bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does Growth Correlate with Turgor-Induced Elastic Strain in Stems? A Re-Evaluation of de Vries' Classical Experiments
Authors: Peters Winfried S. , Farm Maggie S. , Kopf A. Jim 
Published: July 2002

AbstractThe correlation between growth and turgor-induced elastic expansion was studied in hypocotyls of sunflower (Helianthus annuus) seedlings under various growth conditions. Turgor-induced elastic cell wall strain was greater in hypocotyls of faster growing seedlings, i.e. in etiolated versus light-grown ones. It also was higher in rapidly growing young seedlings as compared with nongrowing mature ones. However, analysis of the spatial distribution of elastic strain and growth demonstrated that their correspondence was only apparent. Profiles of elastic strain declined steadily from the top of the hypocotyls toward the basis, whereas the profiles of relative elemental growth rate along the hypocotyls showed maxima within the growing zones. In contrast to earlier hypotheses, we conclude that turgor-induced elastic cell wall strain and growth do not correlate precisely in growing hypocotyls.
Product‐conformation‐driven ligation of peptides by V8 protease
Authors: Srinivasulu Sonati , Acharya A. Seetharama 
Published: July 2002

AbstractOrganic co‐solvent‐induced secondary conformation of α17–40 of human hemoglobin facilitates the splicing of E30‐R31 in a mixture of its complementary segments by V8 protease. The amino acid sequence of α17–40 has been conceptualized by the general structure FRI‐EALER‐FRII and the pentapeptide sequence EALER playing a major role in inducing the α‐helical conformation. The primary structure of α17–40 has been engineered in multiple ways to perturb one, two, or all three regions and the influence of the organic co‐solvent‐induced conformation and the concomitant resistance of E30‐R31 peptide bond to V8 protease digestion has been investigated. The central pentapeptide (EALER), referred to here as splicedon,3Splicedon is a pentapeptide sequence (EALER) sandwiched between the two peptides with intrinsic α‐helical potential and provides the resistance to the spliced peptide bond E‐R by V8 protease once it is integrated as a contiguous segment and the peptide folds into an α‐helical conformation.
appears to dictate a primary role in facilitating the splicing reaction. When the same flanking regions are used, (1) splicedons that carry amino acid residues of low α‐helical potential, for example G at position 2 or 3 of the splicedon, generate a conformational trap of very low thermodynamic stability, giving an equilibrium yield of only 3%–5%; (2) splicedons with amino acid residues of good α‐helical potential generate a conformational trap of medium thermodynamic stability and give an equilibrium yield of 20%–25%; (3) the splicedons with amino residues of good α‐helical potential and also an amino acid that can generate an i, i + 4 side‐chain carboxylate‐guanidino (amino) interaction, a conformational trap of maximum thermodynamic stability is generated, giving an equilibrium yield of 45%–50%; and (4) the thermodynamic stability of the conformational trap of the spliced peptide is also influenced by the amino acid composition of the flanking regions. The V8 protease resistance of the spliced peptide bond is not a direct correlate of the amount of α‐helical conformation induced into the product. The results of this study reflect the unique role of the splicedon in translating the organic co‐solvent‐induced product conformation as a site‐specific stabilization of the spliced peptide bond. It is speculated that the splicedon with higher α‐helical potential as compared to either one of the flanking regions achieves this by integrating its potential with that of the flanking region(s). Exchange of flanking regions with the products of other V8 protease–catalyzed splicing reactions will help to establish the general primary structural requirements of this class of splicing reactions and facilitate their application in modular construction of proteins.
Protein–protein docking with multiple residue conformations and residue substitutions
Authors: Lorber David M. , Udo Maria K. , Shoichet Brian K. 
Published: July 2002

AbstractThe protein docking problem has two major aspects: sampling conformations and orientations, and scoring them for fit. To investigate the extent to which the protein docking problem may be attributed to the sampling of ligand side‐chain conformations, multiple conformations of multiple residues were calculated for the uncomplexed (unbound) structures of protein ligands. These ligand conformations were docked into both the complexed (bound) and unbound conformations of the cognate receptors, and their energies were evaluated using an atomistic potential function. The following questions were considered: (1) does the ensemble of precalculated ligand conformations contain a structure similar to the bound form of the ligand? (2) Can the large number of conformations that are calculated be efficiently docked into the receptors? (3) Can near‐native complexes be distinguished from non‐native complexes? Results from seven test systems suggest that the precalculated ensembles do include side‐chain conformations similar to those adopted in the experimental complexes. By assuming additivity among the side chains, the ensemble can be docked in less than 12 h on a desktop computer. These multiconformer dockings produce near‐native complexes and also non‐native complexes. When docked against the bound conformations of the receptors, the near‐native complexes of the unbound ligand were always distinguishable from the non‐native complexes. When docked against the unbound conformations of the receptors, the near‐native dockings could usually, but not always, be distinguished from the non‐native complexes. In every case, docking the unbound ligands with flexible side chains led to better energies and a better distinction between near‐native and non‐native fits. An extension of this algorithm allowed for docking multiple residue substitutions (mutants) in addition to multiple conformations. The rankings of the docked mutant proteins correlated with experimental binding affinities. These results suggest that sampling multiple residue conformations and residue substitutions of the unbound ligand contributes to, but does not fully provide, a solution to the protein docking problem. Conformational sampling allows a classical atomistic scoring function to be used; such a function may contribute to better selectivity between near‐native and non‐native complexes. Allowing for receptor flexibility may further extend these results.
Heat Transfer in a Two-Pass Rectangular Rotating Channel With 45-deg
Angled Rib Turbulators
Authors: Azad Gm S. , Uddin Mohammad J. , Han Je-Chin , Moon Hee-Koo , Glezer Boris 
Published: July 2002

Abstract
Experimental heat transfer results are presented in a two-pass rectangular channel (aspect ratio=2:1) with smooth and ribbed surfaces for two channel orientations (90 and 135 deg to the direction of rotational plane). The rib turbulators are placed on the leading and trailing sides at an angle 45 deg to the main stream flow. Both 45-deg parallel and cross rib orientations are studied. The results are presented for stationary and rotating cases at three different Reynolds numbers of 5000, 10,000, and 25,000, the corresponding rotation numbers are 0.21, 0.11, and 0.04. The rib height to hydraulic diameter ratio (e/D) is 0.094; the rib pitch-to-height ratio (P/e) is 10 and the inlet wall-to-coolant density ratio (Δρ/ρ) is maintained at 0.115 for all surfaces in the channel. Results show that the rotating ribbed wall heat transfer coefficients increase by a factor of 2 to 3 over the rotating smooth wall results. The heat transfer from the first pass trailing and second pass leading surfaces are enhanced by rotation. However, the first pass leading and the second pass trailing sides show a decrease in heat transfer with rotation. The result show that 45-deg parallel ribs produce a better heat transfer augmentation than 45-deg cross ribs, and a 90-deg channel orientation produces higher heat transfer effect over a 135-deg orientation.
Rayleigh Light Scattering Measurements of Transient Gas Temperature
in a Rapid Chemical Vapor Deposition Reactor
Authors: Horton J. F. , Peterson J. E. 
Published: July 2002

Abstract
A laser-induced Rayleigh light scattering (RLS) system was used to measure transient gas temperatures in a simulated rapid chemical vapor deposition (RCVD) reactor. The test section geometry was an axisymmetric jet of carrier gas directed down, impinging on a heated wafer surface. RLS was used to measure instantaneous gas temperature at several locations above the wafer as it was heated from room temperature to 475 K. Gas flow rate and wafer temperature correspond to jet Reynolds number Rei=60, wafer maximum Grashof number GrH=4.4×106, and maximum mixed convection parameter GrH/Rei2=1200; all conditions typical of impinging jet reactors common in the numerical literature. Uncertainty of RLS transient temperature from a propagated error analysis was ±2–4 K. Peak gas temperature fluctuations were large (in the order of 25 to 75 °C). Both flow visualization and RLS measurements showed that the flow field was momentum dominated prior to heating initiation, but became unstable by GrH/Rei2=5. It then consisted of buoyancy-induced plumes and recirculations. Up to the peak wafer temperature, the flow field continued to be highly three-dimensional, unsteady, and dominated by buoyancy. RLS measurements are shown to provide information on carrier gas instantaneous temperature and flow field stability, both critical issues in RCVD processing. [S0022-1481(00)02401-4]
Molecular-beam epitaxy growth of In0.53 (GaxAl1−x)0.47 As quaternary layers for optointegrated devices
Authors: Genova F. , Morello G. , Rigo C. 
Published: July 2002

High quality In0.53(GaxAl1−x) 0.47 As lattice-matched to InP was obtained by molecular-beam epitaxy (MBE). Most of the work was performed at x = 0.64 because this composition is suitable for low loss waveguiding at 1.55 μm. Device quality material wa obtained showing defect densities as low as 2⋅103 cm−2 and 4 K photoluminescence full width at half-maximum (FWHM) of 23 meV, which represents the state of the art of this material. Double crystal (DC) x-ray profiles showed a FWHM of 17.5′′ of arc, demonstrating the lattice perfection of the material. From low temperature photoluminesence measurements, we evaluated the optimum temperature range for MBE growth.
Ridge waveguides fabricated from these layers showed low loss waveguiding, as low as 2.2 db/cm, at 1.55 μm. The excellent of the grown materials is also confirmed by the narrowest DC x-ray profile linewidth ever reported for one of the ternary limits InGaAs (x = 1), which showed a FWHM of 12′′ of arc. The materials obtained are thus suitable for high performance waveguide optointegrated devices.
Selection and Characterization of Human Immunodeficiency Virus Type 1 Variants Resistant to the (+) and (−) Enantiomers of 2′-Deoxy-3′-Oxa-4′-Thio-5-Fluorocytidine
Authors: Richard Nathalie , Salomon Horacio , Rando Robert , Mansour Tarek , Bowlin Terry L. , Wainberg Mark A. 
Published: July 2002

ABSTRACTHuman immunodeficiency virus (HIV) type 1 (HIV-1) variants were selected for resistance to the (+) and (−) enantiomers of a novel nucleoside analogue, 2′-deoxy-3′-oxa-4′-thio-5-fluorocytidine (dOTFC), by use of the infectious molecular clone HIV HXB2D and the human T-cell line MT-4. The dOTFC-resistant variants that were selected were 10-fold less sensitive than wild-type virus, and cloning and sequencing of the complete reverse transcriptase (RT)-coding region identified the mutation M184V. Studies with mutated recombinant HXB2D virus confirmed the importance of the M184V mutation in conferring resistance to (−)dOTFC in MT-4 cells, although no difference in sensitivity was observed in primary cells. The M184V substitution also displayed decreased susceptibility to (+)dOTFC. Selection with (+)dOTFC also produced variants which were 10-fold more resistant than the wild type, and a novel mutation, D67G, was identified following cloning and sequencing of the RT genes. The D67G mutation was introduced into HXB2D by site-directed mutagenesis, and the data obtained confirmed the importance of this mutation in conferring resistance to both (+)dOTFC and (−)dOTFC. Mutated recombinant molecular clone HXB2D-D67G was further selected with (+)dOTFC, and three of six clones sequenced contained both the D67G and M184V mutations, while the other three of the six clones contained only the D67G mutation. Clinical isolates of HIV-1 which are (−) 2′-deoxy-3′-thiacytidine-resistant also displayed resistance to both (+)dOTFC and (−)dOTFC.
Inhibitors of Sterol Biosynthesis and Amphotericin B Reduce the Viability of
Pneumocystis carinii
f. sp.
carinii
Authors: Kaneshiro Edna S. , Collins Margaret S. , Cushion Melanie T. 
Published: July 2002

ABSTRACT

Pneumocystis carinii
synthesizes sterols with a double bond at C-7 of the sterol nucleus and an alkyl group with one or two carbons at C-24 of the side chain. Also, some human-derived
Pneumocystis carinii
f. sp.
hominis
strains contain lanosterol derivatives with an alkyl group at C-24. These unique sterols have not been found in other pathogens of mammalian lungs. Thus,
P. carinii
may have important differences in its susceptibility to drugs known to block reactions in ergosterol biosynthesis in other fungi. In the present study, inhibitors of 3-hydroxy-3-methyglutaryl coenzyme A reductase, squalene synthase, squalene epoxidase, squalene epoxide-lanosterol cyclase, lanosterol demethylase, Δ
8
to Δ
7
isomerase, and
S
-adenosylmethionine:sterol methyltransferase were tested for their effects on
P. carinii
viability as determined by quantitation of cellular ATP levels in a population of organisms. Compounds within each category varied in inhibitory effect; the most effective included drugs targeted at squalene synthase, squalene epoxide-lanosterol cyclase, and Δ
8
to Δ
7
isomerase. Some drugs that are potent against ergosterol-synthesizing fungi had little effect against
P. carinii
, suggesting that substrates and/or enzymes in
P. carinii
sterol biosynthetic reactions are distinct. Amphotericin B is ineffective in clearing
P. carinii
infections at clinical doses; however, this drug apparently binds to sterols and causes permeability changes in
P. carinii
membranes, since it reduced cellular ATP levels in a dose-dependent fashion.
Efficacy of FK463, a (1,3)-β-
d
-Glucan Synthase Inhibitor, in Disseminated Azole-Resistant
Candida albicans
Infection in Mice
Authors: Maesaki Shigefumi , Hossain Mohammad Ashraf , Miyazaki Yoshitsugu , Tomono Kazunori , Tashiro Takayoshi , Kohno Shigeru 
Published: July 2002

ABSTRACT

The efficacy of FK463, a new (1,3)-β-
d
-glucan synthase inhibitor, against azole-resistant
Candida albicans
strains has been studied. The MIC of FK463 was lower than those of azoles and amphotericin B against
CDR1
-expressing C26 and
CaMDR
-expressing C40 strains. All mice treated with FK463 (1 mg/kg) survived disseminated murine candidiasis. The fungal burden in the kidney after 6 days was markedly reduced after therapy with FK463 and amphotericin B sodium deoxycholate, and plasma (1,3)-β-
d
-glucan concentration was found to be lower in FK463-treated mice. In our study, FK463 was found to be a potent antifungal agent against disseminated infection with azole-resistant
C. albicans
.
In Vitro Activities of Terbinafine against
Aspergillus
Species in Comparison with Those of Itraconazole and Amphotericin B
Authors: Moore Caroline B. , Walls Caroline M. , Denning David W. 
Published: July 2002

ABSTRACT

Compared with the in vitro activities of itraconazole (geometric mean MIC [GM], 0.56 μg/ml) and amphotericin B (GM, 0.66 μg/ml), the in vitro activity of terbinafine was inferior against
Aspergillus fumigatus
(GM, 19.03 μg/ml) (
P
< 0.05) and superior against
A. flavus
(GM, 0.10 μg/ml),
A. terreus
(GM, 0.16 μg/ml), and
A. niger
(GM, 0.19 μg/ml). Clinical correlation is required, as trailing endpoints are problematic.
In Vitro Activities of Ertapenem (MK-0826) against Clinical Bacterial Isolates from 11 North American Medical Centers
Authors: Fuchs Peter C. , Barry Arthur L. , Brown Steven D. 
Published: July 2002

ABSTRACT

This study compared the in vitro activities of the new long-half-life carbapenem ertapenem (also known as MK-0826 and L-749,345) with those of imipenem, amoxicillin-clavulanate, and ciprofloxacin against 5,558 recent clinical isolates from 11 North American medical centers. We confirmed the greater activity of ertapenem than of imipenem against the
Enterobacteriaceae
and the greater activity of imipenem against pseudomonads and gram-positive bacteria.
Variants Other than Aspartic Acid at Codon 69 of the Human Immunodeficiency Virus Type 1 Reverse Transcriptase Gene Affect Susceptibility to Nucleoside Analogs
Authors: Winters Mark A. , Merigan Thomas C. 
Published: July 2002

ABSTRACTThe T69D mutation in the human immunodeficiency virus type 1 reverse transcriptase (RT) gene has been associated with reduced susceptibility to dideoxycytosine (ddC); however, several other mutations at codon 69 have been observed in antiretroviral drug-treated patients. The Stanford HIV RT and Protease Sequence Database was interrogated and showed that 23% of patients treated with nucleoside RT inhibitors (NRTI) had mutations at codon 69. These variants included T69N, -S, -A, -G, -E, -I, and -K mutations that were present in patients treated with NRTI but not in drug-naive patients. Treatment history information showed that a substantial percentage of these codon 69 changes occurred in patients administered non-ddC-containing regimens. Different and specific patterns of other RT gene mutations were associated with the various codon 69 mutations. Drug susceptibility assays showed that viral constructs containing codon 69 variants could have reduced susceptibility to ddC and other RT inhibitors. These results suggest that the T69D mutation is not the only codon 69 variant associated with drug resistance and that ddC is not the only drug affected.
Characterization of Growth and Acid Formation in a
Bacillus subtilis
Pyruvate Kinase Mutant
Authors: Fry B. , Zhu T. , Domach M. M. , Koepsel R. R. , Phalakornkule C. , Ataai M. M. 
Published: July 2002

ABSTRACT

Based on measurements and theoretical analyses, we identified deletion of pyruvate kinase (PYK) activity as a possible route for elimination of acid formation in
Bacillus subtilis
cultures grown on glucose minimal media. Evidence consistent with the attenuation of PYK flux has come from metabolic flux calculations, metabolic pool and enzymatic activity measurements, and a series of nuclear magnetic resonance experiments, all suggesting a nearly complete inhibition of PYK activity for glucose-citrate fed cultures in which the amount of acid formation was nearly zero. In this paper, we report the construction and characterization of a
pyk
mutant of
B. subtilis
. Our results demonstrate an almost complete elimination of acid production in cultures of the
pyk
mutant in glucose minimal medium. The substantial reduction in acid production is accompanied by increased CO
2
production and a reduced rate of growth. Metabolic analysis indicated a dramatic increase in intracellular pools of phosphoenolpyruvate (PEP) and glucose-6-P in the
pyk
mutant. The high concentrations of PEP and glucose-6-P could explain the decreased growth rate of the mutant. The substantial accumulation of PEP does not occur in
Escherichia coli pyk
mutants. The very high concentration of PEP which accumulates in the
B. subtilis pyk
mutant could be exploited for production of various aromatics.
Brachyspira
(
Serpulina
)
hyodysenteriae gyrB
Mutants and Interstrain Transfer of Coumermycin A
1
Resistance
Authors: Stanton Thaddeus B. , Matson Eric G. , Humphrey Samuel B. 
Published: July 2002

ABSTRACT

To further develop genetic techniques for the enteropathogen
Brachyspira hyodysenteriae
, the
gyrB
gene of this spirochete was isolated from a λZAPII library of strain B204 genomic DNA and sequenced. The putative protein encoded by this gene exhibited up to 55% amino acid sequence identity with GyrB proteins of various bacterial species, including other spirochetes.
B. hyodysenteriae
coumermycin A
1
-resistant (Cn
r
) mutant strains, both spontaneous and UV induced, were isolated by plating B204 cells onto Trypticase soy blood agar plates containing 0.5 μg of coumermycin A
1
/ml. The coumermycin A
1
MICs were 25 to 100 μg/ml for the resistant strains and 0.1 to 0.25 μg/ml for strain B204. Four Cn
r
strains had single nucleotide changes in their
gyrB
genes, corresponding to GyrB amino acid changes of Gly
78
to Ser (two strains), Gly
78
to Cys, and Thr
166
to Ala. When Cn
r
strain 435A (Gly
78
to Ser) and Cm
r
Km
r
strain SH (Δ
flaA1
::
cat
Δ
nox
::
kan
) were cultured together in brain heart infusion broth containing 10% (vol/vol) heat-treated (56°C, 30 min) calf serum, cells resistant to chloramphenicol, coumermycin A
1
, and kanamycin could be isolated from the cocultures after overnight incubation, but such cells could not be isolated from monocultures of either strain. Seven Cn
r
Km
r
Cm
r
strains were tested and were determined to have resistance genotypes of both strain 435A and strain SH. Cn
r
Km
r
Cm
r
cells could not be isolated when antiserum to the bacteriophage-like agent VSH-1 was added to cocultures, and the numbers of resistant cells increased fivefold when mitomycin C, an inducer of VSH-1 production, was added. These results indicate that coumermycin resistance associated with a
gyrB
mutation is a useful selection marker for monitoring gene exchange between
B. hyodysenteriae
cells. Gene transfer readily occurs between
B. hyodysenteriae
cells in broth culture, a finding with practical importance. VSH-1 is the likely mechanism for gene transfer.
Synthesis and Fermentation Properties of Novel Galacto-Oligosaccharides by β-Galactosidases from
Bifidobacterium
Species
Authors: Rabiu Bodun A. , Jay Andrew J. , Gibson Glenn R. , Rastall Robert A. 
Published: July 2002

ABSTRACT

β-Galactosidase enzymes were extracted from pure cultures of
Bifidobacterium angulatum, B. bifidum
BB-12,
B. adolescentis
ANB-7,
B. infantis
DSM-20088, and
B. pseudolongum
DSM-20099 and used in glycosyl transfer reactions to synthesize oligosaccharides from lactose. At a lactose concentration of 30% (wt/wt) oligosaccharide yields of 24.7 to 47.6% occurred within 7 h. Examination of the products by thin-layer chromatography and methylation analysis revealed distinct product derived spectra from each enzyme. These were found to be different to that of Oligomate 55, a commercial prebiotic galacto-oligosaccharide. Fermentation testing of the oligosaccharides showed an increase in growth rate, compared to Oligomate 55, with products derived from
B. angulatum, B. bifidum, B. infantis
, and
B. pseudolongum
. However
B. adolescentis
had a lower growth rates on its oligosaccharide compared with Oligomate 55. Mixed culture testing of the
B. bifidum
BS-4 oligosaccharide showed that the overall prebiotic effect was equivalent to that of Oligomate 55.