bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cut rules and explicit substitutions
Authors: VESTERGAARD RENÉ , WELLS JOE 
Published: July 2002

We introduce a method to associate calculi of proof terms and rewrite rules with cut
elimination procedures for logical deduction systems (i.e., Gentzen-style sequent calculi) in
the case of intuitionistic logic. We illustrate this method using two different versions of the
cut rule for a variant of the intuitionistic fragment of Kleene's logical deduction system G3.Our systems are in fact calculi of explicit substitution, where the cut rule introduces an
explicit substitution and the left-→ rule introduces a binding of the result of a function
application. Cut propagation steps of cut elimination correspond to propagation of explicit
substitutions, and propagation of weakening (to eliminate it) corresponds to propagation of
index-updating operations. We prove various subject reduction, termination, and confluence
properties for our calculi.Our calculi improve on some earlier calculi for logical deduction systems in a number of
ways. By using de Bruijn indices, our calculi qualify as first-order term rewriting systems
(TRS's), allowing us to use correctly certain results for TRS's about termination. Unlike in
some other calculi, each of our calculi has only one cut rule and we do not need unusual
features of sequents.We show that the substitution and index-updating mechanisms of our calculi work the same
way as the substitution and index-updating mechanisms of Kamareddine and Ríos' λs and
λt, two well-known systems of explicit substitution for the standard λ-calculus. By a change
in the format of sequents, we obtain similar results for a known λ-calculus with variables
and explicit substitutions, Rose's λbxgc.
Category-based constraint logic
Authors: DIACONESCU RĂZVAN 
Published: July 2002

The research reported in this paper exploits the view of constraint programming as
computation in a logical system, namely constraint logic. The basic ingredients of constraint
logic are: constraint models for the semantics (they form a comma-category over a fixed
model of ‘built-ins’); generalized polynomials in the role of basic syntactic ingredient; and a
constraint satisfaction relation between semantics and syntax. Category-based constraint logic
means the development of the logic is abstract categorical rather than concrete set
theoretical.We show that (category-based) constraint logic is an institution, and we internalize the study
of constraint logic to the abstract framework of category-based equational logic, thus
opening the door for considering constraint logic programming over non-standard structures
(such as CPO's, topologies, graphs, categories, etc.). By embedding category-based constraint
logic into category-based equational logic, we integrate the constraint logic programming
paradigm into (category-based) equational logic programming. Results include completeness
of constraint logic deduction, a novel Herbrand theorem for constraint logic programming
characterizing Herbrand models as initial models in constraint logic, and logical foundations
for the modular combination of constraint solvers based on amalgamated sums of Herbrand
models in the constraint logic institution.
Identification of Novel Human Genes Evolutionarily Conserved inCaenorhabditis elegansby Comparative Proteomics
Authors: Lai Chun-Hung , Chou Chang-Yuan , Ch'ang Lan-Yang , Liu Chung-Shyan , Lin Wen-chang 
Published: July 2002

Modern biomedical research greatly benefits from large-scale genome-sequencing projects ranging from studies of viruses, bacteria, and yeast to multicellular organisms, likeCaenorhabditis elegans. Comparative genomic studies offer a vast array of prospects for identification and functional annotation of human ortholog genes. We presented a novel comparative proteomic approach for assembling human gene contigs and assisting gene discovery. TheC. elegansproteome was used as an alignment template to assist in novel human gene identification from human EST nucleotide databases. Among the available 18,452C. elegansprotein sequences, our results indicate that at least 83% (15,344 sequences) ofC. elegansproteome has human homologous genes, with 7,954 records ofC. elegansproteins matching known human gene transcripts. Only 11% or less ofC. elegansproteome contains nematode-specific genes. We found that the remaining 7,390 sequences might lead to discoveries of novel human genes, and over 150 putative full-length human gene transcripts were assembled upon further database analyses.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.AF132936–AF132973,AF151799–AF151909, andAF152097.]
Evidence for a Ustilago maydis Steroid 5α-Reductase by Functional Expression in Arabidopsis det2-1Mutants
Authors: Basse Christoph W. , Kerschbamer Christine , Brustmann Markus , Altmann Thomas , Kahmann Regine 
Published: July 2002

Abstract
We have identified a gene (udh1) in the basidiomycete Ustilago maydis that is induced during the parasitic interaction with its host plant maize (Zea mays). udh1 encodes a protein with high similarity to mammalian and plant 5α-steroid reductases. Udh1 differs from those of known 5α-steroid reductases by six additional domains, partially predicted to be membrane-spanning. A fusion protein of Udh1 and the green fluorescent protein provided evidence for endoplasmic reticulum localization in U. maydis. The function of the Udh1 protein was demonstrated by complementing Arabidopsisdet2-1 mutants, which display a dwarf phenotype due to a mutation in the 5α-steroid reductase encoding DET2gene. det2-1 mutant plants expressing either theudh1 or the DET2 gene controlled by the cauliflower mosaic virus 35S promoter differed from wild-type Columbia plants by accelerated stem growth, flower and seed development and a reduction in size and number of rosette leaves. The accelerated growth phenotype of udh1 transgenic plants was stably inherited and was favored under reduced light conditions. Truncation of the N-terminal 70 amino acids of the Udh1 protein abolished the ability to restore growth in det2-1 plants. Our results demonstrate the existence of a 5α-steroid reductase encoding gene in fungi and suggest a common ancestor between fungal, plant, and mammalian proteins.
Limits to Sulfur Accumulation in Transgenic Lupin Seeds Expressing a Foreign Sulfur-Rich Protein
Authors: Tabe Linda M. , Droux Michel 
Published: July 2002

Abstract
The low sulfur amino acid content of legume seeds restricts their nutritive value for animals. We have investigated the limitations to the accumulation of sulfur amino acids in the storage proteins of narrow leaf lupin (Lupinus angustifolius) seeds. Variation in sulfur supply to lupin plants affected the sulfur amino acid accumulation in the mature seed. However, when sulfur was in abundant supply, it accumulated to a large extent in oxidized form, rather than reduced form, in the seeds. At all but severely limiting sulfur supply, addition of a transgenic (Tg) sink for organic sulfur resulted in an increase in seed sulfur amino acid content. We hypothesize that demand, or sink strength for organic sulfur, which is itself responsive to environmental sulfur supply, was the first limit to the methionine (Met) and cysteine (Cys) content of wild-type lupin seed protein under most growing conditions. In Tg, soil-grown seeds expressing a foreign Met- and Cys-rich protein, decreased pools of free Met, free Cys, and glutathione indicated that the rate of synthesis of sulfur amino acids in the cotyledon had become limiting. Homeostatic mechanisms similar to those mediating the responses of plants to environmental sulfur stress resulted in an adjustment of endogenous protein composition in Tg seeds, even when grown at adequate sulfur supply. Uptake of sulfur by lupin cotyledons, as indicated by total seed sulfur at maturity, responded positively to increased sulfur supply, but not to increased demand in the Tg seeds.
Inhibition of Trehalase Activity Enhances Trehalose Accumulation in Transgenic Plants
Authors: Goddijn OJM. , Verwoerd T. C. , Voogd E. , Krutwagen RWHH. , de Graff PTHM. , Poels J. , van Dun K. , Ponstein A. S. , Damm B. , Pen J. 
Published: July 2002

Abstract
As a first step toward the exploitation of the disaccharide trehalose as a stress-protective and preservative agent in plants, we engineered trehalose biosynthesis in tobacco (Nicotiana tabacum) and potato (Solanum tuberosum) by introducing the otsA and otsB genes from Escherichia coli, which encode trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase, respectively. In leaves of transgenic tobacco plants, very low levels of trehalose accumulation were obtained (0.11 mg g-1 fresh weight), whereas in transgenic potato tubers, no trehalose accumulated at all. Plant trehalase activity was shown to affect the accumulation of trehalose in these plants. An increase in trehalose accumulation, up to 0.41 and 4.04 mg g-1 fresh weight in tobacco leaves and potato microtubers, respectively, was noted when the potent trehalase inhibitor validamycin A was added to in vitro plants and to hydroponically grown greenhouse plants. Stunted growth and the formation of lancet-shaped leaves by trehalose-accumulating tobacco plants suggest a negative effect of trehalose biosynthesis on N. tabacum development. It is surprising that experiments with wild-type plants cultured in the presence of validamycin A indicate that, despite current belief, the capacity to synthesize trehalose may not be restricted to primitive phyla of vascular plants and certain “resurrection plants,” but may exist throughout the angiosperms.
7-Dehydrobrefeldin A, a Naturally Occurring Brefeldin A Derivative, Inhibits Secretion and Causes a cis-to-trans Breakdown of Golgi Stacks in Plant Cells
Authors: Driouich A. , Jauneau A. , Staehelin L. A. 
Published: July 2002

Abstract
7-Dehydrobrefeldin A (7-oxo-BFA) is a brefeldin A (BFA) analog that, like BFA, is a potent phytotoxin of Alternaria carthami, a fungal pathogen of safflower (Carthamus tinctorius L.) plants. Both BFA and 7-oxo-BFA have been shown to be causal agents of the leaf spot disease of these plants. We have investigated the effects of 7-oxo-BFA on the secretion and the structure of the Golgi stacks of sycamore maple (Acer pseudoplatanus) suspension-cultured cells to determine whether 7-oxo-BFA affects these cells in the same manner as BFA. When applied at 10 [mu]g/mL for 1 h, 7-oxo-BFA inhibits secretion of proteins by approximately 80%, the same value obtained for BFA. However, electron micrographs of high-pressure frozen/freeze-substituted cells demonstrated that 7-oxo-BFA is a more potent disrupter of the Golgi stacks of sycamore maple cells than BFA. In cells treated for 1 h with 10 [mu]g/mL 7-oxo-BFA, very few Golgi stacks can be discerned. Most of those that are left consist of fewer than three cisternae, all of which stain like trans-Golgi cisternae. They are surrounded by clusters of large (150–300 nm in diameter), darkly staining vesicles that are embedded in a fine-filamentous, ribosome-excluding matrix. Similarly sized and stained vesicles are seen budding from the rims of the residual trans-Golgi cisternae. Both the large vesicles and the residual Golgi stack buds stain with anti-xyloglucan polysaccharide antibodies. Recovery of Golgi stacks after removal of 7-oxo-BFA from 1-h-treated cells takes 2 to 6 h, compared with 1 to 2 h for cells treated with BFA. In contrast to 7-oxo-BFA, the BFA breakdown product BFA acid had no effect either on secretion or on the secretory apparatus. This is the first report, to our knowledge, of a BFA analog inhibiting secretion in a eukaryotic cell system.
Proline Accumulation and Salt-Stress-Induced Gene Expression in a Salt-Hypersensitive Mutant of Arabidopsis
Authors: Liu J. , Zhu J. K. 
Published: July 2002

Abstract
The sos1 mutant of Arabidopsis thaliana is more than 20 times more sensitive to NaCl stress than wild-type Arabidopsis. Because proline (Pro) is generally thought to have an important role in plant salt tolerance, the sos1 mutant and the wild type were compared with respect to their capacity to accumulate Pro under NaCl stress, and sos1 mutant plants accumulated more Pro than the wild type. The P5CS gene, which catalyzes the rate-limiting step in Pro biosynthesis, is induced by salt stress to a higher level in sos1 than in the wild type. Although a defective high-affinity K uptake system in sos1 causes K deficiency and inhibits growth in NaCl-treated plants, this decrease is not a sufficient signal for Pro accumulation and P5CS gene expression. Not all salt-stress-induced genes have a higher level of expression in sos1. The expression levels of AtPLC and RD29A, which encode a phospholipase C homolog and a putative protective protein, respectively, are the same in sos1 as in the wild type. However, the expression of AtMYB, which encodes a putative transcriptional factor, is induced to a much higher level by salt stress in sos1. Thus, the SOS1 gene product serves as a negative regulator for the expression of P5CS and AtMYB, but has no effect on AtPLC and RD29A expression.
Gibberellins and Stem Growth in Arabidopsis thaliana (Effects of Photoperiod on Expression of the GA4 and GA5 Loci)
Authors: Xu Y. L. , Gage D. A. , Zeevaart JAD. 
Published: July 2002

Abstract
Arabidopsis thaliana (L.) Heynh. is a quantitative long-day (LD) rosette plant in which stem growth is mediated by gibberellins (GAs). Application of GAs to plants in short-day (SD) conditions resulted in rapid stem elongation and flower formation, with GA4 and GA9 being equally effective, and GA1 showing lower activity. The effects of photoperiod on the levels of endogenous GAs were measured by combined gas chromatography-mass spectrometry with selected ion monitoring. When plants were transferred from SD to LD conditions there was a slight decrease in the level of GA53 and an increase in the levels of C19-GAs, GA9, GA20, GA1, and GA8, indicating that GA 20-oxidase activity is stimulated in LD conditions. Expression of GA5, which encodes GA 20-oxidase, was highest in elongating stems and was correlated with the rate of stem elongation. By contrast, GA4, which encodes 3β-hydroxylase, showed low expression in stems and its expression was not correlated with the rate of stem elongation. We conclude that stem elongation in LD conditions is at least in part due to increased expression of GA5, whereas expression of GA4 is not under photoperiodic control.
Mapping the Functional Roles of Cap Cells in the Response of Arabidopsis Primary Roots to Gravity1
Authors: Blancaflor Elison B. , Fasano Jeremiah M. , Gilroy Simon 
Published: July 2002

AbstractThe cap is widely accepted to be the site of gravity sensing in roots because removal of the cap abolishes root curvature. Circumstantial evidence favors the columella cells as the gravisensory cells because amyloplasts (and often other cellular components) are polarized with respect to the gravity vector. However, there has been no functional confirmation of their role. To address this problem, we used laser ablation to remove defined cells in the cap of Arabidopsis primary roots and quantified the response of the roots to gravity using three parameters: time course of curvature, presentation time, and deviation from vertical growth. Ablation of the peripheral cap cells and tip cells did not alter root curvature. Ablation of the innermost columella cells caused the strongest inhibitory effect on root curvature without affecting growth rates. Many of these roots deviated significantly from vertical growth and had a presentation time 6-fold longer than the controls. Among the two inner columella stories, the central cells of story 2 contributed the most to root gravitropism. These cells also exhibited the largest amyloplast sedimentation velocities. Therefore, these results are consistent with the starch-statolith sedimentation hypothesis for gravity sensing.
The Regulation of Photosynthetic Electron Transport during Nutrient Deprivation inChlamydomonas reinhardtii1
Authors: Wykoff Dennis D. , Davies John P. , Melis Anastasios , Grossman Arthur R. 
Published: July 2002

AbstractThe light-saturated rate of photosynthetic O2 evolution in Chlamydomonas reinhardtii declined by approximately 75% on a per-cell basis after 4 d of P starvation or 1 d of S starvation. Quantitation of the partial reactions of photosynthetic electron transport demonstrated that the light-saturated rate of photosystem (PS) I activity was unaffected by P or S limitation, whereas light-saturated PSII activity was reduced by more than 50%. This decline in PSII activity correlated with a decline in both the maximal quantum efficiency of PSII and the accumulation of the secondary quinone electron acceptor of PSII nonreducing centers (PSII centers capable of performing a charge separation but unable to reduce the plastoquinone pool). In addition to a decline in the light-saturated rate of O2 evolution, there was reduced efficiency of excitation energy transfer to the reaction centers of PSII (because of dissipation of absorbed light energy as heat and because of a transition to state 2). These findings establish a common suite of alterations in photosynthetic electron transport that results in decreased linear electron flow when C. reinhardtii is limited for either P or S. It was interesting that the decline in the maximum quantum efficiency of PSII and the accumulation of the secondary quinone electron acceptor of PSII nonreducing centers were regulated specifically during S-limited growth by theSacI gene product, which was previously shown to be critical for the acclimation of C. reinhardtiito S limitation (J.P. Davies, F.H. Yildiz, and A.R. Grossman [1996] EMBO J 15: 2150–2159).
Temporal Sequence of Cell Wall Disassembly in Rapidly Ripening Melon Fruit1
Authors: Rose Jocelyn K.C. , Hadfield Kristen A. , Labavitch John M. , Bennett Alan B. 
Published: July 2002

AbstractThe Charentais variety of melon (Cucumis melo cv Reticulatus F1 Alpha) was observed to undergo very rapid ripening, with the transition from the preripe to overripe stage occurring within 24 to 48 h. During this time, the flesh first softened and then exhibited substantial disintegration, suggesting that Charentais may represent a useful model system to examine the temporal sequence of changes in cell wall composition that typically take place in softening fruit. The total amount of pectin in the cell wall showed little reduction during ripening but its solubility changed substantially. Initial changes in pectin solubility coincided with a loss of galactose from tightly bound pectins, but preceded the expression of polygalacturonase (PG) mRNAs, suggesting early, PG-independent modification of pectin structure. Depolymerization of polyuronides occurred predominantly in the later ripening stages, and after the appearance of PG mRNAs, suggesting the existence of PG-dependent pectin degradation in later stages. Depolymerization of hemicelluloses was observed throughout ripening, and degradation of a tightly bound xyloglucan fraction was detected at the early onset of softening. Thus, metabolism of xyloglucan that may be closely associated with cellulose microfibrils may contribute to the initial stages of fruit softening. A model is presented of the temporal sequence of cell wall changes during cell wall disassembly in ripening Charentais melon.
Auxin Deprivation Induces Synchronous Golgi Differentiation in Suspension-Cultured Tobacco BY-2 Cells1
Authors: Winicur Zev M. , Feng Zhang Guo , Andrew Staehelin L. 
Published: July 2002

Abstract
To date, the lack of a method for inducing plant cells and their Golgi stacks to differentiate in a synchronous manner has made it difficult to characterize the nature and extent of Golgi retailoring in biochemical terms. Here we report that auxin deprivation can be used to induce a uniform population of suspension-cultured tobacco (Nicotiana tabacum cv BY-2) cells to differentiate synchronously during a 4-d period. Upon removal of auxin, the cells stop dividing, undergo elongation, and differentiate in a manner that mimics the formation of slime-secreting epidermal and peripheral root-cap cells. The morphological changes to the Golgi apparatus include a proportional increase in the number oftrans-Golgi cisternae, a switch to larger-sized secretory vesicles that bud from the trans-Golgi cisternae, and an increase in osmium staining of the secretory products. Biochemical alterations include an increase in large, fucosylated, mucin-type glycoproteins, changes in the types of secreted arabinogalactan proteins, and an increase in the amounts and types of molecules containing the peripheral root-cap-cell-specific epitope JIM 13. Taken together, these findings support the hypothesis that auxin deprivation can be used to induce tobacco BY-2 cells to differentiate synchronously into mucilage-secreting cells.
Conditional Synergism between Cryptochrome 1 and Phytochrome B Is Shown by the Analysis of phyA, phyB, andhy4 Simple, Double, and Triple Mutants in Arabidopsis
Authors: Casal Jorge José , Mazzella Marı́a Agustina 
Published: July 2002

Abstract
Wild-type or phyA,phyB, or hy4 mutant Arabidopsis seedlings lacking phytochrome A (phyA), phytochrome B (phyB), or cryptochrome 1 (cry1), respectively, and the double and triple mutants were used in combination with blue-light treatments given simultaneously with red or far-red light. We investigated the interaction between phytochromes and cry1 in the control of hypocotyl growth and cotyledon unfolding. Under conditions deficient for cry1 (short exposures to blue light) or phyB (far-red background), these photoreceptors acted synergistically: Under short exposures to blue light (3 h/d) added to a red-light background, cry1 activity required phyB (e.g. the hy4 mutant was taller than the wild type but the phyBhy4 mutant was not taller than thephyB mutant). Under prolonged exposures to blue light (24 h/d) added to a far-red light background, phyB activity required cry1 (e.g. the phyAphyB mutant was taller than thephyA mutant but the phyAphyBhy4 mutant was not taller than the phyAhy4 mutant). Under more favorable light inputs, i.e. prolonged exposures to blue light added to a red-light background, the effects of cry1 and phyB were independent. Thus, the synergism between phyB and cry1 is conditional. The effect of cry1 was not reduced by the phyA mutation under any tested light condition. Under continuous blue light the triple mutantphyAphyBhy4 showed reduced hypocotyl growth inhibition and cotyledon unfolding compared with the phyAphyBmutant. The action of cry1 in the phyAphyB double mutant was higher under the red-light than the far-red-light background, indicating a synergistic interaction between cry1 and phytochromes C, D, or E; however, a residual action of cry1 independent of any phytochrome is likely to occur.