bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Arabidopsis Profilin Gene Family (Evidence for an Ancient Split between Constitutive and Pollen-Specific Profilin Genes)
Authors: Huang S. , McDowell J. M. , Weise M. J. , Meagher R. B. 
Published: July 2002

Abstract
Profilin is a ubiquitous eukaryotic protein that regulates the actin cytoskeleton and recently has been identified as a potent allergen in pollen. We examined the profilin gene family in the model plant, Arabidopsis thaliana, and found that it contained approximately 8 to 10 members. Four distinct profilin sequences, three cDNAs, PRF1, PRF2, and PRF3, and two genomic clones, PRF1 and PRF4, were isolated and characterized. These genes encoded four distinct profilin isoforms of 131 to 134 amino acids. Northern and reverse-transcriptase polymerase chain reaction analyses demonstrated that Arabidopsis PRF1 was expressed in all major plant organs, whereas PRF4 was specifically expressed in mature pollen. Gene trees constructed from amino acid sequence data revealed the presence of two ancient, distinct profilin gene classes in plants. PRF4 was in a class with previously identified pollen-specific profilins from monocot and dicot species. PRF1, PRF2, PRF3, and a distant dicot sequence formed a separate novel class, suggesting an ancient separation of plant profilins based on regulation and perhaps function. The coevolution of plant actin and profilin classes with similar patterns of expression is discussed. The similarity of plant, fungal, protist, insect, and nematode profilins and their extreme divergence from the vertebrate profilins has striking implications for the evolution of fungal-spore- and plant-pollen-profilins as allergens.
Evidence That a 77-Kilodalton Protein from the Starch of Pea Embryos Is an Isoform of Starch Synthase That Is Both Soluble and Granule Bound
Authors: Edwards A. , Marshall J. , Denyer K. , Sidebottom C. , Visser RGF. , Martin C. , Smith A. M. 
Published: July 2002

Abstract
In this paper we provide further evidence about the nature of a 77-kD starch synthase (SSII) that is both soluble and bound to the starch granules in developing pea (Pisum sativum L.) embryos. Mature SSII gives rise to starch synthase activity when expressed in a strain of Escherichia coli lacking glycogen synthase. In transgenic potatoes (Solanum tuberosum L.) expressing SSII, the protein is both soluble and bound to the starch granules. These results confirm that SSII is a starch synthase and indicate that partitioning between the soluble and granule-bound fraction of storage organs is an intrinsic property of the protein. A 60-kD isoform of starch synthase found both in the soluble and granule-bound fraction of the pea embryos is probably derived by the processing of SSII and is different gene product from GBSSI, the exclusively granule-bound 59-kD isoform of starch synthase that is similar to starch synthases encoded by the waxy genes of cereals and the amf gene of potatoes. Consistent with this, expression in E. coli of an N-terminally truncated version of SSII gives rise to starch synthase activity.
Evidence for the Critical Role of Sucrose Synthase for Anoxic Tolerance of Maize Roots using a Double Mutant
Authors: Ricard Bérénice , Toai Tara Van , Chourey Prem , Saglio Pierre 
Published: July 2002

Abstract
The induction of the sucrose synthase (SuSy) gene (SuSy) by low O2, low temperature, and limiting carbohydrate supply suggested a role in carbohydrate metabolism under stress conditions. The isolation of a maize (Zea mays L.) line mutant for the two knownSuSy genes but functionally normal showed that SuSy activity might not be required for aerobic growth and allowed the possibility of investigating its importance during anaerobic stress. As assessed by root elongation after return to air, hypoxic pretreatment improved anoxic tolerance, in correlation with the number ofSuSy genes and the level of SuSy expression. Furthermore, root death in double-mutant seedlings during anoxic incubation could be attributed to the impaired utilization of sucrose (Suc). Collectively, these data provide unequivocal evidence that Suc is the principal C source and that SuSy is the main enzyme active in Suc breakdown in roots of maize seedlings deprived of O2. In this situation, SuSy plays a critical role in anoxic tolerance.
Expression of Aluminum-Induced Genes in Transgenic Arabidopsis Plants Can Ameliorate Aluminum Stress and/or Oxidative Stress
Authors: Ezaki Bunichi , Gardner Richard C. , Ezaki Yuka , Matsumoto Hideaki 
Published: July 2002

Abstract
To examine the biological role of Al-stress-induced genes, nine genes derived from Arabidopsis, tobacco (Nicotiana tabacum L.), wheat (Triticum aestivum L.), and yeast (Saccharomyces cerevisiae) were expressed in Arabidopsis ecotype Landsberg. Lines containing eight of these genes were phenotypically normal and were tested in root elongation assays for their sensitivity to Al, Cd, Cu, Na, Zn, and to oxidative stresses. An Arabidopsis blue-copper-binding protein gene (AtBCB), a tobacco glutathione S-transferase gene (parB), a tobacco peroxidase gene (NtPox), and a tobacco GDP-dissociation inhibitor gene (NtGDI1) conferred a degree of resistance to Al. Two of these genes, AtBCB andparB, and a peroxidase gene from Arabidopsis (AtPox) also showed increased resistance to oxidative stress induced by diamide, while parB conferred resistance to Cu and Na. Al content of Al-treated root tips was reduced in the four Al-resistant plant lines compared with wild-type Ler-0, as judged by morin staining. All four Al-resistant lines also showed reduced staining of roots with 2′,7′-dichloro fluorescein diacetate (H2DCFDA), an indicator of oxidative stress. We conclude that Al-induced genes can serve to protect against Al toxicity, and also provide genetic evidence for a link between Al stress and oxidative stress in plants.
The Structure and Expression of the Wheat Starch Synthase III Gene. Motifs in the Expressed Gene Define the Lineage of the Starch Synthase III Gene Family
Authors: Li Zhongyi , Mouille Greg , Kosar-Hashemi Behjat , Rahman Sadequr , Clarke Bryan , Gale Kevin R. , Appels Rudi , Morell Matthew K. 
Published: July 2002

AbstractThe endosperm of hexaploid wheat (Triticum aestivum[L.]) was shown to contain a high molecular weight starch synthase (SS) analogous to the product of the maize du1 gene, starch synthase III (SSIII; DU1). cDNA and genomic DNA sequences encoding wheat SSIII were isolated and characterized. The wheat SSIII cDNA is 5,346 bp long and contains an open reading frame that encodes a 1,628-amino acid polypeptide. A putative N-terminal transit peptide, a 436-amino acid C-terminal catalytic domain, and a central 470-amino acid SSIII-specific domain containing three regions of repeated amino acid similarity were identified in the wheat gene. A fourth region between the transit peptide and the SSIII-specific domain contains repeat motifs that are variable with respect to motif sequence and repeat number between wheat and maize. In dicots, this N-terminal region does not contain repeat motifs and is truncated. The gene encoding wheat SSIII, designated ss3, consists of 16 exons extending over 10 kb, and is located on wheat chromosome I. Expression of ss3 mRNA in wheat was detected in leaves, pre-anthesis florets, and from very early to middle stage of endosperm development. The entire N-terminal variable repeat region and the majority of the SSIII-specific domain are encoded on a single 2,703-bp exon. A gene encoding a class III SS from the Arabidopsis genome sequencing project shows a strongly conserved exon structure to the wheat ss3 gene, with the exception of the N-terminal region. The evolutionary relationships of the genes encoding monocot and dicot class III SSs are discussed.
Computational estimation of specific side chain interaction energies in α helices
Authors: Fisinger Samo , Serrano Luis , Lacroix Emmanuel 
Published: July 2002

AbstractWe have used a structure energy‐based computer program developed for protein design, Perla, to provide theoretical estimates of all specific side chain–side chain interaction energies occurring in α helices. The computed side chain–side chain interaction energies were used as substitutes for the corresponding values used by the helix/coil transition algorithm, AGADIR. Predictions of peptide helical contents were nearly as successful as those obtained with the originally calibrated set of parameters; a correlation to experimentally observed α‐helical populations of 0.91 proved that our theoretical estimates are reasonably correct for amino acid pairs that are frequent in our database of peptides. Furthermore, we have determined experimentally the previously uncharacterized interaction energies for Lys–Ile, Thr–Ile, and Phe–Ile amino acid pairs at i,i + 4 positions. The experimental values compare favorably with the computed theoretical estimates. Importantly, the computed values for Thr–Ile and Phe–Ile interactions are better than the energies based on chemical similarity, whereas for Lys–Ile they are similar. Thus, computational techniques can be used to provide precise energies for amino acid pairwise interactions, a fact that supports the development of structure energy–based computational tools for structure predictions and sequence design.
Structural similarity of the covalent complexes formed between the serpin plasminogen activator inhibitor‐1 and the arginine‐specific proteinases trypsin, LMW u‐PA, HMW u‐PA, and t‐PA: Use of site‐specific fluorescent probes of local environment
Authors: Backovic Marija , Stratikos Efstratios , Lawrence Daniel A. , Gettins Peter G.W. 
Published: July 2002

AbstractWe have used two fluorescent probes, NBD and dansyl, attached site‐specifically to the serpin plasminogen activator inhibitor‐1 (PAI‐1) to address the question of whether a common mechanism of proteinase translocation and full insertion of the reactive center loop is used by PAI‐1 when it forms covalent SDS‐stable complexes with four arginine‐specific proteinases, which differ markedly in size and domain composition. Single‐cysteine residues were incorporated at position 119 or 302 as sites for specific reporter labeling. These are positions ∼30 Å apart that allow discrimination between different types of complex structure. Fluorescent derivatives were prepared for each of these variants using both NBD and dansyl as reporters of local perturbations. Spectra of native and cleaved forms also allowed discrimination between direct proteinase‐induced changes and effects solely due to conformational change within the serpin. Covalent complexes of these derivatized PAI‐1 species were made with the proteinases trypsin, LMW u‐PA, HMW u‐PA, and t‐PA. Whereas only minor perturbations of either NBD and dansyl were found for almost all complexes when label was at position 119, major perturbations in both wavelength maximum (blue shifts) and quantum yield (both increases and decreases) were found for all complexes for both NBD and dansyl at position 302. This is consistent with all four complexes having similar location of the proteinase catalytic domain and hence with all four using the same mechanism of full‐loop insertion with consequent distortion of the proteinase wedged in at the bottom of the serpin.
Approximate Velocities in Mixed Exact-Approximate Position Synthesis of Planar Mechanisms
Authors: Holte Jennifer E. , Chase Thomas R. , Erdman Arthur G. 
Published: July 2002

Abstract
A new approach to the synthesis of planar linkage mechanisms with approximate velocity constraints is proposed. The paper presents the first closed-form complex-number dyad solution to the ground pivot specification problem for two precision positions with velocity specified at one of the positions. The solution is then manipulated in order to add approximate velocity constraints to design methods for two exact positions and an unlimited number of approximate positions. The approximate position and velocity constraints facilitate more realistic representation of design objectives. Solution spaces are presented using two-dimensional ground-pivot maps. Computer implementation of the proposed methodologies would allow designers with little or no knowledge of the synthesis techniques to interactively explore maps of solutions for four-bar motion generation.
Abstract: Microstructure and tensile properties of low-oxygen electrodeposited Cu
Authors: Schuler F.T. , Mansfeld F. 
Published: July 2002

The relationships between microstructure, strength, and ductility of electrodeposited copper (EDCu) has been studied for EDCu in the as-deposited condition. Tensile testing was performed at 25 ° and 370 °C. The EDCu was made from a reagent-grade copper sulfate, 225±10 g/liter, reagent-grade sulfuric acid, 68±5 g/liter, and an electrolyte containing 0.4–0.8 g/liter pentose. The electrolyte temperature was 27 °–32 °C. Anodes were high-purity OFHC copper. Deposition rates were varied from 0.015 to 0.075 mm/h, which is equivalent to current densities of about 1.1–5.5 A/dm2. The EDCu produced under these conditions was very pure (99.995%).
Sheets of EDCu approximately 30×22 cm × 0.125–0.15 cm thick were made on a stainless-steel mandrel, separated from the mandrel, and machined into standard, flat-type tensile coupons having a reduced section 0.635 cm in width and 0.125–0.15 cm thick. Overall sample length was about 11.4 cm.
The ultimate tensile strength at room temperature of the EDCu changed directly with increased deposition rate. A four- to five-fold increase in deposition rate, 0.015 mm/h up to 0.075 mm/h, corresponding to a four- to five-fold increase in current density, produced an increase of 25% or more in tensile strength (242–310 MN/m2). The 0.2% offset yield strength was increased by 40% (105–147 MN/m2) by this same increase in deposition rate. Microstructure of the deposit decreased in size from a large columnar duplex structure to an extremely fine columnar structure as a result of the increased deposition rate. Elongation over a 0.5-in. (1.27-cm) gauge length decreased from over 50% to about 25%.
Tensile strength of the EDCu when tested at 370 °C was 70–90 MN/m2, while yield strength is 35–41 MN/m2, with no assignable effect from the deposition rate. The microstructure shows little or no change after the 370 °C exposure during testing, indicating that increases in as-deposited, room-temperature strength were induced by the deposition process, most likely by internal stresses. However, elongation of the EDCu was consistently higher at 370 °C (15%–20%) for the material deposited at 4–5 A/dm2 than for material deposited at 1–3 A/dm2, which exhibits only 1%–5% elongation.
Impurities such as dissolved organics or fine particulates increase strength above that for pure material, with some EDCu having tensile strength as high as 520 MN/m2. Such material was very brittle when tested at 25 ° and 370 °C. Primary usage of the EDCu has been in electroformed rocket-engine combustion chambers and as a barrier to embrittlement of nickel and nickel alloys used in high-pressure gaseous hydrogen environments.
Identification and Analysis of Bacterial Protein Secretion Inhibitors Utilizing a SecA-LacZ Reporter Fusion System
Authors: Alksne L. E. , Burgio P. , Hu W. , Feld B. , Singh M. P. , Tuckman M. , Petersen P. J. , Labthavikul P. , McGlynn M. , Barbieri L. , McDonald L. , Bradford P. , Dushin R. G. , Rothstein D. , Projan S. J. 
Published: July 2002

ABSTRACT

Protein secretion is an essential process for bacterial growth, yet there are few if any antimicrobial agents which inhibit secretion. An in vivo, high-throughput screen to detect secretion inhibitors was developed based on the translational autoregulation of one of the central protein components, SecA. The assay makes use of a SecA-LacZ fusion reporter construct in
Escherichia coli
which is induced when secretion is perturbed. Several compounds, including two natural product extracts, which had the ability to induce the reporter fusion were identified and the MICs of these compounds for
Staphylococcus aureus
strain MN8 were found to be ≤128 μg/ml. Enzyme-linked immunosorbent assay, Western blotting, and immunoprecipitation techniques were used to analyze the affects of these compounds on protein secretion. Six representative compounds presented here appear to be bona fide secretion inhibitors but were found to have deleterious effects on membranes. It was concluded that, while the method described here for identifying inhibitors of secretion is valid, screens such as this, which are directed against the membrane-bound portion of a pathway, may preferentially identify compounds which affect membrane integrity.
Sequences of the NPS-1 and TLE-1 β-Lactamase Genes
Authors: Pai Hyunjoo , Jacoby George A. 
Published: July 2002

ABSTRACT
The NPS-1 and TLE-1 β-lactamase genes were cloned and sequenced. NPS-1 differed from LCR-1 β-lactamase in 8 of 260 amino acids. TLE-1 differed from TEM-1 by a single Asp(115)→Gly substitution and has been renamed TEM-90.
Overproduction and Biochemical Characterization of the
Chryseobacterium meningosepticum
BlaB Metallo-β-Lactamase
Authors: Vessillier Sandrine , Docquier Jean-Denis , Rival Sandrine , Frere Jean-Marie , Galleni Moreno , Amicosante Gianfranco , Rossolini Gian Maria , Franceschini Nicola 
Published: July 2002

ABSTRACT

The BlaB metallo-β-lactamase of
Chryseobacterium meningosepticum
CCUG4310 was overproduced in
Escherichia coli
by means of a T7 promoter-based expression system. The overproducing system, scaled up in a 15-liter fermentor, yielded approximately 10 mg of BlaB protein per liter, mostly released in the culture supernatant. The enzyme was purified by two ion-exchange chromatographic steps with an overall yield of 66%. Analysis of the kinetic parameters revealed efficient activities (
k
cat
/

K
m

ratios of >10
6
M
−1
s
−1
) toward most penam and carbapenem compounds, with the exception of the 6-α-methoxypenam derivative temocillin and of biapenem, which were poorer substrates. Hydrolysis of cephalosporins was overall less efficient, with a remarkable variability that was largely due to variable affinities of the BlaB enzyme for different compounds. BlaB was also able to hydrolyze serine-β-lactamase inhibitors, including β-iodopenicillanate, sulbactam and, although less efficiently, tazobactam.
A Methylotrophic Pathway Participates in Pectin Utilization by
Candida boidinii
Authors: Nakagawa Tomoyuki , Miyaji Tatsuro , Yurimoto Hiroya , Sakai Yasuyoshi , Kato Nobuo , Tomizuka Noboru 
Published: July 2002

ABSTRACT

The methylotrophic yeast
Candida boidinii
S2 was found to be able to grow on pectin or polygalacturonate as a carbon source. When cells were grown on 1% (wt/vol) pectin,
C. boidinii
exhibited induced levels of the pectin-depolymerizing enzymes pectin methylesterase (208 mU/mg of protein), pectin lyase (673 mU/mg), pectate lyase (673 mU/mg), and polygalacturonase (3.45 U/mg) and two methanol-metabolizing peroxisomal enzymes, alcohol oxidase (0.26 U/mg) and dihydroxyacetone synthase (94 mU/mg). The numbers of peroxisomes also increased ca. two- to threefold in cells grown on these pectic compounds (3.34 and 2.76 peroxisomes/cell for cells grown on pectin and polygalacturonate, respectively) compared to the numbers in cells grown on glucose (1.29 peroxisomes/cell). The cell density obtained with pectin increased as the degree of methyl esterification of pectic compounds increased, and it decreased in strains from which genes encoding alcohol oxidase and dihydroxyacetone synthase were deleted and in a peroxisome assembly mutant. Our study showed that methanol metabolism and peroxisome assembly play important roles in the degradation of pectin, especially in the utilization of its methyl ester moieties.
Degradation of Triphenyltin by a Fluorescent Pseudomonad
Authors: Inoue Hiroyuki , Takimura Osamu , Fuse Hiroyuki , Murakami Katsuji , Kamimura Kazuo , Yamaoka Yukiho 
Published: July 2002

ABSTRACT

Triphenyltin (TPT)-degrading bacteria were screened by a simple technique using a post-column high-performance liquid chromatography using 3,3′,4′,7-tetrahydroxyflavone as a post-column reagent for determination of TPT and its metabolite, diphenyltin (DPT). An isolated strain, strain CNR15, was identified as
Pseudomonas chlororaphis
on the basis of its morphological and biochemical features. The incubation of strain CNR15 in a medium containing glycerol, succinate, and 130 μM TPT resulted in the rapid degradation of TPT and the accumulation of approximately 40 μM DPT as the only metabolite after 48 h. The culture supernatants of strain CNR15, grown with or without TPT, exhibited a TPT degradation activity, whereas the resting cells were not capable of degrading TPT. TPT was stoichiometrically degraded to DPT by the solid-phase extract of the culture supernatant, and benzene was detected as another degradation product. We found that the TPT degradation was catalyzed by low-molecular-mass substances (approximately 1,000 Da) in the extract, termed the TPT-degrading factor. The other fluorescent pseudomonads,
P. chlororaphis
ATCC 9446,
Pseudomonas fluorescens
ATCC 13525, and
Pseudomonas aeruginosa
ATCC 15692, also showed TPT degradation activity similar to strain CNR15 in the solid-phase extracts of their culture supernatants. These results suggest that the extracellular low-molecular-mass substance that is universally produced by the fluorescent pseudomonad could function as a potent catalyst to cometabolite TPT in the environment.
Mannose Phosphate Isomerase Isoenzymes in
Plutella xylostella
Support Common Genetic Bases of Resistance to
Bacillus thuringiensis
Toxins in Lepidopteran Species
Authors: Herrero Salvador , Ferré Juan , Escriche Baltasar 
Published: July 2002

ABSTRACT

A strong correlation between two mannose phosphate isomerase (MPI) isoenzymes and resistance to Cry1A toxins from
Bacillus thuringiensis
has been found in a
Plutella xylostella
population. MPI linkage to Cry1A resistance had previously been reported for a
Heliothis virescens
population. The fact that the two populations share similar biochemical, genetic, and cross-resistance profiles of resistance suggests the occurrence of homologous resistance loci in both species.
Oligophilic Bacteria as Tools To Monitor Aseptic Pharmaceutical Production Units
Authors: Nagarkar Parag P. , Ravetkar Satish D. , Watve Milind G. 
Published: July 2002

ABSTRACT
The bacterial loads of air, surfaces, and personnel in clean rooms are routinely monitored using a set of standard media. Bacteria that can grow on these media are a tiny fraction of the total numbers in any environment. A substantial proportion of bacteria long thought to be unculturable were recently shown to be oligophilic. Oligophile counts in clean rooms in our studies exceeded the standard plate counts by up to 2 orders of magnitude. They responded to disinfection routines in ways similar to the responses of conventional bacteria. We suggest that oligophiles are better tools than conventional bacteria for environmental monitoring in aseptic pharmaceutical production units.