bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic factors in the treatment of generalized aggressive periodontitis: I. Clinical features and initial outcome
Authors: Hughes Francis J. , Syed Mahnaz , Koshy Bindhu , Marinho Valeria , Bostanci Nagihan , McKay Ian J. , Curtis Michael A. , Croucher Raymond E. , Marcenes Wagner 
Published: September 2006

AbstractAims: The aims of this study were to investigate prognostic factors for initial response to non‐surgical periodontal treatment for generalized aggressive periodontitis.Methods: Seventy‐nine patients with generalized aggressive periodontitis were included in this prospective follow‐up intervention study. Patients' clinical and demographic parameters were collected at baseline and 10 weeks following a standard course of treatment (four visits of non‐surgical root surface debridement together with OHI as required). The relationship between clinical variables and treatment outcome were analysed at site‐specific level by χ2 analysis and for patient‐specific variables by logistic regression.Results: In general, there was a good response to the treatment provided. In deep sites the mean pocket depth reduction was 2.11±2.01 mm. Site‐specific analysis showed that the presence of plaque had a small but significant predictive effect on outcome (odds ratio 1.4). Sites on teeth with grade II/III mobility showed a significantly reduced response to treatment.Twenty‐five patients were classified as “non‐responders”. Current smoking was strongly associated with non‐responding patients (odds ratio 3.8) in a logistic regression model; plaque, baseline bleeding and initial pocket depth were not significantly associated with treatment outcomes.Conclusions: Overall, the results emphasize the importance of smoking as a negative prognostic factor, and suggest that treatment outcomes may be determined by a wide range of different determinants requiring further study.
Tudor Religious Cultures in Practice: The Piety and Politics of Grace Mildmay and Her Circle
Authors: Warren Nancy Bradley 
Published: September 2006

AbstractThis essay explores the diversities, complexities, and ambiguities of English religious cultures during the period of religious and political turmoil that constituted the Tudor era. An examination of the religious practices and writings of Grace Sharington Mildmay, members of her natal and conjugal families, and her Northamptonshire neighbors provides a snapshot of the diverse, complex range of Catholicisms and Protestantisms in existence from the beginning of the reign of the first Tudor monarch Henry VII through the end of the Elizabethan regime. The essay emphasizes continuity as well as change, providing an overview of competing versions of the historiography of Tudor religion and underlining the need to reconsider overly simplified understandings of such terms as “Calvinist,”“Puritan,”“recusant,” and “church papist.” It also highlights, through a comparative reading of texts written by Grace Mildmay and the medieval mystic and anchoress Julian of Norwich, the need to rethink the binaries of “medieval” and “early modern” as well as “Catholic” and “Protestant.”
The Emery–Dreifuss muscular dystrophy associated‐protein emerin is phosphorylated on serine 49 by protein kinase A
Authors: Roberts Rhys C. , Sutherland‐Smith Andrew J. , Wheeler Matthew A. , Norregaard Jensen Ole , Emerson Lindsay J. , Spiliotis Ioannis I. , Tate Christopher G. , Kendrick‐Jones John , Ellis Juliet A. 
Published: September 2006

Emerin is a ubiquitously expressed inner nuclear membrane protein of unknown function. Mutations in its gene give rise to X‐linked Emery–Dreifuss muscular dystrophy (X‐EDMD), a neuromuscular condition with an associated life‐threatening cardiomyopathy. We have previously reported that emerin is phosphorylated in a cell cycle‐dependent manner in human lymphoblastoid cell lines [Ellis et al. (1998) Aberrant intracellular targeting and cell cycle‐dependent phosphorylation of emerin contribute to the EDMD phenotype. J. Cell Sci. 111, 781–792]. Recently, five residues in human emerin were identified as undergoing cell cycle‐dependent phosphorylation using a Xenopus egg mitotic cytosol model system (Hirano et al. (2005) Dissociation of emerin from BAF is regulated through mitotic phosphorylation of emerin in a Xenopus egg cell‐free system. J. Biol. Chem.280, 39 925–39 933). In the present paper, recombinant human emerin was purified from a baculovirus‐Sf9 heterogeneous expression system, analyzed by protein mass spectrometry and shown to exist in at least four different phosphorylated species, each of which could be dephosphorylated by treatment with alkaline phosphatase. Further analysis identified three phosphopeptides with m/z values of 2191.9 and 2271.7 corresponding to the singly and doubly phosphorylated peptide 158‐DSAYQSITHYRPVSASRSS‐176, and a m/z of 2396.9 corresponding to the phosphopeptide 47‐RLSPPSSSAASSYSFSDLNSTR‐68. Sequence analysis confirmed that residue S49 was phosphorylated and also demonstrated that this residue was phosphorylated in interphase. Using an in vitro protein kinase A assay, we observed two phospho‐emerin species, one of which was phosphorylated at residue S49. Protein kinase A is thus the first kinase that has been identified to specifically phosphorylate emerin. These results improve our understanding of the molecular mechanisms underlying X‐EDMD and point towards possible signalling pathways involved in regulating emerin's functions.
Comparative Genomic Evidence for a Close Relationship between the Dimorphic Prosthecate Bacteria
Hyphomonas neptunium
and
Caulobacter crescentus
Authors: Badger Jonathan H. , Hoover Timothy R. , Brun Yves V. , Weiner Ronald M. , Laub Michael T. , Alexandre Gladys , Mrázek Jan , Ren Qinghu , Paulsen Ian T. , Nelson Karen E. , Khouri Hoda M. , Radune Diana , Sosa Julia , Dodson Robert J. , Sullivan Steven A. , Rosovitz M. J. , Madupu Ramana , Brinkac Lauren M. , Durkin A. Scott , Daugherty Sean C. , Kothari Sagar P. , Giglio Michelle Gwinn , Zhou Liwei , Haft Daniel H. , Selengut Jeremy D. , Davidsen Tanja M. , Yang Qi , Zafar Nikhat , Ward Naomi L. 
Published: September 2006

ABSTRACT

The dimorphic prosthecate bacteria (DPB) are α-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism
Caulobacter crescentus
. Here we describe the genome sequence of
Hyphomonas neptunium
, a marine member of the DPB that differs from
C. crescentus
in that
H. neptunium
uses its stalk as a reproductive structure. Genome analysis indicates that this organism shares more genes with
C. crescentus
than it does with
Silicibacter pomeroyi
(a closer relative according to 16S rRNA phylogeny), that it relies upon a heterotrophic strategy utilizing a wide range of substrates, that its cell cycle is likely to be regulated in a similar manner to that of
C. crescentus
, and that the outer membrane complements of
H. neptunium
and
C. crescentus
are remarkably similar.
H. neptunium
swarmer cells are highly motile via a single polar flagellum. With the exception of
cheY
and
cheR
, genes required for chemotaxis were absent in the
H. neptunium
genome. Consistent with this observation,
H. neptunium
swarmer cells did not respond to any chemotactic stimuli that were tested, which suggests that
H. neptunium
motility is a random dispersal mechanism for swarmer cells rather than a stimulus-controlled navigation system for locating specific environments. In addition to providing insights into bacterial development, the
H. neptunium
genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging.
Whole-Genome Transcriptional Analysis of Chemolithoautotrophic Thiosulfate Oxidation byThiobacillus denitrificansunder Aerobic versus Denitrifying Conditions
Authors: Beller Harry R. , Letain Tracy E. , Chakicherla Anu , Kane Staci R. , Legler Tina C. , Coleman Matthew A. 
Published: September 2006

ABSTRACTThiobacillus denitrificansis one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur compound oxidation and CO2fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately 10% of the genome) as differentially expressed using RMA (robust multiarray average) statistical analysis and a twofold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochromecbb3oxidase genes,cbbLandcbbS(encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions includednar,nir, andnorgenes (associated, respectively, with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification),cbbM(encoding form II RubisCO), and genes involved with sulfur compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and ofdsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the ordernar>nir>nor>nos. Reverse transcription-quantitative PCR analysis was used to validate these trends.
Lipoprotein PssN of
Rhizobium leguminosarum
bv. trifolii: Subcellular Localization and Possible Involvement in Exopolysaccharide Export
Authors: Marczak Małgorzata , Mazur Andrzej , Król Jarosław E. , Gruszecki Wiesław I. , Skorupska Anna 
Published: September 2006

ABSTRACT

Surface expression of exopolysaccharides (EPS) in gram-negative bacteria depends on the activity of proteins found in the cytoplasmic membrane, the periplasmic space, and the outer membrane.
pssTNOP
genes identified in
Rhizobium leguminosarum
bv. trifolii strain TA1 encode proteins that might be components of the EPS polymerization and secretion system. In this study, we have characterized PssN protein. Employing
pssN
-
phoA
and
pssN
-
lacZ
gene fusions and in vivo acylation with [
3
H]palmitate, we demonstrated that PssN is a 43-kDa lipoprotein directed to the periplasm by an N-terminal signal sequence. Membrane detergent fractionation followed by sucrose gradient centrifugation showed that PssN is an outer membrane-associated protein. Indirect immunofluorescence with anti-PssN and fluorescein isothiocyanate-conjugated antibodies and protease digestion of spheroplasts and intact cells of TA1 provided evidence that PssN is oriented towards the periplasmic space. Chemical cross-linking of TA1 and
E. coli
cells overproducing PssN-His
6
protein showed that PssN might exist as a homo-oligomer of at least two monomers. Investigation of the secondary structure of purified PssN-His
6
protein by Fourier transform infrared spectroscopy revealed the predominant presence of β-structure; however, α-helices were also detected. Influence of an increased amount of PssN protein on the TA1 phenotype was assessed and correlated with a moderate enhancement of EPS production.
Dual Role of the PhoP∼P Response Regulator:Bacillus amyloliquefaciensFZB45 Phytase Gene Transcription Is Directed by Positive and Negative Interactions with thephyCPromoter
Authors: Makarewicz Oliwia , Dubrac Sarah , Msadek Tarek , Borriss Rainer 
Published: September 2006

ABSTRACTSeveralBacillusstrains secrete phytase, an enzyme catalyzing dephosphorylation ofmyo-inositol hexakisphosphate (phytate). We identified thephyC(phytase) gene from environmentalBacillus amyloliquefaciensFZB45 as a member of the phosphate starvation-inducible PhoPR regulon. In vivo and in vitro assays revealed that PhoP∼P is essential forphyC transcription. The transcriptional start site was identified downstream of a σA-like promoter region located 27 bp upstream of the probable translation ATG start codon. Inspection of thephyCpromoter sequence revealed an unusual structure. The− 35 and −10 regions are separated by a window of 21 bp. A pair of tandemly repeated PhoP TT(T/A/C)ACA binding boxes was located within and upstream of the −35 consensus promoter region. A single PhoP box was found within the −10 consensus promoter region. DNase I footprinting experiments performed with isolated PhoP confirmed that PhoP∼P binds at two sites overlapping with thephyC −35 and −10 consensus promoter region. While binding of dimeric PhoP∼P at −35 is essential for activation of thephyCpromoter, binding of PhoP∼P at− 10 suppresses promoter activity. A sixfold enhancement ofphyCgene expression was registered after T:G substitution of nucleotide −13 (mutant MUT13), which eliminates PhoP binding at the single PhoP box without impairing the −10 consensus sequence. Moreover, MUT13 also expressedphyCduring phosphate-replete growth, suggesting that the repressing effect due to binding of PhoP∼P at −10 was abolished. A model is presented in which transcription initiation ofphyCis positively and negatively affected by the actual concentration of the PhoP∼P response regulator.
Modes of Regulation of RpoS by H-NS
Authors: Zhou YanNing , Gottesman Susan 
Published: September 2006

ABSTRACT

Regulated degradation of RpoS requires RssB and ClpXP protease. Mutations in
hns
increase both RpoS synthesis and stability, causing a twofold increase in synthesis and almost complete stabilization of RpoS, independent of effects on synthesis and independent of phosphorylation of RssB. This suggests that H-NS regulates an RssB inhibitor or inhibitors.
The TadV Protein ofActinobacillus actinomycetemcomitansIs a Novel Aspartic Acid Prepilin Peptidase Required for Maturation of the Flp1 Pilin and TadE and TadF Pseudopilins
Authors: Tomich Mladen , Fine Daniel H. , Figurski David H. 
Published: September 2006

ABSTRACTThetadlocus ofActinobacillus actinomycetemcomitansencodes genes for the biogenesis of Flp pili, which allow the bacterium to adhere tenaciously to surfaces and form strong biofilms. Althoughtad(tightadherence) loci are widespread among bacterial and archaeal species, very little is known about the functions of the individual components of the Tad secretion apparatus. Here we characterize the mechanism by which the pre-Flp1 prepilin is processed to the mature pilus subunit. We demonstrate that thetadVgene encodes a prepilin peptidase that is both necessary and sufficient for proteolytic maturation of Flp1. TadV was also found to be required for maturation of the TadE and TadF pilin-like proteins, which we term pseudopilins. Using site-directed mutagenesis, we show that processing of pre-Flp1, pre-TadE, and pre-TadF is required for biofilm formation. Mutation of a highly conserved glutamic acid residue at position +5 of Flp1, relative to the cleavage site, resulted in a processed pilin that was blocked in assembly. In contrast, identical mutations in TadE or TadF had no effect on biofilm formation, indicating that the mechanisms by which Flp1 pilin and the pseudopilins function are distinct. We also determined that two conserved aspartic acid residues in TadV are critical for function of the prepilin peptidase. Together, our results indicate that theA. actinomycetemcomitansTadV protein is a member of a novel subclass of nonmethylating aspartic acid prepilin peptidases.
Structural Basis for Regioselectivity and Stereoselectivity of Product Formation by Naphthalene 1,2-Dioxygenase
Authors: Ferraro Daniel J. , Okerlund Adam L. , Mowers Jonathan C. , Ramaswamy S. 
Published: September 2006

ABSTRACT

Rieske oxygenase (RO) systems are two- and three-component enzyme systems that catalyze the formation of
cis
-dihydrodiols from aromatic substrates. Degradation of pollutants in contaminated soil and generation of chiral synthons have been the major foci of RO research. Substrate specificity and product regio- and stereoselectivity have been shown to vary between individual ROs. While directed evolution methods for altering RO function have been successful in the past, rational engineering of these enzymes still poses a challenge due to the lack of structural understanding. Here we examine the structural changes induced by mutation of Phe-352 in naphthalene 1,2-dioxygenase from
Pseudomonas
sp. strain NCIB 9816-4 (NDO-O
9816-4
). Structures of the Phe-352-Val mutant in native form and in complex with phenanthrene and anthracene, along with those of wild-type NDO-O
9816-4
in complex with phenanthrene, anthracene, and 3-nitrotoluene, are presented. Phenanthrene was shown to bind in a different orientation in the Phe-352-Val mutant active site from that in the wild type, while anthracene was found to bind in similar positions in both enzymes. Two orientations of 3-nitrotoluene were observed, i.e., a productive and a nonproductive orientation. These orientations help explain why NDO-O
9816-4
forms different products from 3-nitrotoluene than those made from nitrobenzene dioxygenase. Comparison of these structures among themselves and with other known ROs bound to substrates reveals that the orientation of substrate binding at the active site is the primary determinant of product regio- and stereoselectivity.
Analysis of RNase P Protein (
rnpA
) Expression in
Bacillus subtilis
Utilizing Strains with Suppressible
rnpA
Expression
Authors: Gößringer Markus , Kretschmer-Kazemi Far Rosel , Hartmann Roland K. 
Published: September 2006

ABSTRACT

Bacterial RNase P is composed of an RNA subunit and a single protein subunit (encoded by the
rnpB
and
rnpA
genes, respectively). We constructed
Bacillus subtilis
mutant strains that conditionally express the RNase P protein under control of the xylose promoter (P

xyl

). In one strain (d7),
rnpA
expression was efficiently repressed in the absence of the inducer xylose, leading to cell growth arrest. Growth could be restored by a second functional
rnpA
allele. This is the first RNase P protein knockdown strain, providing the first direct proof that the
rnpA
gene is essential in
B. subtilis
and, by inference, in other bacteria. We further show (i) that, in the wild-type context,
rnpA
expression is attenuated by transcriptional polarity and (ii) that translation of
rnpA
mRNA in
B. subtilis
can be initiated at two alternative start codons. His-tagged RNase P protein variants are functional in vivo and permit purification of in vivo-assembled holoenzymes by affinity chromatography. Simultaneous expression of plasmid-encoded RNase P RNA and His-tagged protein increased RNase P holoenzyme yields. Massive overproduction of RNase P protein in strain d7 is compatible with cell viability.
FlhF Is Required for Swimming and Swarming in
Pseudomonas aeruginosa
Authors: Murray Thomas S. , Kazmierczak Barbara I. 
Published: September 2006

ABSTRACT

FlhF is a signal recognition particle-like protein present in monotrichous bacteria. The loss of FlhF in various bacteria results in decreased transcription of class II, III, or IV flagellar genes, leads to diminished or absent motility, and results in the assembly of flagella at nonpolar locations on the cell surface. In this work, we demonstrate that the loss of FlhF results in defective swimming and swarming motility of
Pseudomonas aeruginosa
. The FlhF protein localizes to the flagellar pole; in the absence of FlhF, flagellar assembly occurs but is no longer restricted to the pole. Δ
flhF
bacteria swim at lower velocities than wild-type bacteria in liquid media and can no longer swarm when assayed under standard swarming conditions (0.5% agar). However, Δ
flhF
bacteria regain swarming behavior when plated on 0.3% agar. Δ
flhF
organisms show decreased transcription and expression of flagellin (FliC) both in liquid media and on swarming plates compared to wild-type bacteria. However, changes in flagellin expression do not explain the different motility patterns observed for Δ
flhF
bacteria. Instead, the aberrant placement of flagella in Δ
flhF
bacteria may reduce their ability to move this rod-shaped organism effectively.
Genomic Analysis of
Pseudomonas aeruginosa
Phages LKD16 and LKA1: Establishment of the φKMV Subgroup within the T7 Supergroup
Authors: Ceyssens Pieter-Jan , Lavigne Rob , Mattheus Wesley , Chibeu Andrew , Hertveldt Kirsten , Mast Jan , Robben Johan , Volckaert Guido 
Published: September 2006

ABSTRACT

Lytic
Pseudomonas aeruginosa
phages LKD16 and LKA1 were locally isolated and morphologically classified as
Podoviridae
. While LKD16 adsorbs weakly to its host, LKA1 shows efficient adsorption (

k
a

= 3.9 × 10
−9
ml min
−1
). LKA1, however, displays a narrow host range on clinical
P. aeruginosa
strains compared to LKD16. Genome analysis of LKD16 (43,200 bp) and LKA1 (41,593 bp) revealed that both phages have linear double-stranded DNA genomes with direct terminal repeats of 428 and 298 bp and encode 54 and 56 genes, respectively. The majority of the predicted structural proteins were experimentally confirmed as part of the phage particle using mass spectrometry. Phage LKD16 is closely related to bacteriophage φKMV (83% overall DNA homology), allowing a more thoughtful gene annotation of both genomes. In contrast, LKA1 is more distantly related, lacking significant DNA homology and showing protein similarity to φKMV in 48% of its gene products. The early region of the LKA1 genome has diverged strongly from φKMV and LKD16, and intriguing differences in tail fiber genes of LKD16 and LKA1 likely reflect the observed discrepancy in infection-related properties. Nonetheless, general genome organization is clearly conserved among φKMV, LKD16, and LKA1. The three phages carry a single-subunit RNA polymerase gene adjacent to the structural genome region, a feature which distinguishes them from other members of the T7 supergroup. Therefore, we propose that φKMV represents an independent and widespread group of lytic
P. aeruginosa
phages within the T7 supergroup.