bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Characterization and Assembly of the Distal Tail Structure of the Temperate Lactococcal Bacteriophage TP901-1
Authors: Vegge Christina S. , Brøndsted Lone , Neve Horst , Mc Grath Stephen , van Sinderen Douwe , Vogensen Finn K. 
Published: June 2005

ABSTRACT

The tail structures of bacteriophages infecting gram-positive bacteria are largely unexplored, although the phage tail mediates the initial interaction with the host cell. The temperate
Lactococcus lactis
phage TP901-1 of the
Siphoviridae
family has a long noncontractile tail with a distal baseplate. In the present study, we investigated the distal tail structures and tail assembly of phage TP901-1 by introducing nonsense mutations into the late transcribed genes
dit
(
orf46
),

tal
TP901-1

(
orf47
),
bppU
(
orf48
),
bppL
(
orf49
), and
orf50
. Transmission electron microscopy examination of mutant and wild-type TP901-1 phages showed that the baseplate consisted of two different disks and that a central tail fiber is protruding below the baseplate. Evaluation of the mutant tail morphologies with protein profiles and Western blots revealed that the upper and lower baseplate disks consist of the proteins BppU and BppL, respectively. Likewise, Dit and Tal
TP901-1
were shown to be structural tail proteins essential for tail formation, and Tal
TP901-1
was furthermore identified as the tail fiber protein by immunogold labeling experiments. Determination of infection efficiencies of the mutant phages showed that the baseplate is fundamental for host infection and the lower disk protein, BppL, is suggested to interact with the host receptor. In contrast, ORF50 was found to be nonessential for tail assembly and host infection. A model for TP901-1 tail assembly, in which the function of eight specific proteins is considered, is presented.
A Second Outer-Core Region in
Klebsiella pneumoniae
Lipopolysaccharide
Authors: Regué Miguel , Izquierdo Luis , Fresno Sandra , Piqué Núria , Corsaro Maria Michela , Naldi Teresa , De Castro Cristina , Waidelich Dietmar , Merino Susana , Tomás Juan M. 
Published: June 2005

ABSTRACT

Up to now only one major type of core oligosaccharide has been found in the lipopolysaccharide of all
Klebsiella pneumoniae
strains analyzed. Applying a different screening approach, we identified a novel
Klebsiella pneumoniae
core (type 2). Both
Klebsiella
core types share the same inner core and the outer-core-proximal disaccharide, GlcN-(1,4)-GalA, but they differ in the GlcN substituents. In core type 2, the Glc
p
N residue is substituted at the O-4 position by the disaccharide β-Glc
p
(1-6)-α-Glcp(1, while in core type 1 the Glc
p
N residue is substituted at the O-6 position by either the disaccharide α-He
p
(1-4)-α-Kdo(2 or a Kdo residue (Kdo is 3-deoxy-
d
-manno-octulosonic acid). This difference correlates with the presence of a three-gene region in the corresponding core biosynthetic clusters. Engineering of both core types by interchanging this specific region allowed studying the effect on virulence. The replacement of
Klebsiella
core type 1 in a highly type 2 virulent strain (52145) induces lower virulence than core type 2 in a murine infection model.
Defense against Protein Carbonylation by DnaK/DnaJ and Proteases of the Heat Shock Regulon
Authors: Fredriksson Åsa , Ballesteros Manuel , Dukan Sam , Nyström Thomas 
Published: June 2005

ABSTRACT

Protein carbonylation is an irreversible oxidative modification that increases during organism aging and bacterial growth arrest. We analyzed whether the heat shock regulon has a role in defending
Escherichia coli
cells against this deleterious modification upon entry into stationary phase. Providing the cell with ectopically elevated levels of the heat shock transcription factor, σ
32
, effectively reduced stasis-induced carbonylation. Separate overproduction of the major chaperone systems, DnaK/DnaJ and GroEL/GroES, established that the former of these is more important in counteracting protein carbonylation. Deletion of the heat shock proteases Lon and HslVU enhanced carbonylation whereas a
clpP
deletion alone had no effect. However, ClpP appears to have a role in reducing protein carbonyls in cells lacking Lon and HslVU. Proteomic immunodetection of carbonylated proteins in the wild-type,
lon
, and
hslVU
strains demonstrated that the same spectrum of proteins displayed a higher load of carbonyl groups in the
lon
and
hslVU
mutants. These proteins included the β-subunit of RNA polymerase, elongation factors Tu and G, the E1 subunit of the pyruvate dehydrogenase complex, isocitrate dehydrogenase, 6-phosphogluconate dehydrogenase, and serine hydroxymethyltranferase.
Crystal Structure of the
Staphylococcus aureus
pI258 CadC Cd(II)/Pb(II)/Zn(II)-Responsive Repressor
Authors: Ye Jun , Kandegedara Ashoka , Martin Philip , Rosen Barry P. 
Published: June 2005

ABSTRACT

The
Staphylococcus aureus
plasmid pI258
cadCA
operon encodes a P-type ATPase, CadA, that confers resistance to the heavy metals Cd(II), Zn(II), and Pb(II). Expression of this heavy-metal efflux pump is regulated by CadC, a homodimeric repressor that dissociates from the
cad
operator/promoter upon binding of Cd(II), Pb(II), or Zn(II). CadC is a member of the ArsR/SmtB family of metalloregulatory proteins. Here we report the X-ray crystal structure of CadC at 1.9 Å resolution. The dimensions of the protein dimer are approximately 30 Å by 40 Å by 70 Å. Each monomer contains six α-helices and a three-stranded β-sheet. Helices 4 and 5 form a classic helix-turn-helix motif that is the putative DNA binding region. The α1 helix of one monomer crosses the dimer to approach the α4 helix of the other monomer, consistent with the previous proposal that these two regulatory metal binding sites for the inducer cadmium or lead are each formed by Cys-7 and Cys-11 from the N terminus of one monomer and Cys-58 and Cys-60 of the other monomer. Two nonregulatory metal binding sites containing zinc are formed between the two antiparallel α6 helices at the dimerization interface. This is the first reported three-dimensional structure of a member of the ArsR/SmtB family with regulatory metal binding sites at the DNA binding domain and the first structure of a transcription repressor that responds to the heavy metals Cd(II) and Pb(II).
Regulation of Transcription in a Reduced Bacterial Genome: Nutrient-Provisioning Genes of the Obligate SymbiontBuchnera aphidicola
Authors: Moran Nancy A. , Dunbar Helen E. , Wilcox Jennifer L. 
Published: June 2005

ABSTRACTBuchnera aphidicola, the obligate symbiont of aphids, has an extremely reduced genome, of which about 10% is devoted to the biosynthesis of essential amino acids needed by its hosts. Most regulatory genes for these pathways are absent, raising the question of whether and how transcription of these genes responds to the major shifts in dietary amino acid content encountered by aphids. Using full-genome microarrays forB. aphidicolaof the hostSchizaphis graminum, we examined transcriptome responses to changes in dietary amino acid content and then verified behavior of individual transcripts using quantitative reverse transcriptase PCR. The only gene showing a consistent and substantial (>twofold) response wasmetE, which underlies methionine biosynthesis and which is the only amino acid biosynthetic gene retaining its ancestral regulator (metR). In another aphid host,Acyrthosiphon pisum,B. aphidicolahas no functionalmetRand shows no response inmetEtranscript levels to changes in amino acid concentrations. Thus, the only substantial transcriptional response involves the one gene for which an ancestral regulator is retained. This result parallels that from a previous study on heat stress, in which only the few genes retaining the global heat shock promoter showed responses in transcript abundance. The irreversible losses of transcriptional regulators constrain ability to alter gene expression in the context of environmental fluctuations affecting the symbiotic partners.
Overproduction of CcmG and CcmFH
Rc
Fully Suppresses the
c
-Type Cytochrome Biogenesis Defect of
Rhodobacter capsulatus
CcmI-Null Mutants
Authors: Sanders Carsten , Deshmukh Meenal , Astor Doniel , Kranz Robert G. , Daldal Fevzi 
Published: June 2005

ABSTRACT

Gram-negative bacteria like
Rhodobacter capsulatus
use intertwined pathways to carry out the posttranslational maturation of
c
-type cytochromes (Cyts). This periplasmic process requires at least 10 essential components for apo-Cyt
c
chaperoning, thio-oxidoreduction, and the delivery of heme and its covalent ligation. One of these components, CcmI (also called CycH), is thought to act as an apo-Cyt
c
chaperone. In
R. capsulatus
, CcmI-null mutants are unable to produce
c
-type Cyts and thus sustain photosynthetic (Ps) growth. Previously, we have shown that overproduction of the putative heme ligation components CcmF and CcmH
Rc
(also called Ccl1 and Ccl2) can partially bypass the function of CcmI on minimal, but not on enriched, media. Here, we demonstrate that either additional overproduction of CcmG (also called HelX) or hyperproduction of CcmF-CcmH
Rc
is needed to completely overcome the role of CcmI during the biogenesis of
c
-type Cyts on both minimal and enriched media. These findings indicate that, in the absence of CcmI, interactions between the heme ligation and thioreduction pathways become restricted for sufficient Cyt
c
production. We therefore suggest that CcmI, along with its apo-Cyt chaperoning function, is also critical for the efficacy of holo-Cyt
c
formation, possibly via its close interactions with other components performing the final heme ligation steps during Cyt
c
biogenesis.
A Phosphohexomutase from the Archaeon
Sulfolobus solfataricus
Is Covalently Modified by Phosphorylation on Serine
Authors: Ray W. Keith , Keith Sabrina M. , DeSantis Andrea M. , Hunt Jeremy P. , Larson Timothy J. , Helm Richard F. , Kennelly Peter J. 
Published: June 2005

ABSTRACT

A phosphoserine-containing peptide was identified from tryptic digests from
Sulfolobus solfataricus
P1 by liquid chromatography-tandem mass spectrometry. Its amino acid sequence closely matched that bracketing Ser-309 in the predicted protein product of open reading frame sso0207, a putative phosphohexomutase, in the genome of
S. solfataricus
P2. Open reading frame sso0207 was cloned, and its protein product expressed in
Escherichia coli
. The recombinant protein proved capable of interconverting mannose 1-phosphate and mannose 6-phosphate, as well as glucose 1-phosphate and glucose 6-phosphate, in vitro. It displayed no catalytic activity toward glucosamine 6-phosphate or
N
-acetylglucosamine 6-phosphate. Models constructed using the X-ray crystal structure of a homologous phosphohexomutase from
Pseudomonas aeruginosa
predicted that Ser-309 of the archaeal protein lies within the substrate binding site. The presence of a phosphoryl group at this location would be expected to electrostatically interfere with the binding of negatively charged phosphohexose substrates, thus attenuating the catalytic efficiency of the enzyme. Using site-directed mutagenesis, Ser-309 was substituted by aspartic acid to mimic the presence of a phosphoryl group. The
V
max
of the mutationally altered protein was only 4% that of the unmodified form. Substitution of Ser-309 with larger, but uncharged, amino acids, including threonine, also decreased catalytic efficiency, but to a lesser extent—three- to fivefold. We therefore predict that phosphorylation of the enzyme in vivo serves to regulate its catalytic activity.
Integrative Genomic, Transcriptional, and Proteomic Diversity in Natural Isolates of the Human PathogenBurkholderia pseudomallei
Authors: Ou Keli , Ong Catherine , Koh Shze Yung , Rodrigues Fiona , Sim Siew Hoon , Wong Daniel , Ooi Chia Huey , Ng Kim Chong , Jikuya Hiroyuki , Yau Chin Chin , Soon Sou Yen , Kesuma Djohan , Lee May Ann , Tan Patrick 
Published: June 2005

ABSTRACTNatural isolates of pathogenic bacteria can exhibit a broad range of phenotypic traits. To investigate the molecular mechanisms contributing to such phenotypic variability, we compared the genomes, transcriptomes, and proteomes of two natural isolates of the gram-negative bacteriumBurkholderia pseudomallei, the causative agent of the human disease melioidosis. Significant intrinsic genomic, transcriptional, and proteomic variations were observed between the two strains involving genes of diverse functions. We identified 16 strain-specific regions in theB. pseudomalleiK96243 reference genome, and for eight regions their differential presence could be ascribed to either DNA acquisition or loss. A remarkable 43% of the transcriptional differences between the strains could be attributed to genes that were differentially present between K96243 and Bp15682, demonstrating the importance of lateral gene transfer or gene loss events in contributing to pathogen diversity at the gene expression level. Proteins expressed in a strain-specific manner were similarly correlated at the gene expression level, but up to 38% of the global proteomic variation between strains comprised proteins expressed in both strains but associated with strain-specific protein isoforms. Collectively, >65 hypothetical genes were transcriptionally or proteomically expressed, supporting their bona fide biological presence. Our results provide, for the first time, an integrated framework for classifying the repertoire of natural variations existing at distinct molecular levels for an important human pathogen.
Biochemical Characterization of a Prokaryotic Phenylalanine Ammonia Lyase
Authors: Xiang Longkuan , Moore Bradley S. 
Published: June 2005

ABSTRACT

The committed biosynthetic reaction to benzoyl-coenzyme A in the marine bacterium “
Streptomyces maritimus
” is carried out by the novel prokaryotic phenylalanine ammonia lyase (PAL) EncP, which converts the primary amino acid
l
-phenylalanine to
trans
-cinnamic acid. Recombinant EncP is specific for
l
-phenylalanine and shares many biochemical features with eukaryotic PALs, which are substantially larger proteins by ∼200 amino acid residues.
Evolutionary Changes of the
flhDC
Flagellar Master Operon in
Shigella
Strains
Authors: Tominaga Akira , Lan Ruiting , Reeves Peter R. 
Published: June 2005

ABSTRACT

Shigella
strains are nonmotile. The master operon of flagellar synthesis,
flhDC
, was analyzed for genetic damage in 46
Shigella
strains representing all known serotypes. In 11 strains (B1, B3, B6, B8, B10, B18, D5, F1B, D10, F3A, and F3C) the
flhDC
operon was completely deleted. PCR and sequence analysis of the
flhDC
region of the remaining 35 strains revealed many insertions or deletions associated with insertion sequences, and the majority of the strains were found to be defective in their
flhDC
genes. As these genes also play a role in regulation of nonflagellar genes, the loss may have other consequences or be driven by selection pressures other than those against flagellar motility. It has been suggested that
Shigella
strains fall mostly into three clusters within
Escherichia coli
, with five outlier strains, four of which are also within
E. coli
(G. M. Pupo, R. Lan, and P. R. Reeves, Proc. Natl. Acad. Sci. USA 97:10567-10572, 2000). The distribution of genetic changes in the
flhDC
region correlated very well with the three clusters and outlier strains found using housekeeping gene DNA sequences, enabling us to follow the sequence of mutational change in the
flhDC
locus. Two cluster 2 strains were found to have unique
flhDC
sequences, which are most probably due to recombination during the exchange of the adjacent O-antigen gene clusters.
A population based study of reporting patterns and characteristics of men who abuse their female partners
Authors: Peek-Asa C , Zwerling C , Young T , Stromquist A M , Burmeister L F , Merchant J A 
Published: June 2005

Objective:This study estimates the prevalence of male abusive behavior reported by men and their female partners and identifies characteristics of abusive men.Design:Baseline survey from a population based cohort study of general health.Setting:A rural county in Iowa, USA.Subjects:572 men and their cohabitating female partners.Main outcome measures:Male-to-female physical, emotional, and sexual abuse reported by either partner.Results:In this cohort, 13.6% of men had performed at least one act of physical abuse and 34.9% emotional abuse. More than 45% of abusive men reported their own behaviors. Alcohol problems, antisocial personality characteristics, depressive symptoms, and financial stress were all positively associated with both physical and emotional abuse, but suicidal thoughts were less likely among abusers.Conclusion:Identification of common characteristics of abusive men may predict proclivity towards partner violence and barriers to behavior modification.
Traffic calming policy can reduce inequalities in child pedestrian injuries: database study
Authors: Jones S J , Lyons R A , John A , Palmer S R 
Published: June 2005

Objectives:To determine whether area wide traffic calming distribution reflects known inequalities in child pedestrian injury rates. To determine whether traffic calming is associated with changes in childhood pedestrian injury rates.Design:Small area ecological study, longitudinal analysis of injury rates with cross sectional analysis of traffic calming and method of travel to school.Settings:Two cities in the United Kingdom.Participants:4–16 year old children between 1992 and 2000.Main outcome measures:Area wide traffic calming distribution by area deprivation status and changes in injury rate/1000.Results:The most deprived fourth of city A had 4.8 times (95% CI 3.71 to 6.22) the number of traffic calming features per 1000 population compared with the most affluent fourth. Injury rates among the most deprived dropped from 9.42 to 5.07 from 1992–94 to 1998–2000 (95% CI for change 2.82 to 5.91). In city B, the traffic calming ratio of the most to least deprived fourth was 1.88 (95% CI 1.46 to 2.42); injury rates in the deprived areas dropped from 8.92 to 7.46 (95% CI for change −0.84 to 3.77). Similar proportions of 9–12 year olds walked to school in both cities.Conclusions:Area wide traffic calming is associated with absolute reductions in child pedestrian injury rates and reductions in relative inequalities in child pedestrian injury rates.
Group interventions for the prevention of injuries in young children: a systematic review
Authors: Bruce B , McGrath P 
Published: June 2005

Objective:This systematic review examined group based injury prevention interventions that targeted young children to determine the effectiveness of such strategies in enhancing children’s safety behaviors.Methods:A comprehensive (manual and electronic) search of the literature was performed using the following study selection criteria: (1) intervention engaged children under the age of 6 years; (2) included a control group; (3) used a group intervention approach; (4) study written in English language; (5) addressed unintentional injuries; and (6) outcomes included injuries, knowledge, or safety behaviors. Data abstraction was performed independently by two researchers using a standardized approach.Results:Nine studies met the criteria that included safety interventions of road crossing (4), car restraint (2), spinal cord safety (1), poison safety (1), and 911/stranger danger/street crossing (1). The types of interventions included videos, interactive activities, cartoons, stories, puppets, singing, coloring, games, simulation games, demonstrations, modeling/role playing, and rehearsal practice using seat belts, models, and real street crossing. The intensity and duration of interventions varied substantially and only two studies randomly assigned participants. The review revealed a positive effect (knowledge, behaviour, and/or attitude) for five of the studies, three had mixed effect, and one reported no effect.Conclusions:Although no clear conclusions can be drawn from the limited number of studies of diverse design and rigor, researchers should attempt to minimize shortcomings occurring in community based research. Engaging community partners including teachers and parents who influence relationships and outcomes could provide opportunity for more rigorous, comprehensive, and integrated approach to longitudinal research that could identify key factors of successful strategies.
Carotid and vertebral artery dissection syndromes
Authors: Thanvi B , Munshi S K , Dawson S L , Robinson T G 
Published: June 2005

Abstract
Cervicocerebral arterial dissections (CAD) are an important cause of strokes in younger patients accounting for nearly 20% of strokes in patients under the age of 45 years. Extracranial internal carotid artery dissections comprise 70%–80% and extracranial vertebral dissections account for about 15% of all CAD. Aetiopathogenesis of CAD is incompletely understood, though trauma, respiratory infections, and underlying arteriopathy are considered important. A typical picture of local pain, headache, and ipsilateral Horner’s syndrome followed after several hours by cerebral or retinal ischaemia is rare. Doppler ultrasound, MRI/MRA, and CT angiography are useful non-invasive diagnostic tests. The treatment of extracranial CAD is mainly medical using anticoagulants or antiplatelet agents although controlled studies to show their effectiveness are lacking. The prognosis of extracranial CAD is generally much better than that of the intracranial CAD. Recurrences are rare in CAD.
Practical experience and confidence in managing emergencies among preregistration house officers
Authors: Clayton R A E , Henderson J , McCracken S E , Wigmore S J , Paterson-Brown S 
Published: June 2005

Abstract

Objectives
To assess the experience gained by pre-registration house officers (PRHOs) at the end of their first post. To assess confidence in managing common emergencies and experience gained in practical procedures. To compare traditional six month posts with four month posts and to compare the experiences of PRHOs posted in teaching hospitals (THs) with those based in district general hospitals (DGHs).

Design
Interview questionnaire.

Participants
152 graduates from Edinburgh University Medical School in 2000 who had completed their first PRHO post by February 2001.

Results
There were few significant differences in confidence in managing emergencies and in numbers of practical procedures attempted between respondents from four and six month posts or between those holding TH and DGH posts. PRHOs had gained little experience in practical procedures: fewer than 15% had performed five or more of a number of procedures including lumbar puncture, pleural aspiration, chest drainage, and insertion of nasogastric tube. A high proportion of PRHOs indicated that they felt confident initiating management of conditions in specialties of which they had little or no experience.

Conclusions
Rotations of three four month posts do not seem to reduce overall experience in the PRHO year. There is little difference in experience gained between TH and DGH posts. PRHOs perform few practical procedures and some may be overconfident in their own abilities.