bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced Activity of Antioxidant Machinery Is Correlated with Suppression of Totipotency in Plant Protoplasts
Authors: Papadakis Anastasia K. , Siminis Charalambos I. , Roubelakis-Angelakis Kalliopi A. 
Published: July 2002

Abstract
We previously showed that during protoplast isolation, an oxidative burst occurred and the generation of active oxygen species was differentially mediated in tobacco (Nicotiana tabacum) and grapevine (Vitis vinifera), accompanied by significant quantitative differences (A.K. Papadakis, K.A. Roubelakis-Angelakis [1999] Plant Physiol 127: 197–205). We have now further tested if the expression of totipotency in protoplasts is related to the activity of cellular antioxidant machinery during protoplast culture. Totipotent (T) tobacco protoplasts had 2-fold lower contents of intracellular O2 .− and H2O2 and 7-fold lower levels of O2 .− and H2O2 in the culture medium, compared with non-totipotent (NT) tobacco protoplasts. Addition of alkaline dimethylsulfoxide, known to generate O2 .−, resulted in isolation of tobacco protoplasts with reduced viability and cell division potential during subsequent culture. Active oxygen species levels decreased in tobacco and grapevine protoplasts during culturing, although higher contents of O2 .− and H2O2 were still found in NT- compared with T-tobacco protoplasts, after 8 d in culture. In T-tobacco protoplasts, the reduced forms of ascorbate and glutathione predominated, whereas in NT-tobacco and grapevine protoplasts, the oxidized forms predominated. In addition, T-tobacco protoplasts exhibited severalfold lower lipid peroxidation than NT-tobacco and grapevine protoplasts. Furthermore, several antioxidant enzyme activities were increased in T-tobacco protoplasts. Superoxide dismutase activity increased in tobacco, but not in grapevine protoplasts during culturing due to the increased expression of cytoplasmic Cu/Zn-superoxide dismutase. The increase was only sustained in T-tobacco protoplasts for d 8. Together, these results suggest that suppressed expression of totipotency in protoplasts is correlated with reduced activity of the cellular antioxidant machinery.
Flavonoids Act as Negative Regulators of Auxin Transport in Vivo in Arabidopsis
Authors: Brown Dana E. , Rashotte Aaron M. , Murphy Angus S. , Normanly Jennifer , Tague Brian W. , Peer Wendy A. , Taiz Lincoln , Muday Gloria K. 
Published: July 2002

Abstract
Polar transport of the plant hormone auxin controls many aspects of plant growth and development. A number of synthetic compounds have been shown to block the process of auxin transport by inhibition of the auxin efflux carrier complex. These synthetic auxin transport inhibitors may act by mimicking endogenous molecules. Flavonoids, a class of secondary plant metabolic compounds, have been suggested to be auxin transport inhibitors based on their in vitro activity. The hypothesis that flavonoids regulate auxin transport in vivo was tested in Arabidopsis by comparing wild-type (WT) and transparent testa (tt4) plants with a mutation in the gene encoding the first enzyme in flavonoid biosynthesis, chalcone synthase. In a comparison between tt4 and WT plants, phenotypic differences were observed, including three times as many secondary inflorescence stems, reduced plant height, decreased stem diameter, and increased secondary root development. Growth of WT Arabidopsis plants on naringenin, a biosynthetic precursor to those flavonoids with auxin transport inhibitor activity in vitro, leads to a reduction in root growth and gravitropism, similar to the effects of synthetic auxin transport inhibitors. Analyses of auxin transport in the inflorescence and hypocotyl of independent tt4 alleles indicate that auxin transport is elevated in plants with a tt4mutation. In hypocotyls of tt4, this elevated transport is reversed when flavonoids are synthesized by growth of plants on the flavonoid precursor, naringenin. These results are consistent with a role for flavonoids as endogenous regulators of auxin transport.
Biochemical and Crystallographic Characterization of Homologous Non-peptidic Thrombin Inhibitors Having Alternate Binding Modes
Authors: Strickland Corey L. , Fevig John. M. , Galemmo Robert A. , Wells Brian L. , Kettner Charles A. , Weber Patricia C. 
Published: July 2002

The X-ray crystallographic structure of [N-(3-phenylpropionyl)-N-(phenethyl)]-Gly-boroLys-OH (HPBK, Ki
= 0.42 nM, crystallographic R factor to 1.8 Å resolution, 19.6%) complexed with human α-thrombin shows that the boron adopts a tetrahedral geometry and is covalently bonded to the active serine, Ser195. The HPBK phenethyl aromatic ring forms an edge-to-face interaction with the indole side chain of Trp215. Four HPBK analogs containing either electron-withdrawing or electron-donating substitutents at the 3′ position of the phenethyl ring were synthesized in an attempt to modulate ligand affinity by inductive stabilization of the edge-to-face interaction. Refined crystallographic structures of the trifluoromethyl (Ki
= 0.37 nM, crystallographic R factor to 2.0 Å resolution = 18.7%), fluoro (Ki
= 0.60; R factor to 2.3 Å resolution = 18.4%), methoxy (Ki
= 0.91 nM, R factor to 2.2 Å resolution = 19.8%) and methyl (Ki
= 0.20 nM, R factor to 2.5 Å resolution = 16.9%) HPBK analogs complexed with thrombin revealed two binding modes for the closely related com-pounds. A less than 1.5-fold variation in affinity was observed for analogs (trifluoromethyl-HPBK and fluoro-HPBK) binding with the edge-to-face interaction. The slight inductive modulation is consistent with the overall weak nature of the edge-to-face interaction. Owing to an unexpected rotation of the phenethyl aromatic ring, the 3′ substituent of two analogs, methoxy-HPBK and methyl-HPBK, made direct contact with the Trp215 indole side chain. Increased affinity of the 3′ methyl analog is attributed to favorable interactions between the methyl group and the Trp215 indole ring. Differences in inhibitor, thrombin and solvent structure are discussed in detail. These results demonstrate the subtle interplay of weak forces that determine the equilibrium binding orientation of inhibitor, solvent and protein.
Overproduction, purification, crystallization and preliminary X-ray diffraction studies of the human spliceosomal protein U5-15kD
Authors: Reuter Klaus , Ficner Ralf 
Published: July 2002

The gene coding for the human spliceosomal U5 snRNP-specific 15 kDa protein (U5-15kD) was overexpressed in Escherichia coli, its product purified to homogeneity and crystallized. Well diffracting single crystals were obtained by the vapour-diffusion method in hanging drops and subsequent macroseeding. The crystals belong to the orthorhombic space group P21212 with a = 62.3, b = 65.7, c = 37.1 Å. They diffract to at least 3.0 Å and contain one molecule in the asymmetric unit. A selenomethionine derivative of the protein was prepared and crystallized for multiwavelength anomalous diffraction (MAD) data collection.
The CXXC motif: crystal structure of an active-site variant of Escherichia coli thioredoxin
Authors: Schultz L. Wayne , Chivers Peter T. , Raines Ronald T. 
Published: July 2002

The 2.2 Å crystalline structure of an oxidized active-site variant of Escherichia coli thioredoxin (Trx) has been solved. Trx is a 12 kDa enzyme which catalyzes the oxidation of dithiols and the reduction and isomerization of disulfides in other proteins. Its active site contains the common structural motif CXXC. Protein-disulfide isomerase (PDI), a 57 kDa homolog of Trx, contains four Trx-like domains. The three-dimensional structure of PDI is unknown. PDI-deficient Saccharomyces cerevisiae are inviable. An active-site variant of Trx which complements PDI-deficient yeast has the active-site sequence Cys32-Val33-Trp34-Cys35 (CVWC). The reduction potential of oxidized CVWC Trx (E°′ = −0.230 V) is altered significantly from that of the wild-type enzyme (E°′ = −0.270 V). However, the structure of the oxidized CVWC enzyme is almost identical to that of wild-type Trx. The addition of valine and tryptophan in the active site is likely to increase the reduction potential, largely by decreasing the pKa
of the Cys32 thiol in the reduced enzyme. Unlike in wild-type Trx, significant protein–protein contacts occur in the crystal. Protein molecules related by a crystallographic twofold axis form a dimer in the crystal. The dimer forms as an extension of the twisted mixed β-sheet which composes the backbone of each Trx structure.
Crystallization and preliminary X-ray analyses of catabolite control protein A, free and in complex with its DNA-binding site
Authors: Tebbe Jan , Orth Peter , Küster-Schöck Elke , Hillen Wolfgang , Saenger Wolfram , Hinrichs Winfried 
Published: July 2002

The catabolite control protein (CcpA) from Bacillus megaterium is a member of the bacterial repressor protein family GalR/LacI. CcpA with an N-terminal His-tag was used for crystallization. Crystals of free CcpA and of CcpA in complex with the putative operator sequence (catabolite responsive elements, CRE) were obtained by vapour-diffusion techniques at 291 K using the hanging-drop method. CcpA crystals grown in the presence of polyethylene glycol 8000 belong to the hexagonal space group P6122 or P6522, with unit-cell parameters a = 74.4, c = 238.8 Å. These crystals diffract X-rays to 2.55 Å resolution and contain one monomer of the homodimeric protein per asymmetric unit. Crystals of the CcpA–CRE complex were obtained with ammonium sulfate as precipitant and belong to the tetragonal space group I4122, with unit-cell parameters a = 125, c = 400 Å and one complex per asymmetric unit. Although these co-crystals grew to a sufficient size, X-ray diffraction was limited to 8 Å resolution.
Stability and interactions of the amino‐terminal domain of ClpB from Escherichia coli
Authors: Tek Vekalet , Zolkiewski Michal 
Published: July 2002

AbstractClpB is a member of a multichaperone system in Escherichia coli (with DnaK, DnaJ, and GrpE) that reactivates aggregated proteins. The sequence of ClpB contains two ATP‐binding regions that are enclosed between the N‐ and C‐terminal extensions. Whereas it has been found that the N‐terminal region of ClpB is essential for the chaperone activity, the structure of this region is not known, and its biochemical properties have not been studied. We expressed and purified the N‐terminal fragment of ClpB (residues 1–147). Circular dichroism of the isolated N‐terminal region showed a high content of α‐helical structure. Differential scanning calorimetry showed that the N‐terminal region of ClpB is thermodynamically stable and contains a single folding domain. The N‐terminal domain is monomeric, as determined by gel‐filtration chromatography, and the elution profile of the N‐terminal domain does not change in the presence of the N‐terminally truncated ClpB (ClpBΔN). This indicates that the N‐terminal domain does not form strong contacts with ClpBΔN. Consistently, addition of the separated N‐terminal domain does not reverse an inhibition of ATPase activity of ClpBΔN in the presence of casein. As shown by ELISA measurements, full‐length ClpB and ClpBΔN bind protein substrates (casein, inactivated luciferase) with similar affinity. We also found that the isolated N‐terminal domain of ClpB interacts with heat‐inactivated luciferase. Taken together, our results indicate that the N‐terminal fragment of ClpB forms a distinct domain that is not strongly associated with the ClpB core and is not required for ClpB interactions with other proteins, but may be involved in recognition of protein substrates.
Predicting Local Cell Deformations in Engineered Tissue Constructs: A Multilevel Finite Element Approach
Authors: Breuls Roel G. M. , Sengers Bram G. , Oomens Cees W. J. , Bouten Carlijn V. C. , Baaijens Frank P. T. 
Published: July 2002

AbstractA multilevel finite element approach is applied to predict local cell deformations in engineered tissue constructs. Cell deformations are predicted from detailed nonlinear FE analysis of the microstructure, consisting of an arrangement of cells embedded in matrix material. Effective macroscopic tissue behavior is derived by a computational homogenization procedure. To illustrate this approach, we simulated the compression of a skeletal muscle tissue construct and studied the influence of microstructural heterogeneity on local cell deformations. Results show that heterogeneity has a profound impact on local cell deformations, which highly exceed macroscopic deformations. Moreover, microstructural heterogeneity and the presence of neighboring cells leads to complex cell shapes and causes non-uniform deformations within a cell.
Fluconazole plus Cyclosporine: a Fungicidal Combination Effective against Experimental Endocarditis Due to
Candida albicans
Authors: Marchetti O. , Entenza J. M. , Sanglard D. , Bille J. , Glauser M. P. , Moreillon P. 
Published: July 2002

ABSTRACT

Recent observations demonstrated that fluconazole plus cyclosporine (Cy) synergistically killed
Candida albicans
in vitro. This combination was tested in rats with
C. albicans
experimental endocarditis. The MICs of fluconazole and Cy for the test organism were 0.25 and >10 mg/liter, respectively. Rats were treated for 5 days with either Cy, amphotericin B, fluconazole, or fluconazole-Cy. Although used at high doses, the peak concentrations of fluconazole in the serum of rats (up to 4.5 mg/liter) were compatible with high-dose fluconazole therapy in humans. On the other hand, Cy concentrations in serum (up to 4.5 mg/liter) were greater than recommended therapeutic levels. Untreated rats demonstrated massive pseudohyphal growth in both the vegetations and the kidneys. However, only the kidneys displayed concomitant polymorphonuclear infiltration. The therapeutic results reflected this dissociation. In the vegetations, only the fungicidal fluconazole-Cy combination significantly decreased fungal densities compared to all groups, including amphotericin B (
P
< 0.0001). In the kidneys, all regimens except the Cy regimen were effective, but fluconazole-Cy remained superior to amphotericin B and fluconazole alone in sterilizing the organs (
P
< 0.0001). While the mechanism responsible for the fluconazole-Cy interaction is hypothetical, this observation opens new perspectives for fungicidal combinations between azoles and other drugs.
Delavirdine in Combination with Zidovudine in Treatment of Human Immunodeficiency Virus Type 1-Infected Patients: Evaluation of Efficacy and Emergence of Viral Resistance in a Randomized, Comparative Phase III Trial
Authors: Joly Véronique , Moroni Mauro , Concia Ercole , Lazzarin Adriano , Hirschel Bernard , Jost Josef , Chiodo Francesco , Bentwich Zvi , Love W. Campbell , Hawkins David A. , Wilkins Edmund G. L. , Gatell Aritigas J. , Vetter Norbert , Greenwald Cynthia , Freimuth William W. , de Cian Wanda ,   The M/3331/0013B Study Group
Published: July 2002

ABSTRACT

We compared the activity of delavirdine (DLV) plus zidovudine (AZT) (
n
= 300) with that of AZT (
n
= 297) against human immunodeficiency virus type 1 in a randomized, double-blind, placebo-controlled trial. DLV exerted a transient antiviral effect, and mutations for resistance to DLV were found in more than 90% of subjects at week 12. The K103N mutation, which confers nonnucleoside reverse transcriptase inhibitor cross-resistance, was found in 85% of the patients.
Antibiotic Resistance Trends in Enteropathogenic Bacteria Isolated in 1985–1987 and 1995–1998 in Barcelona
Authors: Prats Guillermo , Mirelis Beatriz , Llovet Teresa , Muñoz Carmen , Miró Elisenda , Navarro Ferran 
Published: July 2002

ABSTRACT

Trends in resistance to antimicrobial agents used for therapy have been evaluated with 3,797 enteropathogenic bacteria,
Campylobacter
,
Salmonella
,
Shigella
, and
Yersinia
, between 1985–1987 and 1995–1998. The greater increase in the rate of resistance was observed in
Campylobacter jejuni
for quinolones (from 1 to 82%) and tetracycline (from 23 to 72%) and in gastroenteric salmonellae for ampicillin (from 8 to 44%), chloramphenicol (from 1.7 to 26%), and trimethoprim-sulfamethoxazole and nalidixic acid (from less than 0.5 to 11%). Multidrug resistance was detected in several
Salmonella
serotypes. In the 1995–1998 period, 76% of
Shigella
strains were resistant to trimethoprim-sulfamethoxazole, 43% were resistant to ampicillin, and 39% were resistant to chloramphenicol. Seventy-two percent of
Yersinia enterocolitica
O3 strains were resistant to streptomycin, 45% were resistant to sulfonamides, 28% were resistant to trimethoprim-sulfamethoxazole, and 20% were resistant to chloramphenicol.
Activities of BMS 284756 (T-3811) against
Haemophilus influenzae
,
Moraxella catarrhalis
, and
Streptococcus pneumoniae
Isolates from SENTRY Antimicrobial Surveillance Program Medical Centers in Latin America (1999)
Authors:   SENTRY Participants Group (Latin America), Gales Ana , Sader Helio , Jones Ronald N. 
Published: July 2002

ABSTRACT

The antimicrobial activity of BMS 284756, a novel des-F(6)-quinolone, was comparatively evaluated against 257
Streptococcus pneumoniae
, 198
Haemophilus influenzae
, and 88
Moraxella catarrhalis
strains isolated in Latin America between July and September of 1999 as part of the SENTRY Antimicrobial Surveillance Program. Nearly 28.0% of
S. pneumoniae
strains were nonsusceptible to penicillin. The rank order of quinolone potency versus
S. pneumoniae
was BMS 284756 (MIC at which 90% of isolates were inhibited [MIC
90
], 0.12 μg/ml) > trovafloxacin (MIC
90
, 0.25 μg/ml) > gatifloxacin (MIC
90
, 0.5 μg/ml) > levofloxacin and ciprofloxacin (MIC
90
, 1 to 2 μg/ml). All
S. pneumoniae
strains that were not susceptible to other quinolones were inhibited by BMS 284756 at ≤2 μg/ml. The overall prevalence of β-lactamase production was 15.2% in
H. influenzae
and 98.9% in
M. catarrhalis.
BMS 284756 showed excellent potency and spectrum against this group of pathogens, inhibiting all isolates at ≤0.12 μg/ml. BMS 284756 exhibited activity similar to those displayed by the new fluoroquinolones, such as levofloxacin, trovafloxacin, or gatifloxacin, and could be a therapeutic option for empirical treatment of community-acquired respiratory tract infections.
Amprenavir Inhibitory Quotient and Virological Response in Human Immunodeficiency Virus-Infected Patients on an Amprenavir-Containing Salvage Regimen without or with Ritonavir
Authors: Duval Xavier , Lamotte Claire , Race Ester , Descamps Diane , Damond Florence , Clavel François , Leport Catherine , Peytavin Gilles , Vilde Jean-Louis 
Published: July 2002

ABSTRACT
The efficacy of an amprenavir (APV)-containing therapy without (group A) or with (group B) ritonavir was assessed in patients with failure of previous protease inhibitor therapy for human immunodeficiency virus (HIV) infection. The mean minimal plasma APV concentrations in groups A and B were 58 and 1,320 ng/ml, respectively, corresponding to APV inhibitory quotients of 0.2 (range, 0.03 to 0.70) and 7.0 (range, 1.4 to 145), respectively. At week 24, 2 of 8 and 13 of 14 patients in groups A and B, respectively, had <200 HIV RNA copies/ml of plasma, including 4 of 5 patients infected with APV-resistant viruses.
Distribution of Azithromycin in Plasma and Tonsil Tissue after Repeated Oral Administration of 10 or 20 Milligrams per Kilogram in Pediatric Patients
Authors: Blandizzi Corrado , Malizia Tecla , Batoni Giovanna , Ghelardi Emilia , Baschiera Fabio , Bruschini Paolo , Senesi Sonia , Campa Mario , Del Tacca Mario 
Published: July 2002

ABSTRACT
Azithromycin concentrations in the tonsils of 56 pediatric patients, treated with 10 or 20 mg of the drug per kg of body weight for 3 days, were compared. Azithromycin levels in plasma and tonsil samples were determined up to 8.5 days after the last dose. The 20-mg/kg regimen resulted in an improved tonsillar distribution of azithromycin, suggesting the achievement of enhanced therapeutic concentrations at infective sites of the upper respiratory tract.
Bacterial Community Structure Associated with a Dimethylsulfoniopropionate-Producing North Atlantic Algal Bloom
Authors: González José M. , Simó Rafel , Massana Ramon , Covert Joseph S. , Casamayor Emilio O. , Pedrós-Alió Carlos , Moran Mary Ann 
Published: July 2002

ABSTRACT

The bacteria associated with oceanic algal blooms are acknowledged to play important roles in carbon, nitrogen, and sulfur cycling, yet little information is available on their identities or phylogenetic affiliations. Three culture-independent methods were used to characterize bacteria from a dimethylsulfoniopropionate (DMSP)-producing algal bloom in the North Atlantic. Group-specific 16S rRNA-targeted oligonucleotides, 16S ribosomal DNA (rDNA) clone libraries, and terminal restriction fragment length polymorphism analysis all indicated that the marine
Roseobacter
lineage was numerically important in the heterotrophic bacterial community, averaging >20% of the 16S rDNA sampled. Two other groups of heterotrophic bacteria, the SAR86 and SAR11 clades, were also shown by the three 16S rRNA-based methods to be abundant in the bloom community. In surface waters, the
Roseobacter
, SAR86, and SAR11 lineages together accounted for over 50% of the bacterial rDNA and showed little spatial variability in abundance despite variations in the dominant algal species. Depth profiles indicated that
Roseobacter
phylotype abundance decreased with depth and was positively correlated with chlorophyll
a
, DMSP, and total organic sulfur (dimethyl sulfide plus DMSP plus dimethyl sulfoxide) concentrations. Based on these data and previous physiological studies of cultured
Roseobacter
strains, we hypothesize that this lineage plays a role in cycling organic sulfur compounds produced within the bloom. Three other abundant bacterial phylotypes (representing a cyanobacterium and two members of the α
Proteobacteria
) were primarily associated with chlorophyll-rich surface waters of the bloom (0 to 50 m), while two others (representing
Cytophagales
and δ
Proteobacteria
) were primarily found in deeper waters (200 to 500 m).