bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pcons: A neural‐network–based consensus predictor that improves fold recognition
Authors: Lundström Jesper , Rychlewski Leszek , Bujnicki Janusz , Elofsson Arne 
Published: July 2002

AbstractDuring recent years many protein fold recognition methods have been developed, based on different algorithms and using various kinds of information. To examine the performance of these methods several evaluation experiments have been conducted. These include blind tests in CASP/CAFASP, large scale benchmarks, and long‐term, continuous assessment with newly solved protein structures. These studies confirm the expectation that for different targets different methods produce the best predictions, and the final prediction accuracy could be improved if the available methods were combined in a perfect manner. In this article a neural‐network‐based consensus predictor, Pcons, is presented that attempts this task. Pcons attempts to select the best model out of those produced by six prediction servers, each using different methods. Pcons translates the confidence scores reported by each server into uniformly scaled values corresponding to the expected accuracy of each model. The translated scores as well as the similarity between models produced by different servers is used in the final selection. According to the analysis based on two unrelated sets of newly solved proteins, Pcons outperforms any single server by generating ∼8%–10% more correct predictions. Furthermore, the specificity of Pcons is significantly higher than for any individual server. From analyzing different input data to Pcons it can be shown that the improvement is mainly attributable to measurement of the similarity between the different models. Pcons is freely accessible for the academic community through the protein structure‐prediction metaserver athttp://bioinfo.pl/meta/.
Structural comparison of recombinant human macrophage colony stimulating factor β and a partially reduced derivative using hydrogen deuterium exchange and electrospray ionization mass spectrometry
Authors: Zhang Y. Heidi , Yan Xuguang , Maier Claudia S. , Schimerlik Michael I. , Deinzer Max L. 
Published: July 2002

AbstractHydrogen deuterium exchange, monitored by electrospray ionization mass spectrometry, has been employed to characterize structural features of a derivative of recombinant human macrophage colony stimulating factor beta (rhm‐CSFβ) in which two of the nine disulfide bridges (Cys157/Cys159–Cys′157/Cys′159) were selectively reduced and alkylated. Removal of these two disulfide bridges did not affect the biological activity of the protein. Similarities between CD and fluorescence spectra for rhm‐CSFβ and its derivative indicate that removing the disulfide bonds did not strongly alter the overall three‐dimensional structure of rhm‐CSFβ. However, differences between deuterium exchange data of the intact proteins indicate that more NHs underwent fast deuterium exchange in the derivative than in rhm‐CSFβ. Regions located near the disulfide bond removal site were shown to exhibit faster deuterium exchange behavior in the derivative than in rhm‐CSFβ.
Characterization of Ejl, the cell‐wall amidase coded by the pneumococcal bacteriophage Ej‐1
Authors: Sáiz José L. , López‐Zumel Consuelo , Monterroso Begoña , Varea Julio , Arrondo José Luis R. , Iloro Ibon , García José L. , Laynez José , Menéndez Margarita 
Published: July 2002

AbstractThe Ejl amidase is coded by Ej‐1, a temperate phage isolated from the atypical pneumococcus strain 101/87. Like all the pneumococcal cell‐wall lysins, Ejl has a bimodular organization; the catalytic region is located in the N‐terminal module, and the C‐terminal module attaches the enzyme to the choline residues of the pneumococcal cell wall. The structural features of the Ejl amidase, its interaction with choline, and the structural changes accompanying the ligand binding have been characterized by CD and IR spectroscopies, differential scanning calorimetry, analytical ultracentrifugation, and FPLC. According to prediction and spectroscopic (CD and IR) results, Ejl would be composed of short β‐strands (ca. 36%) connected by long loops (ca. 17%), presenting only two well‐predicted α‐helices (ca. 12%) in the catalytic module. Its polypeptide chain folds into two cooperative domains, corresponding to the N‐ and C‐terminal modules, and exhibits a monomer ↔ dimer self‐association equilibrium. Choline binding induces small rearrangements in Ejl secondary structure but enhances the amidase self‐association by preferential binding to Ejl dimers and tetramers. Comparison of LytA, the major pneumococcal amidase, with Ejl shows that the sequence differences (15% divergence) strongly influence the amidase stability, the organization of the catalytic module in cooperative domains, and the self‐association state induced by choline. Moreover, the ligand affinity for the choline‐binding locus involved in regulation of the amidase dimerization is reduced by a factor of 10 in Ejl. Present results evidence that sequence differences resulting from the natural variability found in the cell wall amidases coded by pneumococcus and its bacteriophages may significantly alter the protein structure and its attachment to the cell wall.
Phagocytosis Affects Biguanide Sensitivity of
Acanthamoeba
spp
Authors: Noble Judith A. , Ahearn Donald G. , Avery Simon V. , Crow Sidney A. 
Published: July 2002

ABSTRACT

The incidence of
Acanthamoeba
keratitis, a disease associated with contact lens wear, has been in apparent decline with the advent of multipurpose contact lens solutions. The concentrations of the biguanides chlorhexidine digluconate (CHX) and particularly polyhexamethylene biguanide (PHMB) included in multipurpose solutions (MPSs) are sublethal for amoebae. We evaluated by flow cytometry the effects of these two biguanides on phagocytosis of particles and the survival of trophozoites of
Acanthamoeba castellanii
and
A. polyphaga
. Trophozoites of
A. castellanii
and
A. polyphaga
(10
6
/ml) were exposed to solutions of 5 and 50 μg of PHMB and CHX per ml in the presence and absence of particles (i.e., heat-killed yeasts and bacteria and latex beads). In addition, trophozoites were exposed to particles treated with these concentrations of the two biguanides. In the absence of particles, trophozoites of
A. polyphaga
appeared to be more resistant to the biguanides than those of
A. castellanii
. In the presence of particles, the rates of survival of both species were decreased. In most instances, particles treated with sublethal concentrations of both biguanides that were adsorbed onto the particles reduced the incidence of phagocytosis. Particles present in MPSs in contact lens cases may be involved in the decreased incidence of
Acanthamoeba
keratitis.
Design and Activity of Antimicrobial Peptides against Sporogonic-Stage Parasites Causing Murine Malarias
Authors: Arrighi Romanico B. G. , Nakamura Chikashi , Miyake Jun , Hurd Hilary , Burgess J. Grant 
Published: July 2002

ABSTRACTInsects produce several types of peptides to combat a broad spectrum of invasive pathogenic microbes, including protozoans. However, despite this defense response, infections are often established. Our aim was to design novel peptides that produce high rates of mortality among protozoa of the genusPlasmodium, the malaria parasites. Using existing antimicrobial peptide sequences as templates, we designed and synthesized three short novel hybrids, designated Vida1 to Vida3. Each has a slightly different predicted secondary structure. The peptides were tested against sporogonic stages of the rodent malaria parasitesPlasmodium berghei(in vitro and in vivo) andP. yoelii nigeriensis(in vitro). The level of activity varied for each peptide and according to the parasite stage targeted. Vida3 (which is predicted to have large numbers of β sheets and coils but no α helices) showed the highest level of activity, killing the early sporogonic stages in culture and causing highly significant reductions in the prevalence and intensity of infection ofP. bergheiafter oral administration or injection inAnopheles gambiaemosquitoes. The secondary structures of these peptides may play a crucial role in their ability to interact with and kill sporogonic forms of the malaria parasite.
Antifungal Triazoles and Polymorphonuclear Leukocytes Synergize To Cause Increased Hyphal Damage toScedosporium prolificansandScedosporium apiospermum
Authors: Gil-Lamaignere Cristina , Roilides Emmanuel , Mosquera Juan , Maloukou Avgi , Walsh Thomas J. 
Published: July 2002

ABSTRACTScedosporium prolificansandScedosporium apiospermum(Pseudallescheria boydii) cause pulmonary and disseminated infections refractory to most currently used antifungal agents in immunocompromised patients. We therefore investigated the potential antifungal activities of the triazoles itraconazole (ITC), voriconazole (VRC), and posaconazole (PSC) in combination with human polymorphonuclear leukocytes (PMNs) against the hyphae of these fungal pathogens. A colorimetric assay with (2,3-bis[2-methoxy-4-nitro-5-sulfophenyl]2H-tetrazolium-5-carboxanilide) sodium salt was used for the measurement of hyphal damage as an indicator of antifungal activity. We found that the newer triazoles VRC and PSC displayed synergistic effects with PMNs againstS. prolificanshyphae after 24 h (P< 0.05), whereas the effect of ITC in combination with PMNs was additive (P< 0.01). All three triazoles displayed additive antifungal activities in combination with PMNs againstS. apiospermumhyphae (P< 0.05). The synergistic or additive effects that these triazoles exhibited, combined with the antifungal activities of human PMNs, may have important therapeutic implications for the management of infections due toS. prolificansandS. apiospermum.
In Vitro Antiviral Interaction of Lopinavir with Other Protease Inhibitors
Authors: Molla Akhteruzzaman , Mo Hongmei , Vasavanonda Sudthida , Han Lixin , Lin C. Thomas , Hsu Ann , Kempf Dale J. 
Published: July 2002

ABSTRACT
The in vitro inhibition of wild-type human immunodeficiency virus (HIV) by combinations of lopinavir and six other protease inhibitors over a range of two-drug combination ratios was evaluated. Combinations of lopinavir with indinavir, nelfinavir, amprenavir, tipranavir, and BMS-232632 generally displayed an additive relationship. In contrast, a consistent, statistically significant synergistic inhibition of HIV type 1 replication with combinations of lopinavir and saquinavir was observed. Analysis of the combination indices indicated that lopinavir with saquinavir was synergistic over the entire range of drug combination ratios tested and at all levels of inhibition in excess of 40%. Cellular toxicity was not observed at the highest drug concentrations tested. These results suggest that administration of combinations of the appropriate dose of lopinavir with other protease inhibitors in vivo may result in enhanced antiviral activity with no associated increase in cellular cytotoxicity. More importantly, the observed in vitro synergy between lopinavir and saquinavir provides a theoretical basis for the clinical exploration of a novel regimen of lopinavir-ritonavir and saquinavir.
Influence of Clarithromycin on Early Atherosclerotic Lesions after
Chlamydia pneumoniae
Infection in a Rabbit Model
Authors: Fong Ignatius W. , Chiu Brian , Viira Esther , Jang Dan , Mahony James B. 
Published: July 2002

ABSTRACT

Chlamydia pneumoniae
may play a role in atherogenesis and vascular diseases, and antibiotics may prove useful in these conditions. Three groups of New Zealand White rabbits (24 per group) were infected via the nasopharynx with
C. pneumoniae
on three separate occasions (2 weeks apart). Group I was untreated and sacrificed at 12 weeks; group II received clarithromycin at 20 mg/kg/day for 8 days, beginning 5 days after each inoculation (early treatment); and group III received a similar dose of clarithromycin starting 2 weeks after the third inoculation and continued for 6 weeks thereafter (delayed treatment). To test for a possible anti-inflammatory effect of clarithromycin, two other groups of uninfected rabbits (12 animals in each) were fed 0.5% cholesterol-enriched chow, and one of these groups was treated with clarithromycin at 30 mg/kg/day for 6 weeks. Of 23 untreated infected rabbits, 8 developed early lesions of atherosclerosis, whereas 2 of the 24 early-treated group II had similar changes (
P
= 0.036 [75% efficacy]). However, in the delayed-treatment group, group III, 3 of 24 rabbits developed early lesions of atherosclerosis, thus demonstrating 62.5% reduction compared to the untreated controls (
P
= 0.07 [trend to statistical significance]).
C. pneumoniae
antigen was detected in 8 of 23 group I (untreated) rabbits versus 1 of 24 of the early-treated (group II) rabbits and 4 of 24 animals in the delayed group III (
P
= 0.009 and 0.138, respectively). All of the untreated, cholesterol-fed rabbits had moderate to advanced atherosclerosis (grade III or IV); clarithromycin had no effect on reducing the prevalence of but did reduce the extent of atherosclerosis in the cholesterol-fed rabbits by 17% compared to untreated controls. Thus, clarithromycin administration modified
C. pneumoniae
-induced atherosclerotic lesions and reduced the ability to detect organism in tissue. Early treatment was more effective than delayed treatment.
Potent and Selective Inhibition of Human Cytomegalovirus Replication by 1263W94, a Benzimidazole
l
-Riboside with a Unique Mode of Action
Authors: Biron Karen K. , Harvey Robert J. , Chamberlain Stanley C. , Good Steven S. , Smith Albert A. , Davis Michelle G. , Talarico Christine L. , Miller Wayne H. , Ferris Robert , Dornsife Ronna E. , Stanat Sylvia C. , Drach John C. , Townsend Leroy B. , Koszalka George W. 
Published: July 2002

ABSTRACT

Benzimidazole nucleosides have been shown to be potent inhibitors of human cytomegalovirus (HCMV) replication in vitro. As part of the exploration of structure-activity relationships within this series, we synthesized the 2-isopropylamino derivative (3322W93) of 1H-β
-d-
ribofuranoside-2-bromo-5,6-dichlorobenzimidazole (BDCRB) and the biologically unnatural
l-
sugars corresponding to both compounds. One of the
l
derivatives, 1H-β
-l-
ribofuranoside-2-isopropylamino-5,6-dichlorobenzimidazole (1263W94), showed significant antiviral potency in vitro against both laboratory HCMV strains and clinical HCMV isolates, including those resistant to ganciclovir (GCV), foscarnet, and BDCRB. 1263W94 inhibited viral replication in a dose-dependent manner, with a mean 50% inhibitory concentration (IC
50
) of 0.12 ± 0.01 μM compared to a mean IC
50
for GCV of 0.53 ± 0.04 μM, as measured by a multicycle DNA hybridization assay. In a single replication cycle, 1263W94 treatment reduced viral DNA synthesis, as well as overall virus yield. HCMV mutants resistant to 1263W94 were isolated, establishing that the target of 1263W94 was a viral gene product. The resistance mutation was mapped to the UL97 open reading frame. The pUL97 protein kinase was strongly inhibited by 1263W94, with 50% inhibition occurring at 3 nM. Although HCMV DNA synthesis was inhibited by 1263W94, the inhibition was not mediated by the inhibition of viral DNA polymerase. The parent benzimidazole
d-
riboside BDCRB inhibits viral DNA maturation and processing, whereas 1263W94 does not. The mechanism of the antiviral effect of
l-
riboside 1263W94 is thus distinct from those of GCV and of BDCRB. In summary, 1263W94 inhibits viral replication by a novel mechanism that is not yet completely understood.
Assessment of Azithromycin in Combination with Other Antimalarial Drugs against
Plasmodium falciparum
In Vitro
Authors: Ohrt Colin , Willingmyre George D. , Lee Patricia , Knirsch Charles , Milhous Wilbur 
Published: July 2002

ABSTRACT

Initial field malaria prophylaxis trials with azithromycin revealed insufficient efficacy against falciparum malaria to develop azithromycin as a single agent. The objective of this in vitro study was to determine the best drug combination(s) to evaluate for future malaria treatment and prophylaxis field trials. In vitro, azithromycin was tested in combination with chloroquine against 10 representative
Plasmodium falciparum
isolates. Azithromycin was also assessed in combination with eight additional antimalarial agents against two or three multidrug-resistant
P. falciparum
isolates. Parasite susceptibility testing was carried out with a modification of the semiautomated microdilution technique. The incubation period was extended from the usual 48 h to 68 h. Fifty percent inhibitory concentrations (IC
50
s) were calculated for each drug alone and for drugs in fixed combinations of their respective IC
50
s (1:1, 3:1, 1:3, 4:1, 1:4, and 5:1). These data were used to calculate fractional inhibitory concentrations and isobolograms. Chloroquine-azithromycin studies revealed a range of activity from additive to synergistic interactions for the eight chloroquine-resistant isolates tested, while an additive response was seen for the two chloroquine-sensitive isolates. Quinine, tafenoquine, and primaquine were additive to synergistic with azithromycin, while dihydroartemisinin was additive with a trend toward antagonism. The remaining interactions appeared to be additive. These results suggest that a chloroquine-azithromycin combination should be evaluated for malaria prophylaxis and that a quinine-azithromycin combination should be evaluated for malaria treatment in areas of drug resistance.
Chemiosmotic Mechanism of Antimicrobial Activity of Ag
+
in
Vibrio cholerae
Authors: Dibrov Pavel , Dzioba Judith , Gosink Khoosheh K. , Häse Claudia C. 
Published: July 2002

ABSTRACT

Although the antimicrobial effects of silver salts were noticed long ago, the molecular mechanism of the bactericidal action of Ag
+
in low concentrations has not been elucidated. Here, we show that low concentrations of Ag
+
induce a massive proton leakage through the
Vibrio cholerae
membrane, which results in complete deenergization and, with a high degree of probability, cell death.
Efficacy of Orally Delivered Cochleates Containing Amphotericin B in a Murine Model of Aspergillosis
Authors: Delmas G. , Park S. , Chen Z. W. , Tan F. , Kashiwazaki R. , Zarif L. , Perlin D. S. 
Published: July 2002

ABSTRACT
Cochleates containing amphotericin B (CAMB) were administered orally at doses ranging from 0 to 40 mg/kg of body weight/day for 14 days in a murine model of systemic aspergillosis. The administration of oral doses of CAMB (20 and 40 mg/kg/day) resulted in a survival rate of 70% and a reduction in colony counts of more than 2 logs in lungs, livers, and kidneys. Orally administered CAMB shows promise for the treatment of aspergillosis.
Topoisomerase Mutations Associated with In Vitro Selection of Resistance to Moxifloxacin in
Streptococcus pneumoniae
Authors: Houssaye Serge , Gutmann Laurent , Varon Emmanuelle 
Published: July 2002

ABSTRACT
We analyzed the frequencies of selection, the order of acquisition, and the mutations selected on moxifloxacin in two wild-type pneumococcal strains, R6 and 5714. The first selection step showed either a single GyrA mutation or no mutation in any of the quinolone resistance-determining regions. Second-step mutants selected had either a second mutation in ParC or in ParE. Moxifloxacin could belong to these fluoroquinolones, which preferentially target GyrA though probably acting equally through both gyrase and topoisomerase IV.
Potential Repair of
Escherichia coli
DNA following Exposure to UV Radiation from Both Medium- and Low-Pressure UV Sources Used in Drinking Water Treatment
Authors: Zimmer J. L. , Slawson R. M. 
Published: July 2002

ABSTRACT

The increased use of UV radiation as a drinking water treatment technology has instigated studies of the repair potential of microorganisms following treatment. This study challenged the repair potential of an optimally grown nonpathogenic laboratory strain of
Escherichia coli
after UV radiation from low- and medium-pressure lamps. Samples were irradiated with doses of 5, 8, and 10 mJ/cm
2
from a low-pressure lamp and 3, 5, 8, and 10 mJ/cm
2
from a medium-pressure UV lamp housed in a bench-scale collimated beam apparatus. Following irradiation, samples were incubated at 37°C under photoreactivating light or in the dark. Sample aliquots were analyzed for up to 4 h following incubation using a standard plate count. Results of this study showed that
E. coli
underwent photorepair following exposure to the low-pressure UV source, but no repair was detectable following exposure to the medium-pressure UV source at the initial doses examined. Minimal repair was eventually observed upon medium-pressure UV lamp exposure when doses were lowered to 3 mJ/cm
2
. This study clearly indicates differences in repair potential under laboratory conditions between irradiation from low-pressure and medium-pressure UV sources of the type used in water treatment.
Klebsiella pneumoniae
Produces No Histamine:
Raoultella planticola
and
Raoultella ornithinolytica
Strains Are Histamine Producers
Authors: Kanki Masashi , Yoda Tomoko , Tsukamoto Teizo , Shibata Tadayoshi 
Published: July 2002

ABSTRACT

Histamine fish poisoning is caused by histamine-producing bacteria (HPB).
Klebsiella pneumoniae
and
Klebsiella oxytoca
are the best-known HPB in fish. However, 22 strains of HPB from fish first identified as
K. pneumoniae
or
K. oxytoca
by commercialized systems were later correctly identified as
Raoultella planticola
(formerly
Klebsiella planticola
) by additional tests. Similarly, five strains of
Raoultella ornithinolytica
(formerly
Klebsiella ornithinolytica
) were isolated from fish as new HPB.
R. planticola
and
R. ornithinolytica
strains were equal in their histamine-producing capabilities and were determined to possess the
hdc
genes, encoding histidine decarboxylase. On the other hand, a collection of 61 strains of
K. pneumoniae
and 18 strains of
K. oxytoca
produced no histamine.
Large Fraction of Dead and Inactive Bacteria in Coastal Marine Sediments: Comparison of Protocols for Determination and Ecological Significance
Authors: Luna G. M. , Manini E. , Danovaro R. 
Published: July 2002

ABSTRACT

It is now universally recognized that only a portion of aquatic bacteria is actively growing, but quantitative information on the fraction of living versus dormant or dead bacteria in marine sediments is completely lacking. We compared different protocols for the determination of the dead, dormant, and active bacterial fractions in two different marine sediments and at different depths into the sediment core. Bacterial counts ranged between (1.5 ± 0.2) × 10
8
cells g
−1
and (53.1 ± 16.0) × 10
8
cells g
−1
in sandy and muddy sediments, respectively. Bacteria displaying intact membrane (live bacterial cells) accounted for 26 to 30% of total bacterial counts, while dead cells represented the most abundant fraction (70 to 74%). Among living bacterial cells, nucleoid-containing cells represented only 4% of total bacterial counts, indicating that only a very limited fraction of bacterial assemblage was actively growing. Nucleoid-containing cells increased with increasing sediment organic content. The number of bacteria responsive to antibiotic treatment (direct viable count; range, 0.3 to 4.8% of the total bacterial number) was significantly lower than nucleoid-containing cell counts. An experiment of nutrient enrichment to stimulate a response of the dormant bacterial fraction determined a significant increase of nucleoid-containing cells. After nutrient enrichment, a large fraction of dormant bacteria (6 to 11% of the total bacterial number) was “reactivated.” Bacterial turnover rates estimated ranged from 0.01 to 0.1 day
−1
but were 50 to 80 times higher when only the fraction of active bacteria was considered (on average 3.2 day
−1
). Our results suggest that the fraction of active bacteria in marine sediments is controlled by nutrient supply and availability and that their turnover rates are at least 1 order of magnitude higher than previously reported.