs Mark , Binns Andrew N. 
Published: January 2011

ABSTRACTThe plant pathogenAgrobacterium tumefaciensresponds to three main signals at the plant-bacterium interface: phenolics, such as acetosyringone (AS), monosaccharides, and acidic pH (∼5.5). These signals are transduced via the chromosomally encoded sugar binding protein ChvE and the Ti plasmid-encoded VirA/VirG two-component regulatory system, resulting in the transcriptional activation of the Ti plasmid virulence genes. Here, we present genetic and physical evidence that the periplasmic domain of VirA dimerizes independently of other parts of the protein, and we examine the effects of several engineered mutations in the periplasmic and transmembrane regions of VirA onvir-inducing capacity as indicated by AS sensitivity and maximal level ofvir-inducing activity at saturating AS levels. The data indicate that helix-breaking mutations throughout the periplasmic domain of VirA or mutations that reposition the second transmembrane domain (TM2) of VirA relieve the periplasmic domain's repressive effects on the maximal activity of this kinase in response to phenolics, effects normally relieved only when ChvE, sugars, and low pH are also present. Such relief, however, does not sensitize VirA to low concentrations of phenolics, the other major effect of the ChvE-sugar and low pH signals. We further demonstrate that amino acid residues in a small Trg-like motif in the periplasmic domain of VirA are crucial for transmission of the ChvE-sugar signal to the cytoplasmic domain. These experiments provide evidence that small perturbations in the periplasmic domain of VirA can uncouple sugar-mediated changes in AS sensitivity from the sugar-mediated effects on maximal activity.
Identification ofEscherichia coliZapC (YcbW) as a Component of the Division Apparatus That Binds and Bundles FtsZ Polymers
Authors: Hale Cynthia A. , Shiomi Daisuke , Liu Bing , Bernhardt Thomas G. , Margolin William , Niki Hironori , de Boer Piet A. J. 
Published: January 2011

ABSTRACTAssembly of the cell division apparatus in bacteria starts with formation of the Z ring on the cytoplasmic face of the membrane. This process involves the accumulation of FtsZ polymers at midcell and their interaction with several FtsZ-binding proteins that collectively organize the polymers into a membrane-associated ring-like configuration. Three such proteins, FtsA, ZipA, and ZapA, have previously been identified inEscherichia coli. FtsA and ZipA are essential membrane-associated division proteins that help connect FtsZ polymers with the inner membrane. ZapA is a cytoplasmic protein that is not required for the fission processper sebut contributes to its efficiency, likely by promoting lateral interactions between FtsZ protofilaments. We report the identification of YcbW (ZapC) as a fourth FtsZ-binding component of the Z ring inE. coli. Binding of ZapC promotes lateral interactions between FtsZ polymers and suppresses FtsZ GTPase activity. This and additional evidence indicate that, like ZapA, ZapC is a nonessential Z-ring component that contributes to the efficiency of the division process by stabilizing the polymeric form of FtsZ.
TheCoxiella burnetiiCryptic Plasmid Is Enriched in Genes Encoding Type IV Secretion System Substrates
Authors: Voth Daniel E. , Beare Paul A. , Howe Dale , Sharma Uma M. , Samoilis Georgios , Cockrell Diane C. , Omsland Anders , Heinzen Robert A. 
Published: January 2011

ABSTRACTThe intracellular bacterial pathogenCoxiella burnetiidirects biogenesis of a phagolysosome-like parasitophorous vacuole (PV), in which it replicates. The organism encodes a Dot/Icm type IV secretion system (T4SS) predicted to deliver to the host cytosol effector proteins that mediate PV formation and other cellular events. AllC. burnetiiisolates carry a large, autonomously replicating plasmid or have chromosomally integrated plasmid-like sequences (IPS), suggesting that plasmid and IPS genes are critical for infection. Bioinformatic analyses revealed two candidate Dot/Icm substrates with eukaryotic-like motifs uniquely encoded by the QpH1 plasmid from the Nine Mile reference isolate. CpeC, containing an F-box domain, and CpeD, possessing kinesin-related and coiled-coil regions, were secreted by the closely relatedLegionella pneumophilaDot/Icm T4SS. An additional QpH1-specific gene,cpeE, situated in a predicted operon withcpeD, also encoded a secreted effector. Further screening revealed that three hypothetical proteins (CpeA, CpeB, and CpeF) encoded by allC. burnetiiplasmids and IPS are Dot/Icm substrates. By use of new genetic tools, secretion of plasmid effectors byC. burnetiiduring host cell infection was confirmed using β-lactamase and adenylate cyclase translocation assays, and a C-terminal secretion signal was identified. When ectopically expressed in HeLa cells, plasmid effectors trafficked to different subcellular sites, including autophagosomes (CpeB), ubiquitin-rich compartments (CpeC), and the endoplasmic reticulum (CpeD). Collectively, these results suggest thatC. burnetiiplasmid-encoded T4SS substrates play important roles in subversion of host cell functions, providing a plausible explanation for the absolute maintenance of plasmid genes by this pathogen.
Inactivation of σ
E
and σ
G
in
Clostridium acetobutylicum
Illuminates Their Roles in Clostridial-Cell-Form Biogenesis, Granulose Synthesis, Solventogenesis, and Spore Morphogenesis
Authors: Tracy Bryan P. , Jones Shawn W. , Papoutsakis Eleftherios T. 
Published: January 2011

ABSTRACT

Central to all clostridia is the orchestration of endospore formation (i.e., sporulation) and, specifically, the roles of differentiation-associated sigma factors. Moreover, there is considerable applied interest in understanding the roles of these sigma factors in other stationary-phase phenomena, such as solvent production (i.e., solventogenesis). Here we separately inactivated by gene disruption the major sporulation-specific sigma factors, σ
E
and σ
G
, and performed an initial analysis to elucidate their roles in sporulation-related morphogenesis and solventogenesis in
Clostridium acetobutylicum
. The terminal differentiation phenotype for the
sigE
inactivation mutant stalled in sporulation prior to asymmetric septum formation, appeared vegetative-like often with an accumulation of DNA at both poles, frequently exhibited two longitudinal internal membranes, and did not synthesize granulose. The
sigE
inactivation mutant did produce the characteristic solvents (i.e., butanol and acetone), but the extent of solventogenesis was dependent on the physiological state of the inoculum. The
sigG
inactivation mutant stalled in sporulation during endospore maturation, exhibiting engulfment and partial cortex and spore coat formation. Lastly, the
sigG
inactivation mutant did produce granulose and exhibited wild-type-like solventogenesis.
Resolution of Holliday Junction Recombination Intermediates by Wild-Type and Mutant IntDOT Proteins
Authors: Kim Seyeun , Gardner Jeffrey F. 
Published: January 2011

ABSTRACT

CTnDOT encodes an integrase that is a member of the tyrosine recombinase family. The recombination reaction proceeds by sequential sets of genetic exchanges between the
attDOT
site in CTnDOT and an
attB
site in the chromosome. The exchanges are separated by 7 base pairs in each site. Unlike most tyrosine recombinases, IntDOT exchanges sites that contain different DNA sequences between the exchange sites to generate Holliday junctions (HJs) that contain mismatched bases. We demonstrate that IntDOT resolves synthetic HJs
in vitro
. Holliday junctions that contain identical sequences between the exchange sites are resolved into both substrates and products, while HJs that contain mismatches are resolved only to substrates. This result implies that resolution of HJs to products requires the formation of a higher-order nucleoprotein complex with natural sites containing IntDOT. We also found that proteins with substitutions of residues (V95, K94, and K96) in a putative alpha helix at the junction of the N and CB domains (coupler region) were defective in resolving HJs. Mutational analysis of charged residues in the coupler and the N terminus of the protein did not provide evidence for a charge interaction between the regions of the protein. V95 may participate in a hydrophobic interaction with another region of IntDOT.
Complete Genome Sequence of
Campylobacter jejuni
Strain S3
Authors: Cooper Kerry K. , Cooper Margarethe A. , Zuccolo Andrea , Law Bibiana , Joens Lynn A. 
Published: January 2011

ABSTRACT

Campylobacter jejuni
is one of the leading causes of bacterial gastroenteritis in the world; however, there is only one complete genome sequence of a poultry strain to date. Here we report the complete genome sequence and annotation of the second poultry strain,
C. jejuni
strain S3. This strain has been shown to be nonmotile, to be a poor invader
in vitro
, and to be a poor colonizer of poultry after minimal
in vitro
passage.
Complete Genome Sequence of the Hyperthermophilic, Piezophilic, Heterotrophic, and Carboxydotrophic Archaeon
Thermococcus barophilus
MP
Authors: Vannier Pauline , Marteinsson Viggo Thor , Fridjonsson Olafur Hedinn , Oger Philippe , Jebbar Mohamed 
Published: January 2011

ABSTRACT

Thermococcus barophilus
is a hyperthermophilic, anaerobic, mixed heterotrophic, and carboxydotrophic euryarchaeon isolated from the deep sea hydrothermal vent Snakepit site on the mid-Atlantic ridge at a depth of 3,550 m.
T. barophilus
is the first true piezophilic, hyperthermophilic archaeon isolated, having an optimal growth at 40 MPa. Here we report the complete genome sequence of strain MP, the type strain of
T. barophilus
. The genome data reveal a close proximity with
T
hermococcus
sibiricus
, another
Thermococcus
isolated from the deep biosphere and a possible connection to life in the depths.
Glycosylation Is Required for Outer Membrane Localization of the Lectin LecB inPseudomonas aeruginosa
Authors: Bartels Kai-Malte , Funken Horst , Knapp Andreas , Brocker Melanie , Bott Michael , Wilhelm Susanne , Jaeger Karl-Erich , Rosenau Frank 
Published: January 2011

ABSTRACTThe fucose-/mannose-specific lectin LecB fromPseudomonas aeruginosais transported to the outer membrane; however, the mechanism used is not known so far. Here, we report that LecB is present in the periplasm ofP. aeruginosain two variants of different sizes. Both were functional and could be purified by their affinity to mannose. The difference in size was shown by a specific enzyme assay to be a result of N glycosylation, and inactivation of the glycosylation sites was shown by site-directed mutagenesis. Furthermore, we demonstrate that this glycosylation is required for the transport of LecB.
Whole Genome Sequence of an UnusualBorrelia burgdorferiSensu Lato Isolate
Authors: Casjens Sherwood R. , Fraser-Liggett Claire M. , Mongodin Emmanuel F. , Qiu Wei-Gang , Dunn John J. , Luft Benjamin J. , Schutzer Steven E. 
Published: January 2011

ABSTRACTHuman Lyme disease is caused by a number of relatedBorrelia burgdorferisensu lato species. We report here the complete genome sequence ofBorreliasp. isolate SV1 from Finland. This isolate is to date the closest known relative ofB. burgdorferisensu stricto, but it is sufficiently genetically distinct from that species that it and its close relatives warrant its candidacy for new-species status. We suggest that this isolate should be named “Borrelia finlandensis.”
Detection of Klebsiella pneumoniae Carbapenemase (KPC) Production in Non-Klebsiella pneumoniae Enterobacteriaceae Isolates by Use of the Phoenix, Vitek 2, and Disk Diffusion Methods
Authors: Doern Christopher D. , Dunne W. Michael , Burnham Carey-Ann D. 
Published: January 2011

ABSTRACT

In this study, we tested the abilities of the Vitek 2, BD Phoenix, and Kirby Bauer disk diffusion tests to detect carbapenemase production in a collection of 14
Klebsiella pneumoniae
carbapenemase (KPC)-producing non-
Klebsiella pneumoniae
isolates. In addition, we evaluated 13 KPC-positive
K. pneumoniae
isolates by using each of these methods and applied both 2009 and 2010 CLSI carbapenem interpretive guidelines.
Mixed mould species in laboratory cultures of respiratory specimens: how should they be reported, and what are the indications for susceptibility testing?: Table 1
Authors: Purcell J , McKenna J , Critten P , Denning D W , Hassan I A 
Published: January 2011

AimsTo investigate how clinical microbiology laboratories should report and interpret mixed mould isolates includingAspergillusspecies from clinical samples and the criteria for susceptibility testing of the isolates.MethodsRetrospectively collected data from our laboratory information system of moulds isolated between January 2005 and December 2007. Patient case notes were also reviewed.ResultsA total of 502 isolates (from 273 patients) were found. 20 patients with clinical diagnosis of a probable fungal infection had mixedAspergillusspecies.ConclusionsIn most instances, the isolation ofAspergillusspecies from non-sterile sites does not represent clinical disease, but only colonisation/contamination. However, for high-risk patients including transplant recipients, a positive culture is associated with invasive disease. Our tertiary centre routinely reports single fungal isolates and mixed cultures with appropriate comments, and those considered significant will also have susceptibility testing carried out. The correlation of culture results with clinical features can differentiate between invasive disease and contamination.
Haemostatic response to hypoxaemic/exercise stress: the dilemma of plasma volume correction: Figure 1
Authors: Fall Lewis , Evans Kevin A , Lewis Michael H , Bailey Damian M 
Published: January 2011

ObjectivePatients with arterial occlusive disease are typically hypoxaemic, and exercise is prescribed for rehabilitation. Both stressors independently contract plasma volume (PV), which may influence clinical interpretation of a patient's thrombogenicity. The aim of the study was to emphasise the conceptual significance of PV correction.Methods and ResultsVenous plasma samples were obtained from 18 healthy men at rest in normoxia for the measurement of fibrinogen, prothrombin (PT), thrombin (TT) and activated partial thromboplastin (aPTT) times. Additional samples were obtained in hypoxia (12% oxygen) after 6 h of rest and immediately after a maximal exercise challenge. Haemostatic parameters were expressed before and after volume-shift correction. Passive hypoxia reduced PV by 3±5% (p<0.05 vs normoxia), with a further decrease observed during exercise (14±5%, p<0.05). The latter increased the absolute concentration of fibrinogen and shortened aPTT (p<0.05), but these changes were no longer apparent after PV correction (p>0.05). Likewise, the lack of change in absolute values for PT and TT (p>0.05) translated into an elongation after correction (p<0.05).ConclusionsThese findings highlight the important, but previously ignored, interpretive implications of PV correction when haemostasis is assessed.
A practical application of analysing weighted kappa for panels of experts and EQA schemes in pathology
Authors: Wright Karen C , Harnden Patricia , Moss Sue , Berney Dan M , Melia Jane 
Published: January 2011

BackgroundKappa statistics are frequently used to analyse observer agreement for panels of experts and External Quality Assurance (EQA) schemes and generally treat all disagreements as total disagreement. However, the differences between ordered categories may not be of equal importance (eg, the difference between grades 1 vs 2 compared with 1 vs 3). Weighted kappa can be used to adjust for this when comparing a small number of readers, but this has not as yet been applied to the large number of readers typical of a national EQA scheme.AimTo develop and validate a method for applying weighted kappa to a large number of readers within the context of a real dataset: the UK National Urological Pathology EQA Scheme for prostatic biopsies.MethodsData on Gleason grade recorded by 19 expert readers were extracted from the fixed text responses of 20 cancer cases from four circulations of the EQA scheme. Composite kappa, currently used to compute an unweighted kappa for large numbers of readers, was compared with the mean kappa for all pairwise combinations of readers. Weighted kappa generalised for multiple readers was compared with the newly developed ‘pairwise-weighted’ kappa.ResultsFor unweighted analyses, the median increase from composite to pairwise kappa was 0.006 (range −0.005 to +0.052). The difference between the pairwise-weighted kappa and generalised weighted kappa for multiple readers never exceeded ±0.01.ConclusionPairwise-weighted kappa is a suitable and highly accurate approximation to weighted kappa for multiple readers.
Mature fat cells in the myocardium of patients with tuberous sclerosis complex: Figure 1
Authors: Adriaensen Miraude E A P M , van Oosterhout Matthijs F M , Feringa Harm H H , Schaefer-Prokop Cornelia M , Zonnenberg Bernard A , Prokop Mathias 
Published: January 2011

AimRoutine abdominal CT scans in patients with tuberous sclerosis complex (TSC) showed characteristic fatty foci in the depicted caudal portions of the myocardium. The purpose of this study was to investigate if areas of abnormal myocardium in patients with TSC could also be found in post-mortem specimens.MethodsA retrospective search of our histopathology database was performed to identify specimens of the heart of patients with TSC. Institutional review board approval was obtained, and patient informed consent was waived. Four specimens were included (mean age, 44 years; range 32–68 years; 2 females).ResultsTwo specimens (50%) of the heart showed areas of mature fat cells in the myocardium, without associated inflammation, without associated fibrosis, without entrapped myocardial cells and without a capsule.ConclusionPost-mortem specimens of the heart of patients with TSC showed areas of mature fat cells in the myocardium which seem to be unique for TSC.
Ethically complex decisions in the neonatal intensive care unit: impact of the new French legislation on attitudes and practices of physicians and nurses: Table 1
Authors: Garel Micheline , Caeymaex Laurence , Goffinet François , Cuttini Marina , Kaminski Monique 
Published: January 2011

ObjectivesA statute enacted in 2005 modified the legislative framework of the rights of terminally ill persons in France. Ten years after the EURONIC study, which described the self-reported practices of neonatal caregivers towards ethical decision-making, a new study was conducted to assess the impact of the new law in neonatal intensive care units (NICU) and compare the results reported by EURONIC with current practices.Setting and designThe study was carried out in the same two NICU as in the EURONIC qualitative study. A third centre was added to increase the sample size. From February to October 2007, 19 physicians and 17 nurses participated in semistructured interviews very similar to those for EURONIC. Content analysis identified the recurring themes emerging from the interviews.ResultsCompared with the EURONIC results, the caregivers reported that they pay greater attention to the views of parents and provided respectful support to the neonates when life-sustaining treatment is withdrawn. Active termination of life has become exceptional. The possibility of withdrawal of treatment, the administration of sedatives to control pain even at the risk of hastening death, the emphasis on sparing parents the burden of decision, and the relative ignorance of the law were very similar to the EURONIC findings.ConclusionBoth the medical and the legal regulation of practices has allowed more dialogue with the parents and more humane care for dying newborns. A new European study is necessary to investigate the possible changes in practices and attitudes also in other countries.