bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulation of the Escherichia coliσE‐dependent envelope stress response
Authors: Alba Benjamin M. , Gross Carol A.
Published: April 2004

The Escherichia coliσE‐dependent stress response pathway controls the expression of genes encoding periplasmic folding catalysts, proteases, biosynthesis enzymes for lipid A (a component of lipopolysaccharide or LPS) and other proteins known or predicted to function in or produce components of the envelope. When E. coli is subjected to heat or other stresses that generate unfolded envelope proteins, σE activity is induced. Four key players in this signal transduction pathway have been identified: RseA, an inner membrane σE antisigma factor; RseB, a periplasmic protein that binds to the periplasmic face of RseA; and the DegS and YaeL proteases. The major point of regulation, the interaction between σE and RseA, is primarily controlled by the stability of RseA. Envelope stress promotes RseA degradation, which occurs by a proteolytic cascade initiated by DegS. There is evidence that one σE‐inducing stress (OmpC overexpression) directly activates DegS to cleave RseA. Secondarily, envelope stress may relieve RseB‐mediated enhancement of RseA activity. Additional levels of control upon σE activity may become evident upon further study of this stress response pathway.
A novel enzyme, citryl‐CoA synthetase, catalysing the first step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK‐6
Authors: Aoshima Miho , Ishii Masaharu , Igarashi Yasuo
Published: April 2004

We attempted to purify ATP citrate lyase (ACL) from Hydrogenobacter thermophilus by following the citrate‐, ATP‐ and CoA‐dependent formation of an acyl‐CoA species that was detected as hydroxamate. However, citryl‐CoA rather than acetyl‐CoA was found, indicating that the purified enzyme was a novel citryl‐CoA synthetase (CCS) rather than ACL. Because the reaction catalysed by CCS corresponds to the first half of that mediated by ACL, CCS may be responsible for citrate cleavage in H. thermophilus. Thus, a novel citrate cleavage pathway, which does not involve ACL, appears to exist in this organism. Citryl‐CoA synthetase is composed of two different polypeptides: a large β subunit of 46 kDa and a small α subunit of 36 kDa. The corresponding genes were cloned and sequenced. The deduced amino acid sequences of the two subunits of CCS display significant similarity to those of succinyl‐CoA synthetase (SCS) in the database. As a comparison, SCS was also purified from H. thermophilus and the corresponding genes were cloned and sequenced. Citryl‐CoA synthetase and SCS were homologous, but showed different substrate specificity. The deduced amino acid sequences of the CCS subunits show similarity to part of the ACL sequence. The evolutionary relationship between CCS, SCS and ACL is discussed.
Stress‐directed adaptive mutations and evolution
Authors: Wright Barbara E.
Published: April 2004

Comparative biochemistry demonstrates that the metabolites, complex biochemical networks, enzymes and regulatory mechanisms essential to all living cells are conserved in amazing detail throughout evolution. Thus, in order to evolve, an organism must overcome new adverse conditions without creating different but equally dangerous alterations in its ongoing successful metabolic relationship with its environment. Evidence suggests that stable long‐term acquisitive evolution results from minor increases in mutation rates of genes related to a particular stress, with minimal disturbance to the balanced and resilient metabolism critical for responding to an unpredictable environment. Microorganisms have evolved specific biochemical feedback mechanisms that direct mutations to genes derepressed by starvation or other stressors in their environment. Transcription of the activated genes creates localized supercoiling and DNA secondary structures with unpaired bases vulnerable to mutation. The resulting mutants provide appropriate variants for selection by the stress involved, thus accelerating evolution with minimal random damage to the genome. This model has successfully predicted mutation frequencies in genes of E. coli and humans. Stressed cells observed in the laboratory over hundreds of generations accumulate mutations that also arise by this mechanism. When this occurs in repair‐deficient mutator strains with high rates of random mutation, the specific stress‐directed mutations are also enhanced.
Leaf beetle grazing does not induce willow trichome defence in the coppicing willow Salix viminalis
Authors: Dalin Peter , Björkman Christer , Eklund Karin
Published: April 2004

Abstract  1 Willows are frequently attacked and defoliated by adult leaf beetles (Phratora vulgatissima L.) early in the season and the plants are then attacked again when new larvae emerge. The native willow Salix cinerea has previously been shown to respond to adult grazing by producing new leaves with an increased trichome density. Subsequent larval feeding was reduced on new leaves. This type of induced plant response may reduce insect damage and could potentially be utilized for plant protection in agricultural systems.

2 Here, we investigated if the willow species most commonly used for biomass production in short rotation coppice, Salix viminalis, also responds to adult beetle grazing by increasing trichome density. Larval performance and feeding behaviour on plants previously exposed to adult beetles was compared with that on undefoliated control plants in a greenhouse.

3 We found an overall decrease in trichome density within all the plants (i.e. trichome density was lower on new leaves compared to that for older basal leaves on S. viminalis). However, leaves of beetle defoliated plants had a higher trichome density compared to control plants. Larval growth and feeding was not affected by this difference between treatments. Larvae appeared to remove trichomes when feeding on S. viminalis, a behaviour that might explain the lack of difference between treatments.
Hylobius pine weevils adult host selection and antifeedants: feeding behaviour on host and non‐host woody scandinavian plants
Authors: Månsson Per E. , Schlyter Fredrik
Published: April 2004

Abstract  1 We searched for antifeedant activity in predomonantly non‐host woody plants to find new compounds for seedling protection of Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) against feeding by pine weevil Hylobius abietis. In total, 38 species from 25 families were compared in choice and no‐choice tests.

2 In choice tests with Empetrum, Juniperus, Ledum, Populus, Betula, Evonymus, Sorbus, Salix, Myrica and Pinus, the weevils preferred Pinus to all others. In no‐choice tests with the same species, the insects removed a similar or even greater area of the bark in three of 10 species than Pinus. The results were clearly different between the test modes.

3 In experiment 4, the areas of outer and inner bark (phloem) removed were quantified separately.The weevils removed significantly less of both outer and inner bark in Ilex, Evonymus, Populus, Syringa, Taxus, Tilia, Viburnum, Lonicera and Sorbus than Pinus.

4 Large areas of outer bark were removed in Juglans, Fraxinus, Sambucus, Aesculus, Quercus, Corylus, Fagus, Salix, Alnus and Acer. However, in the latter cases the insects stopped when reaching the inner bark. Thus, certain plant species have the outer bark removed by the insects but possessed an inner bark with antifeedant qualities.
Worsening of soft tissue calcifications in a hemodialysis patient following parathyroidectomy
Authors: Butman Michael P , Goodman William
Published: April 2004

Hemodialysis patients with soft tissue calcifications present unique challenges to nephrologists who play an integral role in their long‐term management. Although disorders of soft tissue calcification are rare in the general population, calciphylaxis and tumoral calcinosis are encountered in up to 4% of the end‐stage renal disease population. Although they are both associated with the deposition of calcium in the soft tissue, they are distinct entities that differ markedly in respect to their clinical presentation, morbidity, and mortality. It is therefore exceedingly important that the nephrologist be aware of these disorders, be able to recognize them, and be able to differentiate them from each other to diagnose and treat patients appropriately. To achieve this it is necessary that the nephrologist be familiar with the diagnostic tools and the treatment modalities that are available. A case of a patient with soft tissue calcifications is presented followed by an overview of these disorders including a comparison of the clinical, laboratory, radiologic, and histologic findings, as well as treatment.
Remote monitoring in nocturnal home hemodialysis 2003
Authors: Hoy Christopher
Published: April 2004

Over the past several years there has been growth in the number of dialysis units performing remote monitoring in nocturnal home hemodialysis, there has been growth in the technical options available for remote monitoring, and there have been more creative approaches to overcoming previous limitations. This article will review this growth and the diverse factors driving the innovations internationally.
Six years' experience with short daily hemodialysis: Do the early improvements persist in the mid and long term?
Authors: Traeger Jules , Galland Roula , Delawari Ehsan , Arkouche Walid , Hadden Richard
Published: April 2004

Observational studies from several groups have shown consistent beneficial effects in patients treated with short daily hemodialysis (SDHD). The cardiovascular and nutritional changes appear during the first few months after the initiation of SDHD. An extensive review of 17 patients from a group of 36 ESRD patients treated for up to 6 years with SDHD was undertaken to compare the clinicobiologic results during the initial period of standard hemodialysis (3 × 4 hr/week) and the short daily hemodialysis period at 1 year (SDHD1) and subsequent years (SDHD2). The statistical analysis of the clinicobiologic data clearly shows that the initial favorable results obtained during the first year of SDHD do persist in the mid and long term, which shows the more physiologic nature of this dialytic approach. The amelioration of left ventricular hypertrophy is of particular interest, showing a regression of ventricular dilation during the first year followed by a reduction of interventricular septum and posterior wall thickness during the subsequent years.
Ultrapure dialysis fluid: Improving conventional and daily dialysis
Authors: Ledebo Ingrid
Published: April 2004

Dialysis fluid of standard quality contains a certain amount of bacteria and endotoxin. This has been considered acceptable because the dialysis membrane was believed to be a protective barrier to blood. However, improved methods for detection of cellular activation have demonstrated that bacterial products in the dialysate may stimulate monocytes to produce cytokines with most dialysis membranes. Ultrapure dialysis fluid is practically free from bacteria and endotoxin (< 0.1 CFU/mL and < 0.03 EU/mL) and can be prepared from standard‐quality dialysis fluid using a single step of controlled ultrafiltration. The European guidelines for hemodialysis (HD) set the use of ultrapure dialysis fluid as the goal for all dialysis modalities. Several clinical studies report improved inflammatory status in HD patients when ultrapure dialysis fluid is used, compared with standard‐quality dialysate. The benefits include less frequent occurrence of carpal tunnel syndrome, lower C‐reactive protein values, reduced need for erythropoietin, better nutritional status, and even better preservation of residual renal function. For patients on daily dialysis, dialysate quality is especially important because such patients are often treated at home where quality control of incoming water may be less rigorous, and increased treatment frequency leads to exposure to larger volumes of dialysis fluid than with conventional dialysis. The use of ultrapure dialysis fluid together with low‐complement‐activating membranes maximizes the biocompatibility of a dialysis treatment, a goal of treatment, although there is a lack of evidence to date supporting a beneficial effect on mortality. From a physiologic point of view the reduced inflammatory stimulus that can be achieved with ultrapure dialysis fluid is highly desirable. In addition, achieving ultrapure dialysis fluid is realistic, because today it can be practically and economically prepared using modern equipment and applying appropriate microbiologic surveillance techniques.
Hemofiltration as a treatment for end‐stage renal disease
Authors: Zimmerman Deborah L
Published: April 2004

Patients treated for end‐stage renal disease (ESRD) have a poorer quality of life and a higher mortality rate than patients in the general population. In addition, the cost to provide ESRD care is tremendous. Daily hemodialysis programs have been associated with improvements in the patient's quality of life, anemia management, blood pressure, nutrition, and left ventricular hypertrophy. In addition, especially when treated at home, cost savings are possible. Daily hemofiltration may offer additional benefits with enhanced middle‐molecule clearance, improved cardiovascular stability, and perhaps a further reduction in cost. Finally, ease of use of the NxStage System One may encourage patients to undergo their treatment at home.
Does Advertising Overcome Brand Loyalty? Evidence from the Breakfast‐Cereals Market
Authors: Shum Matthew
Published: April 2004

In differentiated product markets where consumer preferences are characterized by brand loyalty, an important role for advertising may be to overcome brand loyalty by encouraging consumers to switch to less familiar brands. Using a scanner panel dataset of breakfast‐cereal purchases, I find evidence consistent with the hypothesis that advertising counteracts the tendencies of brand loyalty toward repeat purchasing. Equivalently, advertising reduces switching costs in this market. Furthermore, counterfactual experiments demonstrate that in markets with brand loyalty, advertising is an attractive and effective option—relative to alternative promotional activities, such as price discounts—of stimulating demand for a brand.
Preference‐Based Discrimination and Profit: On the Profitability of Discriminatory Spatial Policy
Authors: Wallace Rodney B.
Published: April 2004

In many markets, firms are able to conduct discriminatory strategies based on whether a customer prefers a competitors' product or their own. This article considers the impact of such discrimination in duopoly models in which firms set prices and conduct precontract‐customization efforts for some customers. We identify two effects: (1) The ability to conduct preference‐based discrimination increases equilibrium profit as long as long as precontract customization is at least modestly important in competitive dynamics; and (2) The ability to conduct preference‐based discrimination enhances social welfare if any precontract customization is done.
Probabilistic Integrated Assessment of "Dangerous" Climate Change
Authors: Mastrandrea Michael D. , Schneider Stephen H.
Published: April 2004

Climate policy decisions are being made despite layers of uncertainty. Such decisions directly influence the potential for “dangerous anthropogenic interference with the climate system.” We mapped a metric for this concept, based on Intergovernmental Panel on Climate Change assessment of climate impacts, onto probability distributions of future climate change produced from uncertainty in key parameters of the coupled social-natural system—climate sensitivity, climate damages, and discount rate. Analyses with a simple integrated assessment model found that, under midrange assumptions, endogenously calculated, optimal climate policy controls can reduce the probability of dangerous anthropogenic interference from ∼45% under minimal controls to near zero.
Role of a Mutation at Position 167 of CTX-M-19 in Ceftazidime Hydrolysis
Authors: Kimura Soichiro , Ishiguro Masaji , Ishii Yoshikazu , Alba Jimena , Yamaguchi Keizo
Published: April 2004

CTX-M-19 is a recently identified ceftazidime-hydrolyzing extended-spectrum β-lactamase, which differs from the majority of CTX-M-type β-lactamases that preferentially hydrolyze cefotaxime but not ceftazidime. To elucidate the mechanism of ceftazidime hydrolysis by CTX-M-19, the β-lactam MICs of a CTX-M-19 producer, and the kinetic parameters of the enzyme were confirmed. We reconfirmed here that CTX-M-19 is also stable at a high enzyme concentration in the presence of bovine serum albumin (20 μg/ml). Under this condition, we obtained more accurate kinetic parameters and determined that cefotaxime (
k
cat

/K
m

, 1.47 × 10
6
s
−1
M
−1
), cefoxitin (
k
cat

/K
m

, 62.2 s
−1
M
−1
), and aztreonam (
k
cat

/K
m

, 1.34 × 10
3
s
−1
M
−1
) are good substrates and that imipenem (
k
+2
/K
, 1.20 × 10
2
s
−1
M
−1
) is a poor substrate. However, CTX-M-18 and CTX-M-19 exhibited too high a

K
m

value (2.7 to 5.6 mM) against ceftazidime to obtain their catalytic activity (
k
cat
). Comparison of the MICs with the catalytic efficiency (
k
cat

/K
m

) of these enzymes showed that some β-lactams, including cefotaxime, ceftazidime, and aztreonam showed a similar correlation. Using the previously reported crystal structure of the Toho-1 β-lactamase, which belongs to the CTX-M-type β-lactamase group, we have suggested characteristic interactions between the enzymes and the β-lactams ceftazidime, cefotaxime, and aztreonam by molecular modeling. Aminothiazole-bearing β-lactams require a displacement of the aminothiazole moiety due to a severe steric interaction with the hydroxyl group of Ser167 in CTX-M-19, and the displacement affects the interaction between Ser130 and the acidic group such as carboxylate and sulfonate of β-lactams.
Analysis of the Effects of Chlorhexidine on Oral Biofilm Vitality and Structure Based on Viability Profiling and an Indicator of Membrane Integrity
Authors: Hope C. K. , Wilson M.
Published: April 2004

Multispecies biofilms modeling interproximal plaque were grown on a hydroxyapatite substratum in a constant-depth film fermentor and then immersed in a viewing solution containing fluorescent indicators of membrane integrity. Confocal laser scanning microscopy (CLSM) revealed the structure and spatial distribution of cell vitality within the biofilms. Chlorhexidine gluconate (CHX) was added to the viewing solution to achieve concentrations of 0.05 and 0.2% (wt/vol) before further CLSM time-lapse series were captured. Image analysis showed that exposure to 0.2% CHX caused the biofilm to contract at a rate of 1.176 μm min
−1
along the
z
axis and also effected changes in total fluorescence measurements and viability profiles through the biofilms after a delay of 3 to 5 min. At a concentration of 0.05% CHX, total fluorescence measurements for the biofilm exhibited barely detectable changes after 5 min. Fluorescence profiles (fluorescence versus time versus depth), however, clearly showed that a time-dependent effect was present, but the clearest indicator of the effect of dilute CHX over time was viability profiling. These findings suggest the possibility of using fluorescent indicators of membrane integrity in conjunction with viability profiling to evaluate the penetration of the bactericidal effects of membrane-active antimicrobial compounds into biofilm.
Antibiotic Susceptibility in Relation to Penicillin-Binding Protein Genes and Serotype Distribution of
Streptococcus pneumoniae
Strains Responsible for Meningitis in Japan, 1999 to 2002
Authors: Ubukata Kimiko , Chiba Naoko , Hasegawa Keiko , Kobayashi Reiko , Iwata Satoshi , Sunakawa Keisuke
Published: April 2004

The antibiotic susceptibilities, genotypes of penicillin (PEN)-binding protein genes (
pbp
), and serotype distributions of
Streptococcus pneumoniae
isolates from meningitis patients were investigated by a nationwide surveillance group in Japan between 1999 and 2002. We analyzed 146 isolates from children (≤17 years old) and 73 from adults (≥18 years old). Isolates with or without abnormal
pbp1a
,
pbp2x
, or
pbp2b
genes identified by PCR were classified into six genotype patterns and 90% MIC (MIC
90
) values for PEN: (i) strains with three normal genes (17.2% of isolates; MIC
90
, 0.031 μg/ml); (ii) strains with abnormal
pbp2x
(22.1%, 0.063 μg/ml); (iii) strains with abnormal
pbp2b
(1.0%, 0.125 μg/ml); (iv) strains with abnormal
pbp2x
and
pbp2b
(7.4%, 0.25 μg/ml); (v) strains with abnormal
pbp1a
and
pbp2x
(12.7%, 0.25 μg/ml); and (vi) strains with three abnormal PBP genes (39.7%, 4 μg/ml), which are termed genotypic PEN-resistant
S. pneumoniae
(gPRSP). Panipenem, a carbapenem, showed an excellent MIC
90
(0.125 μg/ml) against gPRSP, followed by meropenem and vancomycin (0.5 μg/ml), cefotaxime and ceftriaxone (1 μg/ml), and ampicillin (4 μg/ml). Strains of gPRSP were significantly more prevalent in children (45.2%) than in adults (27.4%). The most frequent serotypes were 6B, 19F, 23F, 6A, and 14 in children and 23F, 22, 3, 10, 6B, and 19F in adults. Serotypes 6B, 6A, 19F, 23F, and 14 predominated among gPRSP. In children, 7- and 11-valent pneumococcal conjugate vaccines would cover 76.2 and 81.3% of isolates, respectively, although coverage would be lower in adults (43.9 and 56.0%, respectively). These findings suggest the need for early introduction of pneumococcal conjugate vaccines and continuous bacteriological surveillance for meningitis.
Rapidly Increasing Prevalence of β-Lactamase-Nonproducing, Ampicillin-Resistant
Haemophilus influenzae
Type b in Patients with Meningitis
Authors: Hasegawa Keiko , Chiba Naoko , Kobayashi Reiko , Murayama Somay Y. , Iwata Satoshi , Sunakawa Keisuke , Ubukata Kimiko
Published: April 2004

A total of 395
Haemophilus influenzae
strains from 226 Japanese institutions participating in the Nationwide Surveillance Study Group for Bacterial Meningitis were received from 1999 to 2002. All strains were analyzed by PCR to identify the resistance genes, and their susceptibilities to β-lactam agents were determined. Of these strains, 29.1% were β-lactamase nonproducing and ampicillin (AMP) susceptible (BLNAS) and lacked all resistance genes; 15.4% were β-lactamase producing and AMP resistant and had the
bla
TEM-1
gene; 30.6% were β-lactamase nonproducing and AMP resistant (low-BLNAR) and had a Lys-526 or His-517 amino acid substitution in
ftsI
encoding PBP 3; 13.9% were β-lactamase nonproducing and AMP resistant (BLNAR) and had an additional substitution of Thr-385 in
ftsI
; 9.1% were amoxicillin-clavulanic acid resistant (BLPACR I) and had the
bla
TEM-1
gene and a Lys-526 or His-517 amino acid substitution in
ftsI
; and 1.8% showed resistance similar to that of the BLPACR I group (BLPACR II) but had
bla
TEM-1
gene and
ftsI
substitutions, as was the case for the BLNAR strains. All but three strains were serotype b. The prevalence of BLNAR strains has increased rapidly: 0% in 1999, 5.8% in 2000, 14.1% in 2001, and 21.3% in 2002. The MICs at which 90% of BLNAR isolates were inhibited were as follows: AMP, 16 μg/ml; cefotaxime, 1 μg/ml; ceftriaxone, 0.25 μg/ml; and meropenem, 0.5 μg/ml. All of these values were higher than those for the BLNAS counterpart strains. The relatively wide distributions of the β-lactam MICs for BLNAR strains presumably reflect variations in
ftsI
gene mutations. Pulsed-field gel electrophoresis suggested the rapid spread of specific
H. influenzae
type b strains throughout Japan. Expedited vaccination, rapid identification, and judicious antibiotic use could slow their spread.
Antibacterial Activities of Rhodamine B-Conjugated Gelsolin-Derived Peptides Compared to Those of the Antimicrobial Peptides Cathelicidin LL37, Magainin II, and Melittin
Authors: Bucki Robert , Pastore Jennifer J. , Randhawa Paramjeet , Vegners Rolands , Weiner Daniel J. , Janmey Paul A.
Published: April 2004

The growing number of antibiotic-resistant bacteria necessitates the search for new antimicrobial agents and the principles by which they work. We report that cell membrane-permeant rhodamine B (RhB)-conjugated peptides based on the phosphatidylinositol-4,5-bisphosphate binding site of gelsolin can kill the gram-negative organismsEscherichia coliandPseudomonas aeruginosaand the gram-positive organismStreptococcus pneumoniae. RhB linkage to the QRLFQVKGRR sequence in gelsolin was essential for the antibacterial function, since the unconjugated peptide had no effect on the bacteria tested. Because RhB-QRLFQVKGRR (also termed PBP10), its scrambled sequence (RhB-FRVKLKQGQR), and PBP10 synthesized fromd-isomer amino acids show similar antibacterial properties, the physical and chemical properties of these derivatives appear to be more important than specific peptide folding for their antibacterial functions. The similar activities of PBP10 and all-d-amino-acid PBP10 also indicate that a specific interaction between RhB derivatives and bacterial proteins is unlikely to be involved in the bacterial killing function of PBP10. By using a phospholipid monolayer system, we found a positive correlation between the antibacterial function of PBP10, as well as some naturally occurring antibacterial peptides, and the intrinsic surface pressure activity at the hydrophobic-hydrophilic interface. Surprisingly, we observed little or no dependence of the insertion of these peptides into lipid monolayers on the phospholipid composition. These studies show that an effective antimicrobial agent can be produced from a peptide sequence with specificity to a phospholipid not found in bacteria, and comparisons with other antimicrobial agents suggest that the surface activities of these peptides are more important than specific binding to bacterial proteins or lipids for their antimicrobial functions.
Effects of Drug Resistance Mutations L100I and V106A on the Binding of Pyrrolobenzoxazepinone Nonnucleoside Inhibitors to the Human Immunodeficiency Virus Type 1 Reverse Transcriptase Catalytic Complex
Authors: Locatelli Giada A. , Campiani Giuseppe , Cancio Reynel , Morelli Elena , Ramunno Anna , Gemma Sandra , Hübscher Ulrich , Spadari Silvio , Maga Giovanni
Published: April 2004

We have previously described a novel class of nonnucleoside reverse transcriptase (RT) inhibitors, the pyrrolobenzoxazepinone (PBO) and the pyridopyrrolooxazepinone (PPO) derivatives, which were effective inhibitors of human immunodeficiency virus type 1 (HIV-1) RT, either wild type or carrying known drug resistance mutations (G. Campiani et al., J. Med. Chem. 42:4462-4470, 1999). The lead compound of the PPO class, (
R
)-(−)-PPO464, was shown to selectively target the ternary complex formed by the viral RT with its substrates nucleic acid and nucleotide (G. Maga et al., J. Biol. Chem. 276:44653-44662, 2001). In order to better understand the structural basis for this selectivity, we exploited some PBO analogs characterized by various substituents at C-3 and by different inhibition potencies and drug resistance profiles, and we studied their interaction with HIV-1 RT wild type or carrying the drug resistance mutations L100I and V106A. Our kinetic and thermodynamic analyses showed that the formation of the complex between the enzyme and the nucleotide increased the inhibition potency of the compound PBO354 and shifted the free energy (energy of activation, ΔG
#
) for inhibitor binding toward more negative values. The V106A mutation conferred resistance to PBO 354 by increasing its dissociation rate from the enzyme, whereas the L100I mutation mainly decreased the association rate. This latter mutation also caused a severe reduction in the catalytic efficiency of the RT. These results provide a correlation between the efficiency of nucleotide utilization by RT and its resistance to PBO inhibition.
Novel 4′-Substituted Stavudine Analog with Improved Anti-Human Immunodeficiency Virus Activity and Decreased Cytotoxicity
Authors: Dutschman Ginger E. , Grill Susan P. , Gullen Elizabeth A. , Haraguchi Kazuhiro , Takeda Shingo , Tanaka Hiromichi , Baba Masanori , Cheng Yung-Chi
Published: April 2004

The antiviral drug 2′,3′-didehydro-3′-deoxythymidine (D4T; also know as stavudine and Zerit), which is used against human immunodeficiency virus (HIV), causes delayed toxicity (peripheral neuropathy) in long-term use. After examining a series of 2′,3′-didehydro-3′-deoxy-4′-substituted thymidine (4′-substituted D4T) analogs, 4′-ethynyl D4T was found to have a fivefold-better antiviral effect and to cause less cellular and mitochondrial toxicity than D4T. The antiviral activity of this compound can be reversed by dThd but not by dCyd. The compound acted synergistically with β-
l
-2′,3′-deoxy-3′-thiacytidine (also known as lamivudine) and β-
l
-2′,3′-dideoxy-2′,3′-didehydro-5-fluorocytidine (also known as elvucitabine) and additively with 2′,3′-dideoxyinosine (also known as didanosine and Videx) and 3′-azido-3′-deoxythymidine (also known as Retovir and zidovudine) against HIV. 4′-Ethynyl D4T is phosphorylated by purified human thymidine kinase 1 (TK-1) from CEM cells with a faster relative
V
max
and a lower

K
m

value than D4T. The efficiency of TK-1 in the phosphorylation of 4′-ethynyl D4T is fourfold better than that of D4T. While D4T is broken down by the catabolic enzyme thymidine phosphorylase, the level of breakdown of 4′-ethynyl D4T was below detection. Since 4′-ethynyl D4T has increased anti-HIV activity and decreased toxicity and interacts favorably with other currently used anti-HIV drugs, it should be considered for further development as an anti-HIV drug.
In Vitro Interactions between Antifungals and Immunosuppressants against
Aspergillus fumigatus
Authors: Steinbach William J. , Schell Wiley A. , Blankenship Jill R. , Onyewu Chiatogu , Heitman Joseph , Perfect John R.
Published: April 2004

The optimal treatment for invasive aspergillosis remains elusive, despite the increased efficacy of newer agents. The immunosuppressants cyclosporine (CY), tacrolimus (FK506), and sirolimus (formerly called rapamycin) exhibit in vitro and in vivo activity against
Candida albicans
,
Cryptococcus neoformans
, and
Saccharomyces cerevisiae
, including fungicidal synergy with azole antifungals. We report here that both FK506 and CY exhibit a clear in vitro positive interaction with caspofungin against
Aspergillus fumigatus
by disk diffusion, microdilution checkerboard, and gross and microscopic morphological analyses. Microscopic morphological analyses indicate that the calcineurin inhibitors delay filamentation, and in combination with caspofungin there is a positive interaction. Our findings suggest a potential role for combination therapy with calcineurin pathway inhibitors and existing antifungal agents to augment activity against
A. fumigatus
.
Peritoneal Fluid Titer Test for Peritoneal Dialysis-Related Peritonitis
Authors: Strijack Christine , Harding Godfrey K. M. , Ariano Robert E. , Zelenitsky Sheryl A.
Published: April 2004

Standard microbiological tests (i.e., MIC) do not account for the unique factors of peritoneal dialysis (PD)-related peritonitis which can significantly influence treatment response. Our goals were to develop a peritoneal fluid titer (PFT) test and to conduct a pilot study of its association with clinical outcome. The methodology was developed by using spent dialysate collected from patients with bacterial PD-related peritonitis prior to the initiation of antibiotics. Dialysate was processed and spiked with antibiotic to simulate two standard intraperitoneal regimens: cefazolin plus tobramycin and cefazolin alone. Thirty-six clinical isolates, including
Staphylococcus epidermidis
,
Staphylococcus aureus
,
Escherichia coli
,
Klebsiella pneumoniae
,
Enterobacter cloacae
, and
Pseudomonas aeruginosa
, were tested. In the pilot study, dialysate was collected from 14 patients with bacterial PD-related peritonitis. Titers were determined by using each patient's dialysate and infecting pathogen. Titers were highly reproducible, with discrepancies in only 1% of cases. Overall, PFTs were notably higher against gram-positive bacteria (
P
< 0.0001). The addition of tobramycin increased titers significantly from zero to values of 1/16 to 1/64 against
E. cloacae
and
P. aeruginosa
(
P
< 0.0001). In the pilot study, peritoneal fluid inhibitory titers were significantly associated with clinical outcome, with a median value of 1/96 for patients who were cured compared to 1/32 for those who failed treatment (
P
= 0.036). In conclusion, this study provides preliminary support for the PFT as a pharmacodynamic index specific to the treatment of PD-related peritonitis. With further characterization and validation in patients, the PFT test may advance the study of antibiotic therapies for PD-related peritonitis.
Screening for Microtubule-Disrupting Antifungal Agents by Using a Mitotic-Arrest Mutant of
Aspergillus nidulans
and Novel Action of Phenylalanine Derivatives Accompanying Tubulin Loss
Authors: Kiso Tetsuo , Fujita Ken-Ichi , Ping Xu , Tanaka Toshio , Taniguchi Makoto
Published: April 2004

The microtubule, which is one of the major targets of anthelmintics, anticancer drugs, and fungicides, is composed mainly of α- and β-tubulins. We focused on a unique characteristic of an
Aspergillus nidulans benA33
mutant to screen for microtubule-disrupting antifungal agents. This mutant, which has a β-tubulin with a mutation of a single amino acid, undergoes mitotic arrest due to the formation of hyperstable microtubules at 37°C. The heat sensitivity of the mutant is remedied by some antimicrotubule agents. We found that an agar plate assay with the mutant was able to distinguish three types of microtubule inhibitors. The growth recovery zones of the mutant were formed around paper disks containing microtubule inhibitors, including four benzimidazoles, ansamitocin P-3, griseofulvin, and rhizoxin, on the agar plate at 37°C. Nocodazole, thiabendazole, and griseofulvin reversed the mitotic arrest of the mutant and promoted its hyphal growth. Ansamitocin P-3 and rhizoxin showed growth recovery zones around the growth-inhibitory zones. Benomyl and carbendazim also reversed mitotic arrest but produced weaker growth recovery than the aforementioned drugs. Other microtubule inhibitors, such as colchicine, Colcemid, paclitaxel, podophyllotoxin, TN-16, vinblastine, and vincristine, as well as some cytoskeletal inhibitors tested, did not show such activity. In our screening, we newly identified two mycotoxins, citrinin and patulin, two sesquiterpene dialdehydes, polygodial and warburganal, and four phenylalanine derivatives, arphamenine A,
l
-2,5-dihydrophenylalanine (DHPA),
N
-tosyl-
l
-phenylalanine chloromethylketone, and
N
-carbobenzoxy-
l
-phenylalanine chloromethyl ketone. In a wild-type strain of
A. nidulans
, DHPA caused selective losses of microtubules, as determined by fluorescence microscopy, and of both α- and β-tubulins, as determined by Western blot analysis. This screening method involving the
benA33
mutant of
A. nidulans
is useful, convenient, and highly selective. The phenylalanine derivatives tested are of a novel type of microtubule-disrupting antifungal agents, producing an accompanying loss of tubulins, and are different from well-known tubulin inhibitors affecting the assembly of tubulin dimers into microtubules.
Crystal Structures of
Escherichia coli
Topoisomerase IV ParE Subunit (24 and 43 Kilodaltons): a Single Residue Dictates Differences in Novobiocin Potency against Topoisomerase IV and DNA Gyrase
Authors: Bellon Steven , Parsons Jonathan D. , Wei Yunyi , Hayakawa Koto , Swenson Lora L. , Charifson Paul S. , Lippke Judith A. , Aldape Robert , Gross Christian H.
Published: April 2004

Topoisomerase IV and DNA gyrase are related bacterial type II topoisomerases that utilize the free energy from ATP hydrolysis to catalyze topological changes in the bacterial genome. The essential function of DNA gyrase is the introduction of negative DNA supercoils into the genome, whereas the essential function of topoisomerase IV is to decatenate daughter chromosomes following replication. Here, we report the crystal structures of a 43-kDa N-terminal fragment of
Escherichia coli
topoisomerase IV ParE subunit complexed with adenylyl-imidodiphosphate at 2.0-Å resolution and a 24-kDa N-terminal fragment of the ParE subunit complexed with novobiocin at 2.1-Å resolution. The solved ParE structures are strikingly similar to the known gyrase B (GyrB) subunit structures. We also identified single-position equivalent amino acid residues in ParE (M74) and in GyrB (I78) that, when exchanged, increased the potency of novobiocin against topoisomerase IV by nearly 20-fold (to 12 nM). The corresponding exchange in gyrase (I78 M) yielded a 20-fold decrease in the potency of novobiocin (to 1.0 μM). These data offer an explanation for the observation that novobiocin is significantly less potent against topoisomerase IV than against DNA gyrase. Additionally, the enzyme kinetic parameters were affected. In gyrase, the ATP

K
m

increased ≈5-fold and the
V
max
decreased ≈30%. In contrast, the topoisomerase IV ATP

K
m

decreased by a factor of 6, and the
V
max
increased ≈2-fold from the wild-type values. These data demonstrate that the ParE M74 and GyrB I78 side chains impart opposite effects on the enzyme's substrate affinity and catalytic efficiency.
Disposition and Metabolic Profiles of [
14
C]Viramidine and [
14
C]Ribavirin in Rat and Monkey Red Blood Cells and Liver
Authors: Lin Chin-Chung , Lourenco David , Xu Guifen , Yeh Li-Tain
Published: April 2004

The disposition and metabolic profiles of [
14
C]viramidine and [
14
C]ribavirin were compared in rat and monkey red blood cells and liver. Our data reveal that the total ribavirin-related components (ribavirin plus its mono-, di-, and triphosphate metabolites) may account for most of the drug in monkey liver following prolonged oral administration of viramidine.
In Vitro Activity of a Novel Diaminopyrimidine Compound, Iclaprim, against
Chlamydia trachomatis
and
C. pneumoniae
Authors: Kohlhoff S. A. , Roblin P. M. , Reznik T. , Hawser S. , Islam K. , Hammerschlag M. R.
Published: April 2004

The in vitro activities of iclaprim, a novel dihydrofolate reductase inhibitor, azithromycin, and levofloxacin were tested against 10 strains of
Chlamydia trachomatis
and 10 isolates of
Chlamydia pneumoniae
. For
C. trachomatis
and
C. pneumoniae
, the iclaprim MIC and minimal bactericidal concentration at which 90% of isolates were inhibited (MIC
90
and MBC
90
) were 0.5 μg/ml, compared to an azithromycin MIC
90
and MBC
90
of 0.125 μg/ml and levofloxacin MIC
90
s and MBC
90
s of 1 μg/ml for
C. trachomatis
and 0.5 μg/ml for
C. pneumoniae
.
Inhibition of Human Immunodeficiency Virus Type 1 Tat-
trans
-Activation-Responsive Region Interaction by an Antiviral Quinolone Derivative
Authors: Richter Sara , Parolin Cristina , Gatto Barbara , Del Vecchio Claudia , Brocca-Cofano Egidio , Fravolini Arnaldo , Palù Giorgio , Palumbo Manlio
Published: April 2004

WM5, a 6-aminoquinolone derivative, binds with high affinity to the bulge of the
trans
-activation-responsive region (TAR), whereas it displays low binding affinity for the loop and stem regions of TAR and for random RNA and DNA sequences. Furthermore, WM5 disrupts the natural protein-nucleic acid complex with a 50% inhibitory concentration in the low micromolar range in both in vitro and in vivo assays.
Downstream migration in Atlantic salmon (Salmo salar) smolt sibling groups
Authors: Olsén K Håkan , Petersson Erik , Ragnarsson Bjarne , Lundqvist Hans , Järvi Torbjörn
Published: April 2004

Previous studies have shown kin recognition abilities in salmonid fish. Some authors have suggested that the attraction of juvenile fish to siblings may indicate preference for shoaling with kin. The aim of the present study is to test the prerequisite for the hypothesis that siblings swim spatially closer than unrelated fish during their seaward migration as smolts. Atlantic salmon (Salmo salar) eggs from three families were each reared in two tanks to create familiar and unfamiliar sibling smolts. Before the experiment started they were tagged individually withpassive integrated transponders (PITs). Twelve individuals from each of six groups were mixed and released together at several occasions in the upper end of the 400-m-long experimental stream. An automatic PIT-monitoring system placed in the outlet recorded the time for passage of each individual leaving the stream. Eighty-five percent of the juveniles monitored by the PIT antenna showed downstream migration at night hours and they migrated significantly more often closer in time to both known and unknown siblings than to unrelated fish. The results suggest that there is a genetic component in the migratory behaviour of Atlantic salmon smolts and support the hypothesis that smolts migrate in kin-structured groups.
Lateral behavior of full-scale concrete-filled carbon composite columns
Authors: Hong Won-Kee , Kim Hee-Cheul , Yoon Suk-Han
Published: April 2004

Full scale concrete-filled carbon composite columns without longitudinal and transverse reinforcing steels are tested to investigate the lateral behavior of columns confined with carbon composite tubes. In the present study, the full-scale circular and square concrete-filled carbon composite tubes (CFCTs) with various winding angles with respect to longitudinal axes of the tubes are subjected to lateral loads under a constant axial load. The influence of thickness and winding angle of carbon tubes on the lateral behavior of concrete columns is studied both experimentally and analytically, demonstrating that the calculated ultimate moment capacity of confined columns compares well with test data. For this analytical process, stress–strain relationships of confined concrete columns uncovered by the authors are used to identify the distribution of confined compressive concrete strength at failure. This stress–strain model considers the influence of winding orientation of carbon fibers on the confining capability of the concrete core.Key words: carbon composite, lateral capacity of confined column, strength, filament winding.
Effect of geometric design consistency on road safety
Authors: Ng Joanne C.W , Sayed Tarek
Published: April 2004

Geometric design consistency is emerging as an important rule in highway design. Identifying and treating any inconsistency on a highway can significantly improve its safety performance. Considerable research has been undertaken to explore this concept including identifying potential consistency measures and developing models to estimate them. However, little work has been carried out to quantify the safety benefits of geometric design consistency. The objectives of this study are to investigate and quantify the relationship between design consistency and road safety. A comprehensive accident and geometric design database of two-lane rural highways is used to investigate the effect of several design consistency measures on road safety. Several accident prediction models that incorporate design consistency measures are developed. The generalized linear regression approach is used for model development. The models can be used as a quantitative tool for the evaluation of the impact of design consistency on road safety. An application is presented where the ability of accident prediction models that incorporate design consistency measures is compared with those that rely on geometric design characteristics. It is found that models that explicitly consider design consistency may identify the inconsistencies more effectively and reflect the resulting impacts on safety more accurately than those that do not.Key words: geometric design consistency, road safety, quantification, accident prediction models.
A recommended specification for recycled content guardrail posts
Authors: Atahan Ali O
Published: April 2004

In this paper, results of an experimental study aimed to assess the suitability of a recycled content guardrail post as a substitute for conventional wooden guardrail post are presented. A series of static and dynamic tests performed on the recycled content guardrail posts show that the strength and energy dissipation of recycled posts are comparable to those of conventional wooden guardrail post. A full-scale crash test, using a 2000-kg pickup truck traveling at 100 km/h and making contact at a 25° angle, is also performed on the recycled content plastic-post W-beam guardrail system to evaluate its strength and structural adequacy. The barrier performed acceptably for National Cooperative Highway Research Program (NCHRP) report 350 test designation 3-11. Results of the crash test show that the recycled content guardrail post and W-beam guardrail can successfully contain and redirect an errant vehicle, and they can be a potential substitute for nationally used guardrail posts. Finally, a recommended specification is developed for the recycled content guardrail posts based on a series of test procedures and performance levels.Key words: recycled plastics, roadside safety, crash test, guardrail post, strong-post guardrail system, recommended specifications, NCHRP report 350.
Using genetic algorithms in solving the one-dimensional cutting stock problem in the construction industry
Authors: Shahin Adham A , Salem Ossama M
Published: April 2004

In the United States, vast amounts of construction waste are produced every year. Construction waste accounts for a significant portion of the municipal waste stream of the United States. One-dimensional stocks are one of the major contributors to construction waste. Cutting one-dimensional stocks to suit needed project lengths results in trim losses, which are the main causes of one-dimensional stock waste. Although part of such waste is recyclable such as steel waste, reduction in the generation of waste can enhance the stock material usage and thereby increase the profit potential of the company. The traditional optimization techniques (i.e., linear programming and integer programming) suffer some drawbacks when they are used to solve the one-dimensional cutting stock problem (CSP). In this paper, a genetic algorithm (GA) model for solving the one-dimensional CSP (GA1D) is presented. Three real life case studies from a local steel workshop in Fargo, North Dakota have been studied, and their solutions (cutting schedules) using the GA approach are presented and compared with the actual workshop cutting schedules. The comparison shows a high potential of savings that could be achieved.Key words: construction waste management, waste reduction, genetic algorithm, GA, cutting stock problem, CSP, optimization, reinforcement steel optimization, rebar optimization.
Ground motion sensitivity of a Vancouver-style high rise
Authors: White Timothy , Ventura Carlos E
Published: April 2004

The purpose of the study discussed in this paper is to evaluate the seismic response of a modern building, designed according to the current building code and to extreme earthquake earthquakes from two different source mechanisms. To this end, a three-dimensional nonlinear dynamic response of a reinforced concrete high-rise building, typical of the type built in Vancouver, British Columbia, is investigated. According to current design practice, the building has been designed to resist lateral loads with a coupled shearwall system. A comparison of the responses of the building to crustal and subduction type earthquakes of similar magnitudes is presented and discussed. The ground motion records selected for this study were derived from recorded crustal and subduction events, which are both considered to be extreme, and beyond the code-based design requirements of the building. A part of this study includes an evaluation of how the dynamic properties of the building change as the building is being damaged by severe ground shaking. The results of the study show that the crustal earthquake imposes large upper levels displacements, and much plastic hinging near the base because the response of the building is governed mainly by the first mode of the "undamaged" system. The subduction earthquake results in displacements smaller than those from the crustal event and causes plastic hinging at mid-height and near the base as well as large torsional rotations, because the behaviour of the building is greatly influenced by the second mode of the "damaged" system.Key words: nonlinear dynamic analysis, seismic, high rise, reinforced concrete, coupled shearwall.