bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recurrent Pleomorphic Adenoma of the Parotid Gland: A Prospective Histopathological and Immunohistochemical Study
Authors: Stennert Eberhard , Wittekindt Claus , Klussmann Jens Peter , Arnold Georg , Guntinas‐Lichius Orlando 
Published: December 2003

AbstractObjectives/Hypothesis Histopathological characteristics and proliferation indices of recurrent pleomorphic adenoma were described in a series of 31 patients who were referred to the authors' clinic for revision surgery.Study Design Prospective series of 31 patients.Methods Serial sections of surgical specimen using the whole‐organ sectioning technique were carried out for light microscopic examination after total parotidectomy and periparotid fat resection. The nodules were examined with special reference to localization, amount, size, histological subtypes, capsular alterations, and the amount of nodule spilling. Expression of proliferation markers (Ki67/MIB‐1) according to the size and histological subtypes of the nodules was also investigated.Results Most recurrences were multinodular, and the number of nodules was much higher than expected, ranging from 1 to 157. The myxoid subtype was predominant. Eighty percent of the patients exhibited widely distributed nodules also lying outside the scar. These nodules contained only a thin pseudocapsule and often lacked complete encapsulation. The majority of multinodular recurrences of parotid pleomorphic adenoma consisted of small nodules (less than 1 mm in diameter). Smaller nodules showed similar or higher levels of proliferative activity than larger nodules.Conclusion The extended multifocal distribution of tumor recurrences after insufficient resection of pleomorphic adenoma (most often after enucleation) can explain a high incidence of further recurrences. Therefore, a total parotidectomy including removal of surrounding fat tissue seems to be appropriate for the initial treatment of recurrent pleomorphic adenoma.
The Methyltransferase from the LlaDII Restriction-Modification System Influences the Level of Expression of Its Own Gene
Authors: Christensen Lisa Lystbæk , Josephsen Jytte 
Published: December 2003

ABSTRACT

The type II restriction-modification (R-M) system LlaDII isolated from
Lactococcus lactis
contains two tandemly arranged genes,
llaDIIR
and
llaDIIM
, encoding a restriction endonuclease (REase) and a methyltransferase (MTase), respectively. Interestingly, two LlaDII recognition sites are present in the
llaDIIM
promoter region, suggesting that they may influence the activity of the promoter through methylation status. In this study, separate promoters for
llaDIIR
and
llaDIIM
were identified, and the regulation of the two genes at the transcriptional level was investigated. DNA fragments containing the putative promoters were cloned in a promoter probe vector and tested for activity in the presence and absence of the active MTase. The level of expression of the MTase was 5- to 10-fold higher than the level of expression of the REase. The results also showed that the presence of M.LlaDII reduced the in vivo expression of the
llaDIIM
promoter (P

llaDIIM

) up to 1,000-fold, whereas the activity of the
llaDIIR
promoter (P

llaDIIR

) was not affected. Based on site-specific mutations it was shown that both of the LlaDII recognition sites within P

llaDIIM

are required to obtain complete repression of transcriptional activity. No regulation was found for
llaDIIR
, which appears to be constitutively expressed.
atxAControlsBacillus anthracisCapsule Synthesis viaacpAand a Newly Discovered Regulator,acpB
Authors: Drysdale Melissa , Bourgogne Agathe , Hilsenbeck Susan G. , Koehler Theresa M. 
Published: December 2003

ABSTRACTTwo regulatory genes,acpAandatxA, have been reported to control expression of theBacillus anthraciscapsule biosynthesis operoncapBCAD. TheatxAgene is located on the virulence plasmid pXO1, while pXO2 carriesacpAand thecapgenes.acpAhas been viewed as the major regulator of thecapoperon because it is essential for capsule gene expression in a pXO1−pXO2+strain.atxAis essential for toxin gene transcription but has also been implicated in control of thecapgenes. The molecular functions of the regulatory proteins are unknown. We examinedcapgene expression in a genetically complete pXO1+pXO2+strain. Our results indicate that another pXO2 gene,acpB(previously called pXO2-53; accession no.NC002146.1:49418-50866), has a role incapexpression. The predicted amino acid sequence of AcpB is 62% similar to that of AcpA and 50% similar to that of AtxA. Assessment ofcapgene transcription revealed thatcapexpression was not affected in a pXO1+pXO2+acpB-null mutant and was slightly reduced in an isogenicacpAmutant. However,capgene expression was abolished in anacpA acpBdouble mutant. Microscopic examination of capsule synthesis by the mutants corroborated these findings.acpAandacpBexpression is controlled byatxA; capsule synthesis and transcription ofacpAandacpBwere markedly reduced in anatxAmutant. The data suggest that, in a strain containing both virulence plasmids,atxAis the major regulator of capsule synthesis and controlscapBCADexpression indirectly, via positive regulation ofacpAandacpB.
The Alternative Sigma Factor σBofBacillus cereus: Response to Stress and Role in Heat Adaptation
Authors: van Schaik Willem , Tempelaars Marcel H. , Wouters Jeroen A. , de Vos Willem M. , Abee Tjakko 
Published: December 2003

ABSTRACTA gene cluster encoding the alternative sigma factor σB, three predicted regulators of σB(RsbV, RsbW, and RsbY), and one protein whose function is not known (Orf4) was identified in the genome sequence of the food pathogenBacillus cereusATCC 14579. Western blotting with polyclonal antibodies raised against σBrevealed that there was 20.1-fold activation of σBafter a heat shock from 30 to 42°C. Osmotic upshock and ethanol exposure also upregulated σB, albeit less than a heat shock. When the intracellular ATP concentration was decreased by exposure to carbonyl cyanidem-chlorophenylhydrazone (CCCP), only limited increases in σBlevels were observed, revealing that stress due to ATP depletion is not an important factor in σBactivation inB. cereus. Analysis of transcription of thesigBoperon by Northern blotting and primer extension revealed the presence of a σB-dependent promoter upstream of the first open reading frame (rsbV) of thesigBoperon, indicating that transcription ofsigBis autoregulated. A second σB-dependent promoter was identified upstream of the last open reading frame (orf4) of thesigBoperon. Production of virulence factors and the nonhemolytic enterotoxin Nhe in asigBnull mutant was the same as in the parent strain. However, σBwas found to play a role in the protective heat shock response ofB. cereus. ThesigBnull mutant was less protected against the lethal temperature of 50°C by a preadaptation to 42°C than the parent strain was, resulting in a more-than-100-fold-reduced survival of the mutant after 40 min at 50°C.
Dihydropteridine Reductase as an Alternative to Dihydrofolate Reductase for Synthesis of Tetrahydrofolate in
Thermus thermophilus
Authors: Wilquet Valérie , Van de Casteele Mark , Gigot Daniel , Legrain Christianne , Glansdorff Nicolas 
Published: December 2003

ABSTRACT

A strategy devised to isolate a gene coding for a dihydrofolate reductase from
Thermus thermophilus
DNA delivered only clones harboring instead a gene (the
T. thermophilus
dehydrogenase [DH

Tt

] gene) coding for a dihydropteridine reductase which displays considerable dihydrofolate reductase activity (about 20% of the activity detected with 6,7-dimethyl-7,8-dihydropterine in the quinonoid form as a substrate). DH

Tt

appears to account for the synthesis of tetrahydrofolate in this bacterium, since a classical dihydrofolate reductase gene could not be found in the recently determined genome nucleotide sequence (A. Henne, personal communication). The derived amino acid sequence displays most of the highly conserved cofactor and active-site residues present in enzymes of the short-chain dehydrogenase/reductase family. The enzyme has no pteridine-independent oxidoreductase activity, in contrast to
Escherichia coli
dihydropteridine reductase, and thus appears more similar to mammalian dihydropteridine reductases, which do not contain a flavin prosthetic group. We suggest that bifunctional dihydropteridine reductases may be responsible for the synthesis of tetrahydrofolate in other bacteria, as well as archaea, that have been reported to lack a classical dihydrofolate reductase but for which possible substitutes have not yet been identified.
Helicobacter acinonychis
: Genetic and Rodent Infection Studies of a
Helicobacter pylori
-Like Gastric Pathogen of Cheetahs and Other Big Cats
Authors: Dailidiene Daiva , Dailide Giedrius , Ogura Keiji , Zhang Maojun , Mukhopadhyay Asish K. , Eaton Kathryn A. , Cattoli Giovanni , Kusters Johannes G. , Berg Douglas E. 
Published: December 2003

ABSTRACT

Insights into bacterium-host interactions and genome evolution can emerge from comparisons among related species. Here we studied
Helicobacter acinonychis
(formerly
H. acinonyx
), a species closely related to the human gastric pathogen
Helicobacter pylori
. Two groups of strains were identified by randomly amplified polymorphic DNA fingerprinting and gene sequencing: one group from six cheetahs in a U.S. zoo and two lions in a European circus, and the other group from a tiger and a lion-tiger hybrid in the same circus. PCR and DNA sequencing showed that each strain lacked the
cag
pathogenicity island and contained a degenerate vacuolating cytotoxin (
vacA
) gene. Analyses of nine other genes (
glmM
,
recA
,
hp519
,
glr
,
cysS
,
ppa
,
flaB
,
flaA
, and
atpA
) revealed a ∼2% base substitution difference, on average, between the two
H. acinonychis
groups and a ∼8% difference between these genes and their homologs in
H. pylori
reference strains such as 26695.
H. acinonychis
derivatives that could chronically infect mice were selected and were found to be capable of persistent mixed infection with certain
H. pylori
strains. Several variants, due variously to recombination or new mutation, were found after 2 months of mixed infection.
H. acinonychis
' modest genetic distance from
H. pylori
, its ability to infect mice, and its ability to coexist and recombine with certain
H. pylori
strains in vivo should be useful in studies of
Helicobacter
infection and virulence mechanisms and studies of genome evolution.
Phage Shock Protein PspA of
Escherichia coli
Relieves Saturation of Protein Export via the Tat Pathway
Authors: DeLisa Matthew P. , Lee Philip , Palmer Tracy , Georgiou George 
Published: December 2003

ABSTRACT

Overexpression of either heterologous or homologous proteins that are routed to the periplasm via the twin-arginine translocation (Tat) pathway results in a block of export and concomitant accumulation of the respective protein precursor in the cytoplasm. Screening of a plasmid-encoded genomic library for mutants that confer enhanced export of a TorA signal sequence (ssTorA)-GFP-SsrA fusion protein, and thus result in higher cell fluorescence, yielded the
pspA
gene encoding phage shock protein A. Coexpression of
pspA
relieved the secretion block observed with ssTorA-GFP-SsrA or upon overexpression of the native Tat proteins SufI and CueO. A similar effect was observed with the
Synechocystis
sp. strain PCC6803 PspA homologue, VIPP1, indicating that the role of PspA in Tat export may be phylogenetically conserved. Mutations in Tat components that completely abolish export result in a marked induction of PspA protein synthesis, consistent with its proposed role in enhancing protein translocation via Tat.
Identification of NAD+Synthetase fromStreptococcus sobrinusas a B-Cell-Stimulatory Protein
Authors: Veiga-Malta Isabel , Duarte Margarida , Dinis Márcia , Madureira Pedro , Ferreira Paula , Videira Arnaldo 
Published: December 2003

ABSTRACTStreptococcus sobrinus, one agent of dental caries, secretes a protein that induces lymphocyte polyclonal activation of the host as a mechanism of immune evasion. We have isolated from culture supernatants of this bacterium a protein with murine B-cell-stimulatory properties and subsequently cloned the relevant gene. It contains an open reading frame of 825 bp encoding a polypeptide with 275 amino acid residues and a molecular mass of 30 kDa. The protein displays high sequence homology with NAD+synthetases from several organisms, including a conserved fingerprint sequence (SGGXD) characteristic of ATP pyrophosphatases. The polypeptide was expressed inEscherichia colias a hexahistidine-tagged protein and purified in an enzymatically active form. The recombinant NAD+synthetase stimulates murine B cells after in vitro treatment of spleen cell cultures, as demonstrated by its ability to induce up-regulation of the expression of CD69, an early marker of lymphocyte activation. Stimulation with the recombinant NAD+synthetase was also observed with other B-cell markers, such as CD19+, B220+, and CD21+. Cell proliferation follows the activation induced by the recombinant NAD+synthetase.
Occurrence and Characterization of Mercury Resistance in the Hyperthermophilic Archaeon
Sulfolobus solfataricus
by Use of Gene Disruption
Authors: Schelert James , Dixit Vidula , Hoang Viet , Simbahan Jessica , Drozda Melissa , Blum Paul 
Published: December 2003

ABSTRACT

Mercury resistance mediated by mercuric reductase (MerA) is widespread among bacteria and operates under the control of MerR. MerR represents a unique class of transcription factors that exert both positive and negative regulation on gene expression. Archaea and bacteria are prokaryotes, yet little is known about the biological role of mercury in archaea or whether a resistance mechanism occurs in these organisms. The archaeon
Sulfolobus solfataricus
was sensitive to mercuric chloride, and low-level adaptive resistance could be induced by metal preconditioning. Protein phylogenetic analysis of open reading frames SSO2689 and SSO2688 clarified their identity as orthologs of MerA and MerR. Northern analysis established that
merA
transcription responded to mercury challenge, since mRNA levels were transiently induced and, when normalized to 7S RNA, approximated values for other highly expressed transcripts. Primer extension analysis of
merA
mRNA predicted a noncanonical TATA box with nonstandard transcription start site spacing. The functional roles of
merA
and
merR
were clarified further by gene disruption. The
merA
mutant exhibited mercury sensitivity relative to wild type and was defective in elemental mercury volatilization, while the
merR
mutant was mercury resistant. Northern analysis of the
merR
mutant revealed
merA
transcription was constitutive and that transcript abundance was at maximum levels. These findings constitute the first report of an archaeal heavy metal resistance system; however, unlike bacteria the level of resistance is much lower. The archaeal system employs a divergent MerR protein that acts only as a negative transcriptional regulator of
merA
expression.
The Sorbitol Phosphotransferase System Is Responsible for Transport of 2-
C
-Methyl-
d
-Erythritol into
Salmonella enterica
Serovar Typhimurium
Authors: Testa Charles A. , Cornish Rita M. , Poulter C. Dale 
Published: December 2003

ABSTRACT

2-
C
-methyl-
d
-erythritol 4-phosphate is the first committed intermediate in the biosynthesis of the isoprenoid precursors isopentenyl diphosphate and dimethylallyl diphosphate. Supplementation of the growth medium with 2-
C
-methyl
-d-
erythritol has been shown to complement disruptions in the
Escherichia coli
gene for 1-deoxy
-d-
xylulose 5-phosphate synthase, the enzyme that synthesizes the immediate precursor of 2-
C
-methyl
-d-
erythritol 4-phosphate. In order to be utilized in isoprenoid biosynthesis, 2-
C
-methyl
-d-
erythritol must be phosphorylated. We describe the construction of
Salmonella enterica
serovar Typhimurium strain RMC26, in which the essential gene encoding 1-deoxy
-d-
xylulose 5-phosphate synthase has been disrupted by insertion of a synthetic mevalonate operon consisting of the yeast
ERG8
,
ERG12
, and
ERG19
genes, responsible for converting mevalonate to isopentenyl diphosphate under the control of an arabinose-inducible promoter. Random mutagenesis of RMC26 produced defects in the sorbitol phosphotransferase system that prevented the transport of 2-
C
-methyl
-d-
erythritol into the cell. RMC26 and mutant strains of RMC26 unable to grow on 2-C-methyl
-d-
erythritol were incubated in buffer containing mevalonate and deuterium-labeled 2-
C
-methyl
-d-
erythritol. Ubiquinone-8 was isolated from these cells and analyzed for deuterium content. Efficient incorporation of deuterium was observed for RMC26. However, there was no evidence of deuterium incorporation into the isoprenoid side chain of ubiquinone Q8 in the RMC26 mutants.
An Evolutionary Hot Spot: the pNGR234
b
Replicon of
Rhizobium
sp. Strain NGR234
Authors: Streit W. R. , Schmitz R. A. , Perret X. , Staehelin C. , Deakin W. J. , Raasch C. , Liesegang H. , Broughton W. J. 
Published: December 2003

ABSTRACT

Rhizobium
sp. strain NGR234 has an exceptionally broad host range and is able to nodulate more than 112 genera of legumes. Since the overall organization of the NGR234 genome is strikingly similar to that of the narrow-host-range symbiont
Rhizobium meliloti
strain 1021 (also known as
Sinorhizobium meliloti
), the obvious question is why are the spectra of hosts so different? Study of the early symbiotic genes of both bacteria (carried by the SymA plasmids) did not provide obvious answers. Yet, both rhizobia also possess second megaplasmids that bear, among many other genes, those that are involved in the synthesis of extracellular polysaccharides (EPSs). EPSs are involved in fine-tuning symbiotic interactions and thus may help answer the broad- versus narrow-host-range question. Accordingly, we sequenced two fragments (total, 594 kb) that encode 575 open reading frames (ORFs). Comparisons revealed 19 conserved gene clusters with high similarity to
R. meliloti
, suggesting that a minimum of 28% (158 ORFs) of the genetic information may have been acquired from a common ancestor. The largest conserved cluster carried the
exo
and
exs
genes and contained 31 ORFs. In addition, nine highly conserved regions with high similarity to
Agrobacterium tumefaciens
C58,
Bradyrhizobium japonicum
USDA110, and
Mesorhizobium loti
strain MAFF303099, as well as two conserved clusters that are highly homologous to similar regions in the plant pathogen
Erwinia carotovora
, were identified. Altogether, these findings suggest that ≥40% of the pNGR234
b
genes are not strain specific and were probably acquired from a wide variety of other microbes. The presence of 26 ORFs coding for transposases and site-specific integrases supports this contention. Surprisingly, several genes involved in the degradation of aromatic carbon sources and genes coding for a type IV pilus were also found.
PmrAB, a Two-Component Regulatory System of
Pseudomonas aeruginosa
That Modulates Resistance to Cationic Antimicrobial Peptides and Addition of Aminoarabinose to Lipid A
Authors: Moskowitz Samuel M. , Ernst Robert K. , Miller Samuel I. 
Published: December 2003

ABSTRACT

Spontaneous polymyxin-resistant mutants of
Pseudomonas aeruginosa
were isolated. The mutations responsible for this phenotype were mapped to a two-component signal transduction system similar to PmrAB of
Salmonella enterica
serovar Typhimurium. Lipid A of these mutants contained aminoarabinose, an inducible modification that is associated with polymyxin resistance. Thus,
P. aeruginosa
possesses a mechanism that induces resistance to cationic antimicrobial peptides in response to environmental conditions.
Biphasic Excitation by Leucine in
Escherichia coli
Chemotaxis
Authors: Khan Shahid , Trentham David R. 
Published: December 2003

ABSTRACT

Leucine concentration jumps (applied by photolysis of inert derivatives) triggered swim or tumble responses in
Escherichia coli
mutants lacking Tsr or Tar, respectively. Wild-type
E. coli
bacteria were attracted in spatial assays when the initial leucine concentration difference was 5 to 120 μM but were repulsed when it was over 0.5 mM. Their responses to concentration jumps confirmed earlier deductions regarding biphasic excitation.
Using simultaneous equation modeling for defining complex phenotypes
Authors: King Terri M 
Published: December 2003

Abstract
Background
Interactions between multiple biological phenotypes are difficult to model. Simultaneous equation modelling (SEM), as used in econometric modelling, may prove an effective tool for this problem. Generalized linear models were used to derive the structural equations defining the interactions between cholesterol, glucose, triglycerides and high-density lipoprotein cholesterol (HDL-C). These structural equations were then applied, using SEM, to Cohort 2 data (replicates 1–100) to estimate the phenotypic structure underlying the simulation. The goal was to determine if this empiric method of deriving structural equations for use in SEM was able to recover the simulation model better than generalized linear models.

Results
First, the underlying structural equations were estimated using generalized linear model techniques, which found strong a relationship between glucose, triglycerides and HDL-C. Using these structural equations, I used SEM to evaluate these relationships jointly. I found that a combination of the empiric structural equations and the SEM method was better at recovering the underlying simulated relationship between biologic measures than generalized linear modelling.

Conclusion
The empiric SEM procedure presented here estimated different relationships between dependent variables than generalized linear modelling. The SEM procedure using empirically developed structural equations was able to recover the underlying simulation relationship partially and thus holds promise as a technique for complex phenotype analysis. Robust methods for determining the structural equations must be developed for application of SEM to population data.
Search for genetic factors predisposing to atherogenic dyslipidemia
Authors: Yip Agustin G , Ma Qianli , Wilcox Marsha , Panhuysen Carolien I , Farrell John , Farrer Lindsay A , Wyszynski Diego F 
Published: December 2003

Abstract
Background
Atherogenic dyslipidemia (AD) is a common feature in persons with premature coronary heart disease. While several linkage studies have been carried out to dissect the genetic etiology of lipid levels, few have investigated the AD lipid triad comprising elevated serum triglyceride, small low density lipoprotein (LDL) particles, and reduced high density lipoprotein (HDL) cholesterol levels. Here we report the results of a whole-genome screen for AD using the Framingham Heart Study population.

Results
Our analyses provide some evidence for linkage to AD on chromosomes 1q31, 3q29, 10q26, 14p12, 14q13, 16q24, 18p11, and 19q13.

Conclusion
AD susceptibility is modulated by multiple genes in different chromosomes. Our study confirms results from other populations and suggests new areas of potential importance.
Genome-wide linkage analysis of systolic blood pressure: a comparison of two approaches to phenotype definition
Authors: Slager Susan L , Iturria Stephen J 
Published: December 2003

AbstractProblem 1 of the Genetic Analysis Workshop 13(GAW13) contains longitudinal data of cardiovascular measurements from 330 pedigrees. The longitudinal data complicates the phenotype definition because multiple measurements are taken on each individual. To address this complication, we propose an approach that uses generalized estimating equations to obtain residuals for each time point for each person. The mean residual is then taken as the new phenotype with which to use in a variance components linkage analysis. We compare our phenotype definition approach to an approach that first reduces the multiple measurements to a single measurement and then models these summary statistics as regression terms in a variance components analysis. For each approach, multipoint linkage analysis was performed using the residuals and the SOLAR computer program. Our results show little difference between the methods based on the LOD scores.