bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of two novel single nucleotide polymorphisms in the promoter of the human interleukin‐18 receptor α
Authors: Cardoso S. P. , Keen L. , Bidwell J. 
Published: March 2004

SummarySingle‐strand conformational polymorphism (SSCP) was used to identify single nucleotide polymorphisms (SNPs) in the promoter region of the human interleukin‐18 receptor α (IL‐18Rα). Two SNPs were identified at positions −69 and −638 relative to the transcriptional start site. Two‐way comparison of the two SNPs revealed strong linkage disequilibrium (χ2 = 63.45, P < 0.001). Three haplotypes were identified, namely C−69C−638, T−69C−638 and C−69T−638, with frequencies of 0.26, 0.39 and 0.35, respectively.
Impact of diverticular disease on hospital costs and activity
Authors: Papagrigoriadis S. , Debrah S. , Koreli A. , Husain A. 
Published: March 2004

AbstractBackground  Diverticulosis is very common in the UK and patients with clinically significant diverticular disease present regularly to departments of surgery as acute emergencies or chronic problems. There are no national data on the hospital prevalence, clinical implications or financial impact of diverticular disease hence the extent of the clinical problem is as yet not quantified.Aim  To detect the prevalence, clinical implications and financial impact of diverticular disease over a one year period in a large district hospital.Methods  Retrospective review of all patients treated for diverticular disease during one financial year. Clinical and cost analysis of inpatient and outpatient investigations, treatment and hospitalization.Results  A total of 148 patients were treated of whom 83 were admitted for more than 1 day, 55 of those were emergency admissions. Five of 83 admitted patients died (in‐patient mortality 6%, peri‐operative mortality 26.3%). There was a total number of 982 hospitalization days of which 94 Intensive Care Unit days and 68 High Dependency Unit days. Nineteen operations were performed (16 sigmoid colectomies, 1 oversewing of perforated sigmoid, 2 reversal of colostomy). The investigations generated were 48 colonoscopies, 77 flexible sigmoidoscopies, 77 Barium enemas, 2 CT scans and 34 ultrasound scans. A total number of 410 clinic appointments were generated. One year after discharge 134/148 (90.5%) patients were alive. The total cost of this activity was £465263 or 5.3% of the total annual budget for General Surgery. Seventy percent of the cost was bed‐days expenses with ICU hospitalization accounting for 25% of the total cost.Conclusion  Diverticular disease is a major cause of morbidity in a large district hospital and a significant burden on resources. More research should be done on prevention of complications and management in the community. The current methods of management do not appear to be cost‐effective and attempts should be made to produce protocols for evidence‐based, cost‐efficient management of the disease. A UK national audit should be undertaken.
Increased expression of minichromosome maintenance protein 2 in active inflammatory bowel disease
Authors: Davies R. J. , Scott I. S. , Morris L. S. , Rushbrook S. M. , Bird K. , Vowler S. L. , Arends M. , Miller R. , Coleman N. 
Published: March 2004

AbstractObjective  Minichromosome maintenance protein 2 (Mcm2) is an accurate indicator of cell cycle entry in tissue samples, but its expression in inflammatory bowel disease (IBD) has not previously been investigated. We have used immunohistochemistry to assess the expression of Mcm2, in comparison to the existing proliferation marker Ki‐67, in active IBD and IBD without inflammatory activity.Materials and methods  For this experimental study, sections from colonic biopsy and resection specimens of 48 patients with IBD (5 inactive/quiescent Crohn's disease (CD), 13 active CD, 19 inactive/quiescent ulcerative colitis (UC) and 11 active UC) and 15 normal controls were immunostained with antibodies to Mcm2 and Ki‐67. The percentage of immunopositive epithelial nuclei was determined by calculating a labelling index (LI) for entire glands and for gland thirds (superficial, middle and basal).Results  The Mcm2 LI was significantly increased in the superficial third of glands in active vs. inactive/quiescent UC (P < 0.0001) and active vs. inactive/quiescent CD (P = 0.001). The Mcm2 LI was significantly greater than the Ki‐67 LI in active IBD, both in entire glands (P < 0.0001) and in the superficial third of glands (UC, P = 0.001; CD, P = 0.0002). Mcm2 LIs for entire glands were significantly higher in UC (all cases) compared to CD (all cases) (P = 0.032).Conclusions  There is increased cell cycle entry, as indicated by expression of Mcm2 and to a lesser extent Ki‐67, in the superficial third of colonic glands in active IBD compared to inactive/quiescent IBD. Detection of Mcm2 may contribute to improved histological assessment of small tissue biopsies and may enable the development of a direct stool‐based test for detection of active IBD and potentially for assessment of disease activity.
Research on Domestic Violence in the 1990s: Making Distinctions
Authors: Johnson Michael P. , Ferraro Kathleen J. 
Published: March 2004

This review of the family literature on domestic violence suggests that two broad themes of the 1990s provide the most promising directions for the future. The first is the importance of distinctions among types or contexts of violence. Some distinctions are central to the theoretical and practical understanding of the nature of partner violence, others provide important contexts for developing more sensitive and comprehensive theories, and others may simply force us to question our tendency to generalize carelessly from one context to another. Second, issues of control, although most visible in the feminist literature that focuses on men using violence to control “their” women, also arise in other contexts, calling for more general analyses of the interplay of violence, power, and control in relationships. In addition to these two general themes, our review covers literature on coping with violence, the effects on victims and their children, and the social effects of partner violence.She wandered the streets, looking in shop windows. Nobody knew her here. Nobody knew what he did when the door was closed. Nobody knew.(Brant, 1996, pp. 281)
Chimeric Nature of Two Plasmids of
Hafnia alvei
Encoding the Bacteriocins Alveicins A and B
Authors: Wertz John E. , Riley Margaret A. 
Published: March 2004

ABSTRACT

The complete nucleotide sequences of two bacteriocin-encoding plasmids isolated from
Hafnia alvei
(pAlvA and pAlvB) were determined. Both plasmids resemble ColE1-type replicons and carry mobilization genes, as well as colicin-like bacteriocin operons. These bacteriocins appear to be chimeras consisting of translocation domains from Tol-dependent colicins, unique binding domains, and killing and immunity domains similar to those of the pore-forming colicin Ia. Just as is found for colicin Ia, these
H. alvei
bacteriocins (alveicins) lack lysis genes. The alveicins are unusually small at 408 and 358 amino acids for alveicin A and B, respectively, which would make alveicin B the smallest pore-forming bacteriocin yet discovered. The pattern of nucleotide substitution in the alveicins suggests that the dominant forces in the evolution of their killing domains and immunity genes are neutral mutation and random genetic drift rather than diversifying selection, which has been implicated in the evolution of other colicins. Five of six bacteriocinogenic isolates of
H. alvei
were found to carry plasmids identical to pAlvA. Comparisons of the levels of nucleotide divergence in five housekeeping genes to the levels of divergence in their respective plasmids led us to conclude that pAlvA is transferring laterally through the
H. alvei
population relatively rapidly.
Regulation ofEscherichia coliHemolysin E Expression by H-NS andSalmonellaSlyA
Authors: Wyborn Neil R. , Stapleton Melanie R. , Norte Valia A. , Roberts Ruth E. , Grafton Jamie , Green Jeffrey 
Published: March 2004

ABSTRACTTheEscherichia coli hlyEgene (also known asclyAorsheA) codes for a novel pore-forming toxin. Previous work has shown that the global transcription factors FNR and CRP positively regulatehlyEexpression by binding at the same site. Here in vivo transcription studies reveal that FNR occupies thehlyEpromoter more frequently than CRP, providing a mechanism for the moderate upregulation ofhlyEexpression in response to two distinct environmental signals (oxygen and glucose starvation). It has been reported that H-NS interacts with two large regions of thehlyEpromoter (PhlyE), one upstream of the −35 element and one downstream of the −10 element. Here we identify two high-affinity H-NS sites, H-NS I, located at the 3′ end of the extended upstream footprint, and H-NS II, located at the 5′ end of the extended downstream footprint. It is suggested that these high-affinity sites initiate the progressive formation of higher order complexes, allowing a range of H-NS-mediated regulatory effects at PhlyE. Finally, the identification of a SlyA binding site that overlaps the H-NS I site in PhlyEsuggests a mechanism to explain how SlyA overproduction enhanceshlyEexpression by antagonizing the negative effects of H-NS.
Phosphatidylethanolamine Is Not Essential for Growth of
Sinorhizobium meliloti
on Complex Culture Media
Authors: Sohlenkamp Christian , de Rudder Karel E. E. , Geiger Otto 
Published: March 2004

ABSTRACT

In addition to phosphatidylglycerol (PG), cardiolipin (CL), and phosphatidylethanolamine (PE),
Sinorhizobium meliloti
also possesses phosphatidylcholine (PC) as a major membrane lipid. The biosynthesis of PC in
S. meliloti
can occur via two different routes, either via the phospholipid N-methylation pathway, in which PE is methylated three times in order to obtain PC, or via the phosphatidylcholine synthase (Pcs) pathway, in which choline is condensed with CDP-diacylglycerol to obtain PC directly. Therefore, for
S. meliloti
, PC biosynthesis can occur via PE as an intermediate or via a pathway that is independent of PE, offering the opportunity to uncouple PC biosynthesis from PE biosynthesis. In this study, we investigated the first step of PE biosynthesis in
S. meliloti
catalyzed by phosphatidylserine synthase (PssA). A sinorhizobial mutant lacking PE was complemented with an
S. meliloti
gene bank, and the complementing DNA was sequenced. The gene coding for the sinorhizobial phosphatidylserine synthase was identified, and it belongs to the type II phosphatidylserine synthases. Inactivation of the sinorhizobial
pssA
gene leads to the inability to form PE, and such a mutant shows a greater requirement for bivalent cations than the wild type. A sinorhizobial PssA-deficient mutant possesses only PG, CL, and PC as major membrane lipids after growth on complex medium, but it grows nearly as well as the wild type under such conditions. On minimal medium, however, the PE-deficient mutant shows a drastic growth phenotype that can only partly be rescued by choline supplementation. Therefore, although choline permits Pcs-dependent PC formation in the mutant, it does not restore wild-type-like growth in minimal medium, suggesting that it is not only the lack of PC that leads to this drastic growth phenotype.
DNA Amplification and Rearrangements in Archival
Salmonella enterica
Serovar Typhimurium LT2 Cultures
Authors: Porwollik Steffen , Wong Rita Mei-Yee , Helm R. Allen , Edwards Kelly K. , Calcutt Michael , Eisenstark Abraham , McClelland Michael 
Published: March 2004

ABSTRACT

Variations in genome size and gene order were observed in archival
Salmonella enterica
serovar Typhimurium cultures stored for over 40 years. In one strain, microarray analysis revealed a large, stable amplification. PCR analysis of the same strain revealed a genomic duplication that underwent a translocation. Other strains had smaller duplications and deletions. These results demonstrate that storage in stabs over time at room temperature not only allows for further bacterial growth but also may produce an environment that selects for a variety of mutations, including genomic rearrangements.
Mutational Analysis of the Signal-Sensing Domain of ResE Histidine Kinase fromBacillus subtilis
Authors: Baruah Avanti , Lindsey Brett , Zhu Yi , Nakano Michiko M. 
Published: March 2004

ABSTRACTTheBacillus subtilisResD-ResE two-component regulatory system activates genes involved in nitrate respiration in response to oxygen limitation or nitric oxide (NO). The sensor kinase ResE activates the response regulator ResD through phosphorylation, which then binds to the regulatory region of genes involved in anaerobiosis to activate their transcription. ResE is composed of an N-terminal signal input domain and a C-terminal catalytic domain. The N-terminal domain contains two transmembrane subdomains and a large extracytoplasmic loop. It also has a cytoplasmic PAS subdomain between the HAMP linker and C-terminal kinase domain. In an attempt to identify the signal-sensing subdomain of ResE, a series of deletions and amino acid substitutions were generated in the N-terminal domain. The results indicated that cytoplasmic ResE lacking the transmembrane segments and the extracytoplasmic loop retains the ability to sense oxygen limitation and NO, which leads to transcriptional activation of ResDE-dependent genes. This activity was eliminated by the deletion of the PAS subdomain, demonstrating that the PAS subdomain participates in signal reception. The study also raised the possibility that the extracytoplasmic region may serve as a second signal-sensing subdomain. This suggests that the extracytoplasmic region could contribute to amplification of ResE activity leading to the robust activation of genes required for anaerobic metabolism inB. subtilis.
Regulation of Expression of the Divergent
ulaG
and
ulaABCDEF
Operons Involved in
l
-Ascorbate Dissimilation in
Escherichia coli
Authors: Campos Evangelina , Baldoma Laura , Aguilar Juan , Badia Josefa 
Published: March 2004

ABSTRACT

The
ula
regulon, responsible for the utilization of
l
-ascorbate in
Escherichia coli
, is formed by two divergently transcribed operons,
ulaG
and
ulaABCDEF
. The regulon is negatively regulated by a repressor of the DeoR family which is encoded by the constitutive gene
ulaR
located downstream of
ulaG
. Full repression of the
ula
regulon requires simultaneous interaction of the repressor with both divergent promoters and seems to be dependent on repressor-mediated DNA loop formation, which is helped by the action of integration host factor. Two operator sites have been identified in each promoter. Lack of either of the two sets of operators partially relieved the repression of the other operon; thus, each promoter is dependent on the UlaR operator sites of the other promoter to enhance repression. Electrophoretic mobility shift assays with purified UlaR protein and promoter deletion analyses revealed a conserved sequence, present in each of the four operators, acting as a UlaR binding site. Glucose represses the
ula
regulon via at least two mechanisms, one dependent on cyclic AMP (cAMP)-cAMP receptor protein (CRP) and the other (possibly inducer exclusion) independent of it. Glucose effects mediated by other global regulators cannot be ruled out with the present information. Changes in cAMP-CRP levels affected only the expression of the
ulaABCDEF
operon.
Sustained Photoevolution of Molecular Hydrogen in a Mutant of
Synechocystis
sp. Strain PCC 6803 Deficient in the Type I NADPH-Dehydrogenase Complex
Authors: Cournac Laurent , Guedeney Geneviève , Peltier Gilles , Vignais Paulette M. 
Published: March 2004

ABSTRACT

The interaction between hydrogen metabolism, respiration, and photosynthesis was studied in vivo in whole cells of
Synechocystis
sp. strain PCC 6803 by continuously monitoring the changes in gas concentrations (H
2
, CO
2
, and O
2
) with an online mass spectrometer. The in vivo activity of the bidirectional [NiFe]hydrogenase [H
2
:NAD(P) oxidoreductase], encoded by the
hoxEFUYH
genes, was also measured independently by the proton-deuterium (H-D) exchange reaction in the presence of D
2
. This technique allowed us to demonstrate that the hydrogenase was insensitive to light, was reversibly inactivated by O
2
, and could be quickly reactivated by NADH or NADPH (+H
2
). H
2
was evolved by cells incubated anaerobically in the dark, after an adaptation period. This dark H
2
evolution was enhanced by exogenously added glucose and resulted from the oxidation of NAD(P)H produced by fermentation reactions. Upon illumination, a short (less than 30-s) burst of H
2
output was observed, followed by rapid H
2
uptake and a concomitant decrease in CO
2
concentration in the cyanobacterial cell suspension. Uptake of both H
2
and CO
2
was linked to photosynthetic electron transport in the thylakoids. In the
ndhB
mutant M55, which is defective in the type I NADPH-dehydrogenase complex (NDH-1) and produces only low amounts of O
2
in the light, H
2
uptake was negligible during dark-to-light transitions, allowing several minutes of continuous H
2
production. A sustained rate of photoevolution of H
2
corresponding to 6 μmol of H
2
mg of chlorophyll
−1
h
−1
or 2 ml of H
2
liter
−1
h
−1
was observed over a longer time period in the presence of glucose and was slightly enhanced by the addition of the O
2
scavenger glucose oxidase. By the use of the inhibitors DCMU [3-(3,4-dichlorophenyl)-1,1-dimethylurea] and DBMIB (2,5-dibromo-3-methyl-6-isopropyl-
p
-benzoquinone), it was shown that two pathways of electron supply for H
2
production operate in M55, namely photolysis of water at the level of photosystem II and carbohydrate-mediated reduction of the plastoquinone pool.
Interaction of the Crystalline Bacterial Cell Surface Layer Protein SbsB and the Secondary Cell Wall Polymer of
Geobacillus stearothermophilus
PV72 Assessed by Real-Time Surface Plasmon Resonance Biosensor Technology
Authors: Mader Christoph , Huber Carina , Moll Dieter , Sleytr Uwe B. , Sára Margit 
Published: March 2004

ABSTRACT

The interaction between S-layer protein SbsB and the secondary cell wall polymer (SCWP) of
Geobacillus stearothermophilus
PV72/p2 was investigated by real-time surface plasmon resonance biosensor technology. The SCWP is an acidic polysaccharide that contains
N
-acetylglucosamine,
N
-acetylmannosamine, and pyruvic acid. For interaction studies, recombinant SbsB (rSbsB) and two truncated forms consisting of either the S-layer-like homology (SLH) domain (3SLH) or the residual part of SbsB were used. Independent of the setup, the data showed that the SLH domain was exclusively responsible for SCWP binding. The interaction was found to be highly specific, since neither the peptidoglycan nor SCWPs from other organisms nor other polysaccharides were recognized. Data analysis from that setup in which 3SLH was immobilized on a sensor chip and SCWP represented the soluble analyte was done in accordance with a model that describes binding of a bivalent analyte to a fixed ligand in terms of an overall affinity for all binding sites. The measured data revealed the presence of at least two binding sites on a single SCWP molecule with a distance of about 14 nm and an overall
K

d

of 7.7 × 10
−7
M. Analysis of data from the inverted setup in which the SCWP was immobilized on a sensor chip was done in accordance with an extension of the heterogeneous-ligand model, which indicated the existence of three binding sites with low (
K

d

= 2.6 × 10
−5
M), medium (
K

d

= 6.1 × 10
−8
M), and high (
K

d

= 6.7 × 10
−11
M) affinities. Since in this setup 3SLH was the soluble analyte and the presence of small amounts of oligomers in even monomeric protein solutions cannot be excluded, the high-affinity binding site may result from avidity effects caused by binding of at least dimeric 3SLH. Solution competition assays performed with both setups confirmed the specificity of the protein-carbohydrate interaction investigated.
Accessory Gene Regulator Control of Staphyloccoccal Enterotoxin D Gene Expression
Authors: Tseng Ching Wen , Zhang Shuping , Stewart George C. 
Published: March 2004

ABSTRACT

The quorum-sensing system of
Staphylococcus aureus
, the accessory gene regulator (Agr) system, is responsible for increased transcription of certain exoprotein genes and decreased transcription of certain cell wall-associated proteins during the postexponential phase of growth. This regulation is important for virulence, as evidenced by a reduction in virulence associated with a loss of the Agr system. The enterotoxin D (
sed
) determinant is upregulated by the Agr system. To define the Agr-regulated
cis
element(s) within the
sed
promoter region, we utilized promoters not regulated by Agr to create hybrid promoters. Hybrid promoters were created by using
sed
sequences combined with the enterotoxin A (
sea
) promoter or the
S. aureus lac
operon promoter sequences. The results obtained indicated that the Agr control element of the
sed
promoter resides within the −35 promoter element and at the Pribnow box to the +1 site of the promoter. At these positions of the
sed
promoter, a directly repeated 6-bp sequence was found. This repeat is important for overall promoter activity, and maximal regulation of the promoter activity requires both repeat elements. Furthermore, Agr control of
sed
promoter activity was found to be dependent upon the presence of a functional Rot protein. Therefore, the postexponential increase in
sed
transcription results from the Agr-mediated reduction in Rot activity rather than as a direct effect of the Agr system.
Characterization of Glycerol Trinitrate Reductase (NerA) and the Catalytic Role of Active-Site Residues
Authors: Marshall Samantha J. , Krause Doreen , Blencowe Dayle K. , White Graham F. 
Published: March 2004

ABSTRACT

Glycerol trinitrate reductase (NerA) from
Agrobacterium radiobacter
, a member of the old yellow enzyme (OYE) family of oxidoreductases, was expressed in and purified from
Escherichia coli
. Denaturation of pure enzyme liberated flavin mononucleotide (FMN), and spectra of NerA during reduction and reoxidation confirmed its catalytic involvement. Binding of FMN to apoenzyme to form the holoenzyme occurred with a dissociation constant of ca. 10
−7
M and with restoration of activity. The NerA-dependent reduction of glycerol trinitrate (GTN; nitroglycerin) by NADH followed ping-pong kinetics. A structural model of NerA based on the known coordinates of OYE showed that His-178, Asn-181, and Tyr-183 were close to FMN in the active site. The NerA mutation H178A produced mutant protein with bound FMN but no activity toward GTN. The N181A mutation produced protein that did not bind FMN and was isolated in partly degraded form. The mutation Y183F produced active protein with the same
k
cat
as that of wild-type enzyme but with altered

K
m

values for GTN and NADH, indicating a role for this residue in substrate binding. Correlation of the ratio of

K
m

GTN
to

K
m

NAD(P)H
, with sequence differences for NerA and several other members of the OYE family of oxidoreductases that reduce GTN, indicated that Asn-181 and a second Asn-238 that lies close to Tyr-183 in the NerA model structure may influence substrate specificity.