bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overexpression of Genes of the Cell Wall Stimulon in Clinical Isolates ofStaphylococcus aureusExhibiting Vancomycin-Intermediate-S. aureus-Type Resistance to Vancomycin
Authors: McAleese Fionnuala , Wu Shang Wei , Sieradzki Krzysztof , Dunman Paul , Murphy Ellen , Projan Steven , Tomasz Alexander 
Published: January 2006

ABSTRACTCustom-designed gene chips (Affymetrix) were used to determine genetic relatedness and gene expression profiles inStaphylococcus aureusisolates with increasing MICs of vancomycin that were recovered over a period of several weeks from the blood and heart valve of a patient undergoing extensive vancomycin therapy. The isolates were found to be isogenic as determined by the GeneChip based genotyping approach and thus represented a unique opportunity to study changes in gene expression that may contribute to the vancomycin resistance phenotype. No differences in gene expression were detected between the parent strain, JH1, and JH15, isolated from the nares of a patient contact. Few expression changes were observed between blood and heart valve isolates with identical vancomycin MICs. A large number of genes had altered expression in the late stage JH9 isolate (MIC = 8 μg/ml) compared to JH1 (MIC = 1 μg/ml). Most genes with altered expression were involved in housekeeping functions or cell wall biosynthesis and regulation. The sortase-encoding genes,srtAandsrtB, as well as several surface protein-encoding genes were downregulated in JH9. Two hypothetical protein-encoding genes, SAS016 and SA2343, were dramatically overexpressed in JH9. Interestingly, 27 of the genes with altered expression in JH9 grown in drug-free medium were found to be also overexpressed when the parental strain JH1 was briefly exposed to inhibitory concentrations of vancomycin, and more than half (17 of 27) of the genes with altered expression belonged to determinants that were proposed to form part of a general cell wall stress stimulon (S. Utaida et al., Microbiology 149:2719-2732, 2003).
Regulation and Physiologic Significance of the Agmatine Deiminase System of
Streptococcus mutans
UA159
Authors: Griswold Ann R. , Jameson-Lee Max , Burne Robert A. 
Published: January 2006

ABSTRACT

We previously demonstrated that
Streptococcus mutans
expresses a functional agmatine deiminase system (AgDS) encoded by the agmatine-inducible
aguBDAC
operon (A. R. Griswold, Y. Y. Chen, and R. A. Burne, J. Bacteriol.
186:
1902-1904, 2004). The AgDS yields ammonia, CO
2
, and ATP while converting agmatine to putrescine and is proposed to augment the acid resistance properties and pathogenic potential of
S. mutans
. To initiate a study of
agu
gene regulation, the
aguB
transcription initiation site was identified by primer extension and a putative σ
70
-like promoter was mapped 5′ to
aguB
. Analysis of the genome database revealed an open reading frame (SMU.261c) encoding a putative transcriptional regulator located 239 bases upstream of
aguB
. Inactivation of SMU.261c decreased AgD activity by sevenfold and eliminated agmatine induction. AgD was also found to be induced by certain environmental stresses, including low pH and heat, implying that the AgDS may also be a part of a general stress response pathway of this organism. Interestingly, an AgDS-deficient strain was unable to grow in the presence of 20 mM agmatine, suggesting that the AgDS converts a growth-inhibitory substance into products that can enhance acid tolerance and contribute to the competitive fitness of the organism at low pH. The capacity to detoxify and catabolize agmatine is likely to have major ramifications on oral biofilm ecology.
ohrR
and
ohr
Are the Primary Sensor/Regulator and Protective Genes against Organic Hydroperoxide Stress in
Agrobacterium tumefaciens
Authors: Chuchue Tatsanee , Tanboon Weerachai , Prapagdee Benjaphorn , Dubbs James M. , Vattanaviboon Paiboon , Mongkolsuk Skorn 
Published: January 2006

ABSTRACT

The genes involved in organic hydroperoxide protection in
Agrobacterium tumefaciens
were functionally evaluated. Gene inactivation studies and functional analyses have identified
ohr
, encoding a thiol peroxidase, as the gene primarily responsible for organic hydroperoxide protection in
A. tumefaciens
. An
ohr
mutant was sensitive to organic hydroperoxide killing and had a reduced capacity to metabolize organic hydroperoxides.
ohr
is located next to, and is divergently transcribed from,
ohrR
, encoding a sensor and transcription regulator of organic hydroperoxide stress. Transcription of both
ohr
and
ohrR
was induced by exposure to organic hydroperoxides but not by exposure to other oxidants. This induction required functional
ohrR
. The results of gel mobility shift and DNase I footprinting assays with purified OhrR, combined with in vivo promoter deletion analyses, confirmed that OhrR regulated both
ohrR
and
ohr
by binding to a single OhrR binding box that overlapped the
ohrR
and
ohr
promoters.
ohrR
and
ohr
are both required for the establishment of a novel cumene hydroperoxide-induced adaptive response. Inactivation or overexpression of other Prx family genes (
prx1
,
prx2
,
prx3
,
bcp1
, and
bcp2
) did not affect either the resistance to, or the ability to degrade, organic hydroperoxide. Taken together, the results of biochemical, gene regulation and physiological studies support the role of
ohrR
and
ohr
as the primary system in sensing and protecting
A. tumefaciens
from organic hydroperoxide stress.
Domains Required for Transcriptional Activation Show Conservation in the Mga Family of Virulence Gene Regulators
Authors: Vahling Cheryl M. , McIver Kevin S. 
Published: January 2006

ABSTRACT

Mga, or the multigene regulator of the group A streptococcus (GAS) (
Streptococcus pyogenes
), is a transcriptional regulator of virulence genes important for colonization and immune evasion. All serotypes of the GAS possess one of two divergent
mga
alleles (
mga-1
or
mga-2
), and orthologues of Mga have also been identified in other pathogenic streptococci. To date, the only functional motifs established within Mga are two amino-terminal DNA-binding domains (HTH-3 and HTH-4). To uncover novel domains, a random mutagenesis screen using an M6 Mga (
mga-1
) was undertaken to find mutations leading to a defect in transcriptional activation of the Mga-regulated
emm
gene. In addition to mutations in the established DNA-binding domains, the screen also revealed mutations in a region conserved among several Mga orthologues. Alanine scanning helped resolve the boundaries of this
c
onserved
M
ga
d
omain (CMD-1) spanning from residues 10 to 15 of the protein, with the two flanking amino acid residues likely involved in protein stability. Transcriptional reporter analyses demonstrated the importance of CMD-1 for activation of P
emm
and autoactivation of P
mga
in the serotype M6 Mga. Mutational analyses showed that both CMD-1 and HTH-4 are also necessary for activation of the promoter target P
mrp
in a divergent serotype M4 Mga (
mga-2
), suggesting a conserved functionality. However, in contrast to M6, the M4 Mga mutants did not show a defect in autoregulation. Mutation of similar conserved residues in the Mga-like regulator DmgB from
S. dysgalactiae
subsp.
dysgalactiae
showed that CMD-1 and HTH-4 are critical for transcriptional activation in this orthologue, implying that a common mechanism of virulence gene activation may exist for members of the Mga family of regulators.
The
yjeB
(
nsrR
) Gene of
Escherichia coli
Encodes a Nitric Oxide-Sensitive Transcriptional Regulator
Authors: Bodenmiller Diane M. , Spiro Stephen 
Published: January 2006

ABSTRACT

Microarray studies of the
Escherichia coli
response to nitric oxide and nitrosative stress have suggested that additional transcriptional regulators of this response remain to be characterized. We identify here the product of the
yjeB
gene as a negative regulator of the transcription of the
ytfE
,
hmpA
and
ygbA
genes, all of which are known to be upregulated by nitrosative stress. Transcriptional fusions to the promoters of these genes were expressed constitutively in a
yjeB
mutant, indicating that all three are targets for repression by YjeB. An inverted repeat sequence that overlaps the −10 element of all three promoters is proposed to be a binding site for the YjeB protein. A similar inverted repeat sequence was identified in the
tehA
promoter, which is also known to be sensitive to nitrosative stress. The
ytfE
,
hmpA
,
ygbA
, and
tehA
promoters all caused derepression of a
ytfE
-
lacZ
transcriptional fusion when present in the cell in multiple copies, presumably by a repressor titration effect, suggesting the presence of functional YjeB binding sites in these promoters. However, YjeB regulation of
tehA
was weak, as judged by the activity of a
tehA
-
lacZ
fusion, perhaps because YjeB repression of
tehA
is masked by other regulatory mechanisms. Promoters regulated by YjeB could be derepressed by iron limitation, which is consistent with an iron requirement for YjeB activity. The YjeB protein is a member of the Rrf2 family of transcriptional repressors and shares three conserved cysteine residues with its closest relatives. We propose a regulatory model in which the YjeB repressor is directly sensitive to nitrosative stress. On the basis of similarity to the nitrite-responsive repressor NsrR from
Nitrosomonas europaea
, we propose that the
yjeB
gene of
E. coli
be renamed
nsrR
.
Anatomy of the Replication Origin of Plasmid ColE2-P9
Authors: Yagura Masaru , Nishio Shin-ya , Kurozumi Hideki , Wang Cheng-fu , Itoh Tateo 
Published: January 2006

ABSTRACT
The plasmid ColE2-P9 origin is a 32-bp region which is specifically recognized by the plasmid-specified Rep protein to initiate DNA replication. We analyzed the structural and functional organization of the ColE2 origin by using various derivatives carrying deletions and single-base-pair substitutions. The origin may be divided into three subregions: subregion I, which is important for stable binding of the Rep protein; subregion II, which is important for binding of the Rep protein and for initiation of DNA replication; and subregion III, which is important for DNA replication but apparently not for binding of the Rep protein. The Rep protein might recognize three specific DNA elements in subregions I and II. The relative transformation frequency of the autonomously replicating plasmids carrying deletions in subregion I is lower, and nevertheless the copy numbers of these plasmids in host bacteria are higher than those of the wild-type plasmid. Efficient and stable binding of the Rep protein to the origin might be important for the replication efficiency to be at the normal (low) level. Subregion II might be essential for interaction with the catalytic domain of the Rep protein for primer RNA synthesis. The 8-bp sequence across the border of subregions II and III, including the primer sequence, is conserved in the (putative) origins of many plasmids, the putative Rep proteins of which are related to the ColE2-P9 Rep protein. Subregion III might be required for a step that is necessary after Rep protein binding has taken place.
IMPLEMENTING THE MODEL EVOLUTION CALCULUS
Authors: BAUMGARTNER PETER , FUCHS ALEXANDER , TINELLI CESARE 
Published: January 2006

Darwin is the first implementation of the Model Evolution Calculus by Baumgartner and Tinelli. The Model Evolution Calculus lifts the DPLL procedure to first-order logic. Darwin is meant to be a fast and clean implementation of the calculus, showing its effectiveness and providing a base for further improvements and extensions. Based on a brief summary of the Model Evolution Calculus, we describe in the main part of the paper Darwin's proof procedure and its data structures and algorithms, discussing the main design decisions and features that influence Darwin's performance. We also report on practical experiments carried out with problems from the CASC-J2 system competition and parts of the TPTP Problem Library, and compare the results with those of other state-of-the-art theorem provers.
Epigenetic Heterogeneity of High-Grade Prostatic Intraepithelial Neoplasia: Clues for Clonal Progression in Prostate Carcinogenesis
Authors: Henrique Rui , Jerónimo Carmen , Teixeira Manuel R. , Hoque Mohammad O. , Carvalho André L. , Pais Irene , Ribeiro Franclim R. , Oliveira Jorge , Lopes Carlos , Sidransky David 
Published: January 2006

Abstract
High-grade prostatic intraepithelial neoplasia (PIN) is the most likely precursor of prostate adenocarcinoma, but the frequency and timing of epigenetic changes found in prostate carcinogenesis has not been extensively documented. Thus, the promoters of three genes (APC, GSTP1, and RARβ2) involved in prostate carcinogenesis were tested by quantitative methylation-specific PCR in tissue DNA from 30 prostate carcinomas, 128 high-grade PIN lesions, and 30 normal prostate tissue samples dissected from 30 radical prostatectomy specimens using laser capture microdissection. The percentage of methylated alleles (PMA) was calculated for each gene, and hierarchical cluster analysis was used to define the degree of similarity of epigenetic alterations among the various samples. We found that PMA values of APC and RARβ2 were higher than those of GSTP1 in all three types of tissue samples and median PMA values for all three genes were higher in prostate cancer. By cluster analysis, 26 of 30 prostate carcinomas and 82 of 128 high-grade PIN lesions were grouped in the “high methylation” branch, whereas 24 of 30 normal prostate tissue samples were allocated in the “low methylation” branch. Although high-grade PIN lesions are epigenetically more similar to prostate carcinoma than to normal prostate tissue, paired prostate carcinoma and high-grade PIN lesions did not always segregate together. We concluded that APC and RARβ2 hypermethylation is frequent in normal prostate tissue and the progressive enrichment in cells carrying methylated alleles observed in high-grade PIN and prostate carcinoma is consistent with clonal progression. Because GSTP1 promoter methylation is mainly observed in prostate carcinoma and some high-grade PIN lesions, it represents an important marker for the transition of in situ to invasive neoplasia. (Mol Cancer Res 2006;4(1):1–8)
An assessment of the current and future options for domestic waste management in Kaunas, Lithuania
Authors: Wade Andreas , Denafas Gintaras , Račys Viktoras , Rimaityte Ingrida , Povilaitytė Renata 
Published: January 2006

The main purpose of this study was to carry out a retrospective analysis of solid waste generation in Kaunas city from 1994 to 2003 and to calculate the theoretical waste generation in the future. This paper also presents measurements of the annual variations of waste amounts and calculations on a theoretical waste incineration facility. Two waste treatment scenarios were considered. •Scenario A: waste deposit at the landfill with ‘implementation of domestic waste separation and recycling’. •Scenario B: waste removal to a landfill with ‘multi-treatment: household separation, recycling and energetic recovery’. Three levels of waste treatment were proposed. The first level was implementation of the recycling system, which included household waste separation. The next step involved mechanical-biological treatment. The third level was the construction and operation of a new waste incineration plant in Kaunas. Two sites in Kaunas city were proposed; however, more detailed analysis, including the economic factors, will need to be done.
Switching of NR5A Proteins Associated with the Inhibin α-Subunit Gene Promoter after Activation of the Gene in Granulosa Cells
Authors: Weck Jennifer , Mayo Kelly E. 
Published: January 2006

AbstractThe inhibin α-subunit gene is transcriptionally activated by FSH in ovarian granulosa cells during follicular growth. We have investigated the roles of the NR5A family nuclear receptors steroidogenic factor 1 (SF-1) and liver receptor homolog 1 (LRH-1) in transcriptional activation of the inhibin α-subunit gene. Transfection assays using an inhibin α-subunit promoter reporter in GRMO2 granulosa cells show that LRH-1 and SF-1 act similarly to increase promoter activity, and that the activity of both transcription factors is augmented by the coactivators cAMP response element-binding protein-binding protein and steroid receptor coactivator 1. However, chromatin immunoprecipitation experiments illustrate differential dynamic association of LRH-1 and SF-1 with the α-subunit inhibin promoter in both primary cells and the GRMO2 granulosa cell line such that hormonal stimulation of transcription results in an apparent replacement of SF-1 with LRH-1. Transcriptional stimulation of the inhibin α-subunit gene is dependent on MAPK kinase activity, as is the dynamic association/disassociation of SF-1 and LRH-1 with the promoter. Inhibition of the phosphatidylinositol 3-kinase signaling pathway influences promoter occupancy and transcriptional activation by SF-1 but not LRH-1, suggesting a possible mechanistic basis for the distinct functions of these NR5A proteins in inhibin α-subunit gene regulation.
Successful protocol of anaesthesia for measuring transepithelial nasal potential difference in spontaneously breathing mice
Authors: Leal T , Lebacq J , Vanbinst R , Lederman Ch , De Kock M , Wallemacq P 
Published: January 2006

Numerous difficulties arise during in vivo measurements of transepithelial nasal potential difference (PD) in mice, such as inadequate duration and depth of anaesthesia, bronchoaspiration of solutions perfused in the nose, and respiratory and/or cardiovascular depression. Anaesthesia was induced in adult C57 mice with intraperitoneal injection of a combination of fentanyl, droperidol and medetomidine, each of these at either a small dose (0.20, 10 and 0.33 mg/kg, respectively) or at a large dose (0.40, 20 and 0.40 mg/kg, respectively), combined with a fixed dose of 0.375 μg clonidine. In order to establish a pharmacokinetic–pharmacodynamic relationship, blood concentrations of the first three drugs were measured in 24 animals by liquid-chromatography tandem mass spectrometry. At the end of the experiment, naloxone, a competitive morphinic antagonist, and atipamezole, an α-2 adrenergic antagonist, were administered. Bronchoaspiration was prevented by tilting the animal head downwards and by absorbing the excess fluid from the opposite nostril and from the oral cavity. Optimal assessment of anaesthesia associated with regular respiration, loss of blink, pupillary and pedal withdrawal reflexes was obtained with doses of fentanyl, droperidol and medetomidine corresponding to 0.20, 20 and 0.40 mg/kg, respectively. Blood concentrations of fentanyl around 17 ng/mL induced loss of respiratory efforts and were followed by death during the experiment. Integrity of ion transport was demonstrated under continuous perfusion by successive depolarization after amiloride and repolarization after chloride-free solution. The combination investigated in this study lead to adequate surgical anaesthesia (stage III, plane 2) for prolonged nasal PD measurements in spontaneously breathing mice.
The preparation of ciprofloxacin hydrochloride-loaded chitosan and pectin microspheres
Authors: Orhan Z. , Cevher E. , Mülazimoglu L. , Gürcan D. , Alper M. , Araman A. , Özsoy Y. 
Published: January 2006

Ciprofloxacin hydrochloride-loaded microspheres were prepared by a spray-drying method using pectin and chitosan. The effects of different polymers and drug ratios were investigated. The most appropriate carriers were selected by in vitro testing. A rat methicillin-resistant Staphylococcus aureus osteomyelitis model was used to evaluate the effects of the loaded microspheres. The drug was released rapidly from the pectin carrier but this was more sustained in the chitosan formulation. Chitosan microspheres loaded with ciprofloxacin hydrochloride were more effective for the treatment of osteomyelitis than equivalent intramuscular antibiotics.
Are systemic emboli reduced in computer-assisted knee surgery?
Authors: Kalairajah Y. , Cossey A. J. , Verrall G. M. , Ludbrook G. , Spriggins A. J. 
Published: January 2006

We undertook a prospective, randomised study using a non-invasive transcranial Doppler device to evaluate cranial embolisation in computer-assisted navigated total knee arthroplasty (n = 14) and compared this with a standard conventional surgical technique using intramedullary alignment guides (n = 10). All patients were selected randomly without the knowledge of the patient, anaesthetists (before the onset of the procedure) and ward staff. The operations were performed by a single surgeon at one hospital using a uniform surgical approach, instrumentation, technique and release sequence. The only variable in the two groups of patients was the use of single tracker pins of the imageless navigation system in the tibia and femur of the navigated group and intramedullary femoral and tibial alignment jigs in the non-navigated group. Acetabular Doppler signals were obtained in 14 patients in the computer-assisted group and nine (90%) in the conventional group, in whom high-intensity signals were detected in seven computer-assisted patients (50%) and in all of the non-navigated patients. In the computer-assisted group no patient had more than two detectable emboli, with a mean of 0.64 (SD 0.74). In the non-navigated group the number of emboli ranged from one to 43 and six patients had more than two detectable emboli, with a mean of 10.7 (sd 13.5). The difference between the two groups was highly significant using the Wilcoxon non-parametric test (p = 0.0003). Our findings show that computer-assisted total knee arthroplasty, when compared with conventional jig-based surgery, significantly reduces systemic emboli as detected by transcranial Doppler ultrasonography.
A comparison of three methods of wound closure following arthroplasty
Authors: Khan R. J. K. , Fick D. , Yao F. , Tang K. , Hurworth M. , Nivbrant B. , Wood D. 
Published: January 2006

We carried out a blinded prospective randomised controlled trial comparing 2-octylcyanoacrylate (OCA), subcuticular suture (monocryl) and skin staples for skin closure following total hip and total knee arthroplasty. We included 102 hip replacements and 85 of the knee.OCA was associated with less wound discharge in the first 24 hours for both the hip and the knee. However, with total knee replacement there was a trend for a more prolonged wound discharge with OCA. With total hip replacement there was no significant difference between the groups for either early or late complications. Closure of the wound with skin staples was significantly faster than with OCA or suture. There was no significant difference in the length of stay in hospital, Hollander wound evaluation score (cosmesis) or patient satisfaction between the groups at six weeks for either hips or knees.We consider that skin staples are the skin closure of choice for both hip and knee replacements.
Subperiosteal elevation of the ulnar nerve during internal fixation for fractures of the distal humerus assessed by intra-operative neurophysiological monitoring
Authors: Krkovič M. , Kordaš M. , Tonin M. , Bošnjak R. 
Published: January 2006

Ulnar nerve function, during and after open reduction and internal fixation of fractures of the distal humerus with subperiosteal elevation of the nerve, was assessed by intra-operative neurophysiological monitoring. Intermittent recording of the compound muscle action potentials was taken from the hypothenar muscles in 18 neurologically asymptomatic patients. The mean amplitude of the compound muscle action potential after surgery was 98.1% (sd 17.6; −37% to +25%). The amplitude improved in six patients following surgery. Despite unremarkable recordings one patient had progressive paresis. Motor impairment is unlikely if the compound muscle action potential is continuously preserved and not reduced by more than 40% at the end of surgery. Temporary decreases in amplitude by up to 70% were tolerated without clinical consequences. However, repeated clinical examination is obligatory to recognise and treat early post-operative palsy.