bluuebunny/crossref_metadata_2025_split huggingface dataset:
SCH 503034, a Mechanism-Based Inhibitor of Hepatitis C Virus NS3 Protease, Suppresses Polyprotein Maturation and Enhances the Antiviral Activity of Alpha Interferon in Replicon Cells
Authors: Malcolm B. A. , Liu R. , Lahser F. , Agrawal S. , Belanger B. , Butkiewicz N. , Chase R. , Gheyas F. , Hart A. , Hesk D. , Ingravallo P. , Jiang C. , Kong R. , Lu J. , Pichardo J. , Prongay A. , Skelton A. , Tong X. , Venkatraman S. , Xia E. , Girijavallabhan V. , Njoroge F. G. 
Published: February 2006

ABSTRACTCleavage of the hepatitis C virus (HCV) polyprotein by the viral NS3 protease releases functional viral proteins essential for viral replication. Recent studies by Foy and coworkers strongly suggest that NS3-mediated cleavage of host factors may abrogate cellular response to alpha interferon (IFN-α) (E. Foy, K. Li, R. Sumpter, Jr., Y.-M. Loo, C. L. Johnson, C. Wang, P. M. Fish, M. Yoneyama, T. Fujita, S. M. Lemon, and M. Gale, Jr., Proc. Natl. Acad. Sci. USA102:2986-2991, 2005, and E. Foy, K. Li, C. Wang, R. Sumpter, Jr., M. Ikeda, S. M. Lemon, and M. Gale, Jr., Science300:1145-1148, 2003). Blockage of NS3 protease activity therefore is expected to inhibit HCV replication by both direct suppression of viral protein production as well as by restoring host responsiveness to IFN. Using structure-assisted design, a ketoamide inhibitor, SCH 503034, was generated which demonstrated potent (overall inhibition constant, 14 nM) time-dependent inhibition of the NS3 protease in cell-free enzyme assays as well as robust in vitro activity in the HCV replicon system, as monitored by immunofluorescence and real-time PCR analysis. Continuous exposure of replicon-bearing cell lines to six times the 90% effective concentration of SCH 503034 for 15 days resulted in a greater than 4-log reduction in replicon RNA. The combination of SCH 503034 with IFN was more effective in suppressing replicon synthesis than either compound alone, supporting the suggestion of Foy and coworkers that combinations of IFN with protease inhibitors would lead to enhanced therapeutic efficacy.
Susceptibility of
Cryptococcus neoformans
Biofilms to Antifungal Agents In Vitro
Authors: Martinez Luis R. , Casadevall Arturo 
Published: February 2006

ABSTRACT

Microbial biofilms contribute to virulence and resistance to antibiotics by shielding microbial cells from host defenses and antimicrobial drugs, respectively.
Cryptococcus neoformans
was demonstrated to form biofilms in polystyrene microtiter plates. The numbers of CFU of disaggregated biofilms, 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl]-2
H
-tetrazolium hydroxide reduction, and light and confocal microscopy were used to measure the fungal mass, the metabolic activity, and the appearance of
C. neoformans
biofilms, respectively. Biofilm development by
C. neoformans
followed a standard sequence of events: fungal surface attachment, microcolony formation, and matrix production. The susceptibilities of
C. neoformans
cells of the biofilm and planktonic phenotypes to four antifungal agents were examined. The exposure of
C. neoformans
cells or preformed cryptococcal biofilms to fluconazole or voriconazole did not result in yeast growth inhibition and did not affect the metabolic activities of the biofilms, respectively. In contrast, both
C. neoformans
cells and preformed biofilms were susceptible to amphotericin B and caspofungin. However,
C. neoformans
biofilms were significantly more resistant to amphotericin B and caspofungin than planktonic cells, and their susceptibilities to these drugs were further reduced if cryptococcal cells contained melanin. A spot enzyme-linked immunosorbent assay and light and confocal microscopy were used to investigate how antifungal drugs affected
C. neoformans
biofilm formation. The mechanism by which amphotericin B and caspofungin interfered with
C. neoformans
biofilm formation involved capsular polysaccharide release and adherence. Our results suggest that biofilm formation may diminish the efficacies of some antifungal drugs during cryptococcal infection.
Potent Antiscrapie Activities of Degenerate Phosphorothioate Oligonucleotides
Authors: Kocisko David A. , Vaillant Andrew , Lee Kil Sun , Arnold Kevin M. , Bertholet Nadine , Race Richard E. , Olsen Emily A. , Juteau Jean-Marc , Caughey Byron 
Published: February 2006

ABSTRACTAlthough transmissible spongiform encephalopathies (TSEs) are incurable, a key therapeutic approach is prevention of conversion of the normal, protease-sensitive form of prion protein (PrP-sen) to the disease-specific protease-resistant form of prion protein (PrP-res). Here degenerate phosphorothioate oligonucleotides (PS-ONs) are introduced as low-nM PrP-res conversion inhibitors with strong antiscrapie activities in vivo. Comparisons of various PS-ON analogs indicated that hydrophobicity and size were important, while base composition was only minimally influential. PS-ONs bound avidly to PrP-sen but could be displaced by sulfated glycan PrP-res inhibitors, indicating the presence of overlapping binding sites. Labeled PS-ONs also bound to PrP-sen on live cells and were internalized. This binding likely accounts for the antiscrapie activity. Prophylactic PS-ON treatments more than tripled scrapie survival periods in mice. Survival times also increased when PS-ONs were mixed with scrapie brain inoculum. With these antiscrapie activities and their much lower anticoagulant activities than that of pentosan polysulfate, degenerate PS-ONs are attractive new compounds for the treatment of TSEs.
Mefloquine Induces Dose-Related Neurological Effects in a Rat Model
Authors: Dow G. , Bauman R. , Caridha D. , Cabezas M. , Du F. , Gomez-Lobo R. , Park M. , Smith K. , Cannard K. 
Published: February 2006

ABSTRACT
Mefloquine is one of the drugs approved by the FDA for malaria chemoprophylaxis. Mefloquine is also approved for the treatment of malaria and is widely used for this purpose in combination with artesunate. However, the clinical utility of the compound has been compromised by reports of adverse neurological effects in some patients. In the present study, the potential neurological effects of mefloquine were investigated with six 7-week-old female rats given a single oral dose of the compound. Potential mefloquine-induced neurological effects were monitored using a standard functional observational battery, automated open field tests, automated spontaneous activity monitoring, a beam traverse task, and histopathology. Plasma mefloquine concentrations were determined 72 h after dosing by using liquid chromatography-mass spectrometry. Mefloquine induced dose-related changes in endpoints associated with spontaneous activity and impairment of motor function and caused degeneration of specific brain stem nuclei (nucleus gracilis). Increased spontaneous motor activity was observed only during the rats' normal sleeping phase, suggesting a correlate to mefloquine-induced sleep disorders. The threshold dose for many of these effects was 187 mg/kg of body weight. This dose yielded plasma mefloquine concentrations after 72 h that are similar to those observed in humans after the treatment dose. Collectively, these data suggest that there may be a biological basis for some of the clinical neurological effects associated with mefloquine.
Inactivation of Herpes Simplex Virus Clinical Isolates by Using a Combination Microbicide
Authors: Isaacs Charles E. , Rohan Lisa , Xu Weimin , Jia Jun Hua , Mietzner Timothy , Hillier Sharon 
Published: February 2006

ABSTRACT
A combination microbicide using the lipid-ether 1-0-octyl-sn-glycerol (OG) (3 mM) and peptide LSA5 (9 μM) synergistically inactivated six clinical isolates of herpes simplex virus type 2 (HSV-2) by 30- to 100-fold and five of six HSV-1 isolates by 10-fold more than the sum of OG and LSA5 used individually within 30 min. OG plus LSA5 inactivated all HSV clinical isolates by ≥1,000-fold in 10 to 40 min.
Medium Plays a Role in Determining Expression of
acrB
,
marA
, and
soxS
in
Escherichia coli
Authors: Bailey Andrew M. , Webber Mark A. , Piddock Laura J. V. 
Published: February 2006

ABSTRACT

Analysis of expression of
acrB
,
marA
, and
soxS
in rich and minimal media, at early and late logarithmic growth phases, showed that
acrB
had increased expression in minimal medium compared to rich medium, but expression decreased dose dependently upon exposure to ciprofloxacin.
Correlation between Reduced Daptomycin Susceptibility and Vancomycin Resistance in Vancomycin-Intermediate
Staphylococcus aureus
Authors: Cui Longzhu , Tominaga Eiji , Neoh Hui-min , Hiramatsu Keiichi 
Published: February 2006

ABSTRACT

We present here findings of a strong positive correlation between reduced daptomycin susceptibility and vancomycin resistance in vancomycin-intermediate
Staphylococcus aureus
(VISA). This correlation is related to cell wall thickening, suggesting that, similar to the case with vancomycin resistance in VISA, the physical barrier of a thickened cell wall may contribute to daptomycin resistance in
S. aureus
.
Potent In Vitro Synergism of Fluconazole and Berberine Chloride against Clinical Isolates of
Candida albicans
Resistant to Fluconazole
Authors: Quan Hua , Cao Ying-Ying , Xu Zheng , Zhao Jing-Xia , Gao Ping-Hui , Qin Xiao-Feng , Jiang Yuan-Ying 
Published: February 2006

ABSTRACT

In vitro interaction of fluconazole and berberine chloride was investigated against 40 fluconazole-resistant clinical isolates of
Candida albicans
. Synergism in fungistatic activity was found with the checkerboard microdilution assay. The findings of agar diffusion tests and time-kill curves confirmed the synergistic interaction, but no antagonistic action was observed.
Effects of Lipid Formulations of Amphotericin B on Activity of Human Monocytes against
Aspergillus fumigatus
Authors: Dotis J. , Simitsopoulou M. , Dalakiouridou M. , Konstantinou T. , Taparkou A. , Kanakoudi-Tsakalidou F. , Walsh T. J. , Roilides E. 
Published: February 2006

ABSTRACT

The immunomodulatory effects of liposomal amphotericin B (LAMB), amphotericin B lipid complex, and amphotericin B colloidal dispersion (ABCD) on antifungal activity of human monocytes (MNCs), an important component of antifungal host defense, against
Aspergillus fumigatus
were compared to those of deoxycholate amphotericin B (DAMB). MNCs from healthy volunteers were incubated with 1 or 5 μg/ml DAMB and 5 or 25 μg/ml lipid formulations for 22 h. Drug-pretreated or untreated MNCs were then washed and assayed for the following: (i) activity against
A. fumigatus
hyphae by XTT assay at MNC:hypha ratios of 10:1 and 20:1; (ii) production of superoxide anion (O
2
−
) from MNCs in response to hyphae by cytochrome
c
reduction; (iii) production of hydrogen peroxide (H
2
O
2
) and H
2
O
2
-dependent intracellular intermediates (DIIs), such as OH
−
and HOCl, from MNCs in response to
A. fumigatus
culture supernatant by flow cytometric measurement of dihydrorhodamine-1,2,3 oxidation. With the exception of 1 μg/ml DAMB and 5 μg/ml LAMB or ABCD at 10:1, all amphotericin B formulations at both concentrations and MNC:hypha ratios enhanced MNC-induced damage of
A. fumigatus
hyphae compared to results with untreated cells (
P
< 0.01). While MNC O
2
−
production upon hyphal challenge, an early event in oxidative burst, was not affected by the drugs, production of H
2
O
2
and DIIs, late events, were significantly increased by all four drugs (
P
< 0.01). At clinically relevant concentrations, both conventional amphotericin B and its lipid formulations enhance antihyphal activity of MNCs against
A. fumigatus
in association with significant augmentation of H
2
O
2
and DIIs but not O
2
−
, further demonstrating the immunomodulatory antifungal activities of these agents.
Age-Related Effects on Nelfinavir and M8 Pharmacokinetics: a Population Study with 182 Children
Authors: Hirt Déborah , Urien Saïk , Jullien Vincent , Firtion Ghislaine , Rey Elisabeth , Pons Gérard , Blanche Stéphane , Treluyer Jean-Marc 
Published: February 2006

ABSTRACTAs a relationship between nelfinavir antiretroviral efficacy and plasma concentrations has been previously established, nelfinavir pharmacokinetics was investigated in order to optimize the individual treatment schedule in a pediatric population. A population pharmacokinetic model was developed to describe the concentration-time course of nelfinavir and its active metabolite M8. Individual characteristics were used to explain the large interindividual variability in children. Data from therapeutic drug monitoring in 182 children treated with nelfinavir were analyzed with NONMEM. Then Food and Drug Administration (FDA) current recommendations were evaluated estimating the percentage of children who reached the target minimum plasma concentration (0.8 mg/liter) by using Bayesian estimates. Nelfinavir pharmacokinetics was described by a one- compartment model with linear absorption and elimination. Pharmacokinetic estimates and the corresponding intersubject variabilities for the model were as follows: nelfinavir total clearance, 0.93 liters/h/kg (39%); volume of distribution, 6.9 liters/kg (109%); absorption rate, 0.5 h−1; formation clearance fraction to hydroxy-tert-butylamide (M8), 0.025; M8 elimination rate, 1.88 h−1(49%). Apparent nelfinavir total clearance and volume of distribution decreased as a function of age. M8 elimination rate was increased by concomitant administration of nevirapine or efavirenz. Our data confirm that the FDA recommendations for children from 2 to 13 years are optimal and that the dose recommended for children younger than 2 years is adequate for the children from 2 months to 2 years old. However, in children younger than 2 months, the proposed nelfinavir newborn dose of 40 mg/kg of body weight twice daily is inadequate and we suggest increasing the dose to 50 to 60 mg/kg administered thrice daily. This assumption should be further evaluated.
Artesunate Suppositories versus Intramuscular Artemether for Treatment of Severe Malaria in Children in Papua New Guinea
Authors: Karunajeewa Harin A. , Reeder John , Lorry Kerry , Dabod Elizah , Hamzah Juliana , Page-Sharp Madhu , Chiswell Gregory M. , Ilett Kenneth F. , Davis Timothy M. E. 
Published: February 2006

ABSTRACTDrug treatment of severe malaria must be rapidly effective. Suppositories may be valuable for childhood malaria when circumstances prevent oral or parenteral therapy. We compared artesunate suppositories (n= 41; 8 to 16 mg/kg of body weight at 0 and 12 h and then daily) with intramuscular (i.m.) artemether (n= 38; 3.2 mg/kg at 0 h and then 1.6 mg/kg daily) in an open-label, randomized trial with children with severePlasmodium falciparummalaria in Papua New Guinea (PNG). Parasite density and temperature were measured every 6 h for ≥72 h. Primary endpoints included times to 50% and 90% parasite clearance (PCT50and PCT90) and the time to per os status. In a subset of 29 patients, plasma levels of artemether, artesunate, and their common active metabolite dihydroartemisinin were measured during the first 12 h. One suppository-treated patient with multiple complications died within 2 h of admission, but the remaining 78 recovered uneventfully. Compared to the artemether-treated children, those receiving artesunate suppositories had a significantly earlier mean PCT50(9.1 versus 13.8 h;P= 0.008) and PCT90(15.6 versus 20.4 h;P= 0.011). Mean time to per os status was similar for each group. Plasma concentrations of primary drug plus active metabolite were significantly higher in the artesunate suppository group at 2 h postdose. The earlier initial fall in parasitemia with artesunate is clinically advantageous and mirrors higher initial plasma concentrations of active drug/metabolite. In severely ill children with malaria in PNG, artesunate suppositories were at least as effective as i.m. artemether and may, therefore, be useful in settings where parenteral therapy cannot be given.
Involvement of the HP0165-HP0166 Two-Component System in Expression of Some Acidic-pH-Upregulated Genes of
Helicobacter pylori
Authors: Wen Yi , Feng Jing , Scott David R. , Marcus Elizabeth A. , Sachs George 
Published: February 2006

ABSTRACT

About 200 genes of the gastric pathogen
Helicobacter pylori
increase expression at medium pHs of 6.2, 5.5, and 4.5, an increase that is abolished or much reduced by the buffering action of urease. Genes up-regulated by a low pH include the two-component system HP0165-HP0166, suggesting a role in the regulation of some of the pH-sensitive genes. To identify targets of HP0165-HP0166, the promoter regions of genes up-regulated by a low pH were grouped based on sequence similarity. Probes for promoter sequences representing each group were subjected to electrophoretic mobility shift assays (EMSA) with recombinant HP0166-His
6
or a mutated response regulator, HP0166-D52N-His
6
, that can specifically determine the role of phosphorylation of HP0166 in binding (including a control EMSA with in-vitro-phosphorylated HP0166-His
6
). Nineteen of 45 promoter-regulatory regions were found to interact with HP0166-His
6
. Seven promoters for genes encoding α-carbonic anhydrase,
omp11
,
fecD
,
lpp20
,
hypA
, and two with unknown function (
p
HP1397-1396 and
p
HP0654-0675) were clustered in gene group A, which may respond to changes in the periplasmic pH at a constant cytoplasmic pH and showed phosphorylation-dependent binding in EMSA with HP0166-D52N-His
6
. Twelve promoters were clustered in groups B and C whose up-regulation likely also depends on a reduction of the cytoplasmic pH at a medium pH of 5.5 or 4.5. Most of the target promoters in groups B and C showed phosphorylation-dependent binding with HP0166-D52N-His
6
, but promoters for
ompR
(p
HP0166
-
0162
), p
HP0682
-
0681
, and p
HP1288
-
1289
showed phosphorylation-independent binding. These findings, combined with DNase I footprinting, suggest that HP0165-0166 is an acid-responsive signaling system affecting the expression of pH-sensitive genes. Regulation of these genes responds either to a decrease in the periplasmic pH alone (HP0165 dependent) or also to a decrease in the cytoplasmic pH (HP0165 independent).
Gene Products Required for De Novo Synthesis of Polysialic Acid in
Escherichia coli
K1
Authors: Andreishcheva Ekaterina N. , Vann Willie F. 
Published: February 2006

ABSTRACT

Escherichia coli
K1 is responsible for 80% of
E. coli
neonatal meningitis and is a common pathogen in urinary tract infections. Bacteria of this serotype are encapsulated with the α(2-8)-polysialic acid NeuNAc(α2-8), common to several bacterial pathogens. The gene cluster encoding the pathway for synthesis of this polymer is organized into three regions: (i)
kpsSCUDEF
, (ii)
neuDBACES
, and (iii)
kpsMT
. The K1 polysialyltransferase, NeuS, cannot synthesize polysialic acid de novo without other products of the gene cluster. Membranes isolated from strains having the entire K1 gene cluster can synthesize polysialic acid de novo. We designed a series of plasmid constructs containing fragments of regions 1 and 2 in two compatible vectors to determine the minimum number of gene products required for de novo synthesis of the polysialic acid from CMP-NeuNAc in K1
E. coli
. We measured the ability of the various combinations of region 1 and 2 fragments to restore polysialyltransferase activity in vitro in the absence of exogenously added polysaccharide acceptor. The products of region 2 genes
neuDBACES
alone were not sufficient to support de novo synthesis of polysialic acid in vitro. Only membrane fractions harboring NeuES and KpsCS could form sialic polymer in the absence of exogenous acceptor at the concentrations formed by wild-type
E. coli
K1 membranes. Membrane fractions harboring NeuES and KpsC together could form small quantities of the sialic polymer de novo.
Epistasis Analysis of Four Genes from
Anabaena
sp. Strain PCC 7120 Suggests a Connection between PatA and PatS in Heterocyst Pattern Formation
Authors: Orozco Christine C. , Risser Douglas D. , Callahan Sean M. 
Published: February 2006

ABSTRACT

The
hetR
,
patA
,
hetN
, and
patS
genes are part of a regulatory network that regulates the differentiation and patterning of heterocysts in the filamentous cyanobacterium
Anabaena
sp. strain PCC 7120. In this report, the epistatic interactions of mutant alleles of these four genes have been used to refine our understanding of their relationships to one another. The
hetR
gene was necessary for differentiation in genetic backgrounds that normally give rise to excessive differentiation, supporting its role as the master regulator of differentiation and indicating that HetR directly regulates factors in addition to
hetR
and
patS
genes that regulate differentiation. A functional
patS
gene was necessary for the delayed multiple-contiguous-heterocyst phenotype observed in
hetN
mutants as well as for the relative lack of intercalary heterocysts in
patA
mutants. Epistasis results with mutant alleles of these three genes suggested that PatA attenuates the negative effects of both PatS and HetN on differentiation and promotes differentiation independent of its antagonistic effects on PatS and HetN activity. Cooverxpression of
patS
and
hetR
in a synthetic operon indicated that
patS
acts at a point downstream of
hetR
transcription in the regulatory network controlling differentiation. A model for the regulation of differentiation that is consistent with these and previous findings is presented.
Global Analysis of Heat Shock Response in
Desulfovibrio vulgaris
Hildenborough
Authors: Chhabra S. R. , He Q. , Huang K. H. , Gaucher S. P. , Alm E. J. , He Z. , Hadi M. Z. , Hazen T. C. , Wall J. D. , Zhou J. , Arkin A. P. , Singh A. K. 
Published: February 2006

ABSTRACT

Desulfovibrio vulgaris
Hildenborough belongs to a class of sulfate-reducing bacteria (SRB) and is found ubiquitously in nature. Given the importance of SRB-mediated reduction for bioremediation of metal ion contaminants, ongoing research on
D. vulgaris
has been in the direction of elucidating regulatory mechanisms for this organism under a variety of stress conditions. This work presents a global view of this organism's response to elevated growth temperature using whole-cell transcriptomics and proteomics tools. Transcriptional response (1.7-fold change or greater; Z ≥ 1.5) ranged from 1,135 genes at 15 min to 1,463 genes at 120 min for a temperature up-shift of 13°C from a growth temperature of 37°C for this organism and suggested both direct and indirect modes of heat sensing. Clusters of orthologous group categories that were significantly affected included posttranslational modifications; protein turnover and chaperones (up-regulated); energy production and conversion (down-regulated), nucleotide transport, metabolism (down-regulated), and translation; ribosomal structure; and biogenesis (down-regulated). Analysis of the genome sequence revealed the presence of features of both negative and positive regulation which included the CIRCE element and promoter sequences corresponding to the alternate sigma factors σ
32
and σ
54
. While mechanisms of heat shock control for some genes appeared to coincide with those established for
Escherichia coli
and
Bacillus subtilis
, the presence of unique control schemes for several other genes was also evident. Analysis of protein expression levels using differential in-gel electrophoresis suggested good agreement with transcriptional profiles of several heat shock proteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), and AhpC (DVU2247). The proteomics study also suggested the possibility of posttranslational modifications in the chaperones DnaK, AhpC, GroES (DVU1977), and GroEL (DVU1976) and also several periplasmic ABC transporters.