bluuebunny/crossref_metadata_2025_split huggingface dataset:
Special issue on ‘Logic Programming and the INTERNET’
Authors: STERLING LEON , NAISH LEE , HERMENEGILDO MANUEL 
Published: July 2002

Computational logic systems can offer an attractive environment for developing
Internet applications. They share many of the important characteristics of popular
network programming tools, including dynamic memory management, well-behaved
structure and pointer manipulation, robustness, and compilation to architecture-independent
bytecode. However, in addition, computational logic systems offer
some unique features such as very powerful symbolic processing capabilities, constraint
solving, dynamic databases, search facilities, grammars, sophisticated meta-programming,
and well understood semantics. Such features can often make it very
easy to code simple applications.This special issue concerned with applications is the third of its kind in a journal
sponsored by the Association for Logic Programming. The first appeared in 1990,
and showed the potential for logic programming to be extended. The second issue
highlighted some papers from the Practical Applications of Prolog conference that
had been held. This third time, the applications are concerned with the Internet and
reflect the profound impact that the Internet has had on the computing landscape.
Impact of sawfly defoliation on growth of Scots pine Pinus sylvestris (Pinaceae) and associated economic losses
Authors: Lyytikäinen-Saarenmaa P. , Tomppo E. 
Published: July 2002

AbstractNeedle defoliation by diprionid sawflies decreases the increment and timber yield of Scots pine Pinus sylvestris L. The aim of this study was to provide approximate estimates of this decrease and preliminary estimates of the economic value of growth losses and tree mortality. Growth loss after needle damage by Diprion pini(Linnaeus) was studied in western Finland. Increment cores were sampled for radial growth measurements from trees subjected to slight, moderate and heavy defoliation. A literature survey was carried out to estimate radial growth losses after defoliation by Neodiprion sertifer (Geoffroy). Calculations for economic consequences were based on previous estimates and on the ongoing 9th Finnish National Forest Inventory. Moderate defoliation by N. sertifer and D. pini reduced volume growth by 21% and 86% and heavy defoliation by 38% and 94%, respectively. Tree mortality in defoliated stands was recorded as approximately 4%after an outbreak of N. sertifer and 30% after an outbreak of D. pini. The estimated average economic value of the losses due to reduced growth and tree mortality reached $40 ha−1 after a single-year outbreak of N. sertifer and $310 ha−1 in the case of D. pini. These preliminary estimates of economic losses indicate a much higher impact of pine sawflies than those revealed by the few earlier studies in Europe.
Potential impact of global warming on deciduous oak dieback caused by ambrosia fungus Raffaelea sp. carried by ambrosia beetle Platypus quercivorus (Coleoptera: Platypodidae) in Japan
Authors: Kamata N. , Esaki K. , Kato K. , Igeta Y. , Wada K. 
Published: July 2002

AbstractDeciduous oak dieback in Japan has been known since the 1930s, but in the last ten years epidemics have intensified and spread to the island’s western coastal areas. The symbiotic ambrosia fungus Raffaelea sp. is the causal agent of oak dieback, and is vectored by Platypus quercivorus (Murayama). This is the first example of an ambrosia beetle fungus that kills vigorous trees. Mortality of Quercus crispula was approximately 40% but much lower for associated species of Fagaceae, even though each species had a similar number of beetle attacks. It is likely that other oaks resistant to the fungus evolved under a stable relationship between the tree, fungus and beetle during a long evolutionary process. Quercus crispula was probably not part of this coevolution. This hypothesis was supported by the fact that P. quercivorus showed the least preference for Q. crispulayet exhibited highest reproductive success in this species. Therefore, P. quercivorus could spread more rapidly in stands with a high composition of Q. crispula. The present oak dieback epidemic in Japan probably resulted from the warmer climate that occurred from the late 1980s which made possible the fateful encounter of P. quercivorus with Q. cripsula by allowing the beetle to extend its distribution to more northerly latitudes and higher altitudes. Future global warming will possibly accelerate the overlapping of the distributions of P. quercivorus and Q. crispula with the result that oak dieback in Q. crispula will become more prevalent in Japan.
Extensive Conservation of Sex Chromosome Organization Between Cat and Human Revealed by Parallel Radiation Hybrid Mapping
Authors: Murphy William J. , Sun Shan , Chen Zhang-Qun , Pecon-Slattery Jill , O'Brien Stephen J. 
Published: July 2002

A radiation hybrid (RH)-derived physical map of 25 markers on the feline X chromosome (including 19 Type I coding loci and 6 Type II microsatellite markers) was compared to homologous marker order on the human and mouse X chromosome maps. Complete conservation of synteny and marker order was observed between feline and human X chromosomes, whereas the same markers identified a minimum of seven rearranged syntenic segments between mouse and cat/human X chromosome marker order. Within the blocks, the feline, human, and mouse marker order was strongly conserved. Similarly, Y chromosome locus order was remarkably conserved between cat and human Y chromosomes, with only one marker (SMCY) position rearranged between the species. Tight linkage and a conserved gene order for a segment encoding three genes,DFFRY–DBY–UTY in human, mouse, and cat Y chromosomes, coupled with demonstrated deletion effects of these genes on reproductive impairment in both human and mouse, implicates the region as critical for Y-mediated sperm production.[The sequence data described in this paper have been submitted to the GenBank data library under accession numbers AF197956–AF197962 andAF197964–AF197972.]
The Rice Mutant esp2 Greatly Accumulates the Glutelin Precursor and Deletes the Protein Disulfide Isomerase
Authors: Takemoto Yoko , Coughlan Sean J. , Okita Thomas W. , Satoh Hikaru , Ogawa Masahiro , Kumamaru Toshihiro 
Published: July 2002

Abstract
Rice (Oryza sativa) accumulates prolamins and glutelins as storage proteins. The latter storage protein is synthesized on the endoplasmic reticulum (ER) as a 57-kD proglutelin precursor, which is then processed into acidic and basic subunits in the protein storage vacuole. Three esp2mutants, CM1787, EM44, and EM747, contain larger amounts of the 57-kD polypeptide and corresponding lower levels of acidic and basic glutelin subunits than normal. Electron microscopic observation revealed thatesp2 contained normal-appearing glutelin-containing protein bodies (PB-II), but lacked the normal prolamin-containing PB (PB-I). Instead, numerous small ER-derived PBs of uniform size (0.5 μm in diameter) and low electron density were readily observed. Immunoblot analysis of purified subcellular fractions and immunocytochemistry at the electron microscopy level showed that these new PBs contained the 57-kD proglutelin precursor and prolamin polypeptides. The 57-kD proglutelin was extracted with 1% (v/v) lactic acid solution only after removal of cysteine-rich prolamin polypeptides, suggesting that these proteins form glutelin-prolamin aggregates via interchain disulfide bonds within the ER lumen. The endosperm of esp2 mutants contains the lumenal chaperones, binding protein and calnexin, but lacks protein disulfide isomerase (PDI) at the protein and RNA levels. The transcript of PDI was expressed in the seed only during the early stage of seed development in the wild type. These results suggest that PDI plays an essential role in the segregation of proglutelin and prolamin polypeptides within the ER lumen.
Mutants at the Slender1 Locus of Barley cv Himalaya. Molecular and Physiological Characterization
Authors: Chandler Peter Michael , Marion-Poll Annie , Ellis Marc , Gubler Frank 
Published: July 2002

Abstract
A dominant dwarf mutant of barley (Hordeum vulgare) that resembles dominant gibberellin (GA) “-insensitive” or “-nonresponsive” mutants in other species is described. α-Amylase production by endosperm half-grains of the mutant required GA3 at concentrations about 100 times that of the WT. The mutant showed only a slight growth response to GA3, even at very high concentrations. However, when additionally dwarfed, growth rate responded to GA3over the normal concentration range, although only back to the original (dwarf) elongation rate. Genetic studies indicated that the dominant dwarf locus was either closely linked or identical to theSln1 (Slender1) locus. A barley sequence related to Arabidopsis GAI/RGA was isolated, and shown to represent the Sln1 locus by the analysis ofsln1 mutants. The dominant dwarf mutant was also altered in this sequence, indicating that it too is an allele atSln1. Thus, mutations at Sln1 generate plants of radically different phenotypes; either dwarfs that are largely dominant and GA “-insensitive/-nonresponsive,” or the recessive slender types in which GA responses appear to be constitutive. Immunoblotting studies showed that in growing leaves, SLN1 protein localized almost exclusively to the leaf elongation zone. In mutants at the Sln1 locus, there were differences in both the abundance and distribution of SLN1 protein, and large changes in the amounts of bioactive GAs, and of their metabolic precursors and catabolites. These results suggest that there are dynamic interactions between SLN1 protein and GA content in determining leaf elongation rate.
Phosphorus Deficiency in Lupinus albus (Altered Lateral Root Development and Enhanced Expression of Phosphoenolpyruvate Carboxylase)
Authors: Johnson J. F. , Vance C. P. , Allan D. L. 
Published: July 2002

Abstract
The development of clustered tertiary lateral roots (proteoid roots) and the expression of phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31) in roots were studied in white lupin (Lupinus albus L.) grown with either 1 mM P (+P-treated) or without P (-P-treated). The +P-treated plants initiated fewer clustered tertiary meristems and the emergence of these meristems was delayed compared with -P-treated plants. Proteoid root zones could be identified 9 d after emergence in both P treatments. Amounts of PEPC mRNA, PEPC specific activity, and enzyme protein were greater in proteoid roots than in normal roots beginning at 10, 12, and 14 d after emergence, respectively. The increases in PEPC mRNA, PEPC enzyme, and PEPC specific activity suggest that this enzyme is in part under transcriptional regulation. Recovery of organic acids from root exudates coincided with the increases in PEPC specific activity. The -P-treated plants exuded 40-, 20-, and 5-fold more citrate, malate, and succinate, respectively, than did +P-treated plants. Data presented support the hypothesis that white lupin has concerted regulation of proteoid root development, transcriptional regulation of PEPC, and biosynthesis of organic acids for exudation in response to P deficiency.
Phytochrome B Affects Responsiveness to Gibberellins in Arabidopsis
Authors: Reed J. W. , Foster K. R. , Morgan P. W. , Chory J. 
Published: July 2002

Abstract
Plant responses to red and far-red light are mediated by a family of photoreceptors called phytochromes. Arabidopsis thaliana seedlings lacking one of the phytochromes, phyB, have elongated hypocotyls and other tissues, suggesting that they may have an alteration in hormone physiology. We have studied the possibility that phyB mutations affect seedling gibberellin (GA) perception and metabolism by testing the responsiveness of wild-type and phyB seedlings to exogenous GAs. The phyB mutant elongates more than the wild type in response to the same exogenous concentrations of GA3 or GA4, showing that the mutation causes an increase in responsiveness to GAs. Among GAs that we were able to detect, we found no significant difference in endogenous levels between wild-type and phyB mutant seedlings. However, GA4 levels were below our limit of detectability, and the concentration of that active GA could have varied between wild-type and phyB mutant seedlings. These results suggest that, although GAs are required for hypocotyl cell elongation, phyB does not act primarily by changing total seedling GA levels but rather by decreasing seedling responsiveness to GAs.
Cloning of an Enzyme That Synthesizes a Key Nucleotide-Sugar Precursor of Hemicellulose Biosynthesis from Soybean:UDP-Glucose Dehydrogenase
Authors: Tenhaken R. , Thulke O. 
Published: July 2002

Abstract
Hemicellulose is a major component of primary plant cell walls. Many of the glycosyl residues found in hemicellulose are derived from the sugar precursor UDP-glucuronic acid, which can be converted into UDP-arabinose, UDP-apiose, UDP-galacturonic acid, and UDP-xylose. The enzyme controlling the biosynthesis of UDP-glucuronic acid, UDP-glucose dehydrogenase (EC 1.1.1.22), was cloned from soybean (Glycine max [L.] Merr.) by an antibody screening procedure. This enzyme is surprisingly homologous to the bovine sequence, which is the only other eukaryotic UDP-glucose dehydrogenase sequence known. The characteristic motifs of the enzyme, the catalytic center, a NAD-binding site, and two proline residues for main chain bends, are conserved within the prokaryotic and eukaryotic sequences. The soybean full-length cDNA clone encodes a protein of 480 amino acids with a predicted size of 52.9 kD. The enzyme is highly expressed in young roots, but lower expression levels were observed in expanding tissues of the epicotyl and in young leaves. The expression pattern of the enzyme in different developmental stages strengthens the argument that UDP-glucose dehydrogenase is a key regulator for the availability of hemicelluose precursors.
Increased Resistance to Oxidative Stress in Transgenic Plants by Targeting Mannitol Biosynthesis to Chloroplasts
Authors: Shen B. , Jensen R. G. , Bohnert H. J. 
Published: July 2002

Abstract
To investigate the potential role of a polyol, mannitol, in oxidative stress protection, a bacterial mannitol-1-phosphate dehydrogenase gene was targeted to chloroplasts by the addition of an amino-terminal transit peptide. Transgenic tobacco (Nicotiana tabacum) lines accumulate mannitol at concentrations ranging from 2.5 to 7 [mu]mol/g fresh weight. Line BS1-31 accumulated approximately 100 mM mannitol in chloroplasts and was identical to the wild type in phenotype and photosynthetic performance. The presence of mannitol in chloroplasts resulted in an increased resistance to methyl viologen (MV)-induced oxidative stress, documented by the increased retention of chlorophyll in transgenic leaf tissue following MV treatment. In the presence of MV, isolated mesophyll cells of BS1-31 exhibited higher CO2 fixation than the wild type. When the hydroxyl radical probe dimethyl sulfoxide was introduced into cells, the initial formation rate of methane sulfinic acid was significantly lower in cells containing mannitol in the chloroplast compartment than in wild-type cells, indicating an increased hydroxyl radical-scavenging capacity in BS1-31 tobacco. We suggest that the chloroplast location of mannitol can supplement endogenous radical-scavenging mechanisms and reduce oxidative damage of cells by hydroxyl radicals.
Seed Germination of Arabidopsis thaliana phyA/phyB Double Mutants Is under Phytochrome Control
Authors: Poppe C. , Schafer E. 
Published: July 2002

Abstract
We examined the photocontrol of seed germination in the phyA/phyB double mutants of Arabidopsis thaliana seeds. Dormant phyA/phyB seeds showed a red/far-red light (R/FR)-reversible induction of seed germination. This suggests the involvement of at least one other phytochrome, phyC, D, and/or E, in controlling seed germination. We designated this spectrally active phytochrome in phyA/phyB as phyX. The full reversibility of the R-induced germination by subsequent FR pulses, and the observation that the response is reversible by FR, even after a 3-h R treatment, indicates that this phyX response belongs to the low-fluence-response type. Thus, this phyX response is functionally related to phyB-mediated responses. However, in contrast to phyB-controlled seed germination, this phyX-mediated response needs a prolonged imbibition period and exhibits reversibility kinetics different from that needed for phyB. Furthermore, this phyX response requires a prolonged irradiation time and shows a fluence rate response dependency, showing a similarity to the high irradiance response of photomorphogenesis. Thus, phyX, with regard to its control of seed germination, is a functionally new phytochrome that shares some characteristics of both phyA- and phyB-mediated responses.
Characterization of Regions within the N-Terminal 6-Kilodalton Domain of Phytochrome A That Modulate Its Biological Activity
Authors: Jordan E. T. , Marita J. M. , Clough R. C. , Vierstra R. D. 
Published: July 2002

Abstract
Phytochrome A (phyA) is a red/far-red (FR) light photoreceptor responsible for initiating numerous light-mediated plant growth and developmental responses, especially in FR light-enriched environments. We previously showed that the first 70 amino acids of the polypeptide contain at least two regions with potentially opposite functions (E.T. Jordan, J.R. Cherry, J.M. Walker, R.D. Vierstra [1996] Plant J 9: 243–257). One region is required for activity and correct apoprotein/chromophore interactions, whereas the second appears to regulate phytochrome activity. We have further resolved these functional regions by analysis of N-terminal deletion and alanine-scanning mutants of oat (Avena sativa) phyA in transgenic tobacco (Nicotiana tabacum). The results indicate that the region involved in chromophore/apoprotein interactions contains two separate segments (residues 25–33 and 50–62) also required for biological activity. The region that regulates phyA activity requires only five adjacent serines (Sers) (residues 8–12). Removal or alteration of these Sers generates a photoreceptor that increases the sensitivity of transgenic seedlings to red and FR light more than intact phyA. Taken together, these data identify three distinct regions in the N-terminal domain necessary for photoreceptor activity, and further define the Ser-rich region as an important site for phyA regulation.
Protein Repair L-Isoaspartyl Methyltransferase in Plants (Phylogenetic Distribution and the Accumulation of Substrate Proteins in Aged Barley Seeds)
Authors: Mudgett M. B. , Lowenson J. D. , Clarke S. 
Published: July 2002

Abstract
Protein L-isoaspartate (D-aspartate) O-methyltransferases (MTs; EC 2.1.1.77) can initiate the conversion of detrimental L-isoaspartyl residues in spontaneously damaged proteins to normal L-aspartyl residues. We detected this enzyme in 45 species from 23 families representing most of the divisions of the plant kingdom. MT activity is often localized in seeds, suggesting that it has a role in their maturation, quiescence, and germination. The relationship among MT activity, the accumulation of abnormal protein L-isoaspartyl residues, and seed viability was explored in barley (Hordeum vulgare cultivar Himalaya) seeds, which contain high levels of MT. Natural aging of barley seeds for 17 years resulted in a significant reduction in MT activity and in seed viability, coupled with increased levels of “unrepaired” L-isoaspartyl residues. In seeds heated to accelerate aging, we found no reduction of MT activity, but we did observe decreased seed viability and the accumulation of isoaspartyl residues. Among populations of accelerated aged seed, those possessing the highest levels of L-isoaspartyl-containing proteins had the lowest germination percentages. These results suggest that the MT present in seeds cannot efficiently repair all spontaneously damaged proteins containing altered aspartyl residues, and their accumulation during aging may contribute to the loss of seed viability.
Induction of Microbial Genes for Pathogenesis and Symbiosis by Chemicals from Root Border Cells
Authors: Zhu Y. , Pierson III L. S. , Hawes M. C. 
Published: July 2002

Abstract
Reporter strains of soil-borne bacteria were used to test the hypothesis that chemicals released by root border cells can influence the expression of bacterial genes required for the establishment of plant-microbe associations. Promoters from genes known to be activated by plant factors included virE, required for Agrobacterium tumefaciens pathogenesis, and common nod genes from Rhizobium leguminosarum bv viciae and Rhizobium meliloti, required for nodulation of pea (Pisum sativum) and alfalfa (Medicago sativum), respectively. Also included was phzB, an autoinducible gene encoding the biosynthesis of antibiotics by Pseudomonas aureofaciens. The virE and nod genes were activated to different degrees, depending on the source of border cells, whereas phzB activity remained unaffected. The homologous interaction between R. leguminosarum bv viciae and its host, pea, was examined in detail. Nod gene induction by border cells was dosage dependent and responsive to environmental signals. The highest levels of gene induction by pea (but not alfalfa) border cells occurred at low temperatures, when little or no bacterial growth was detected. Detached border cells cultured in distilled water exhibited increased nod gene induction (ini) in response to signals from R. leguminosarum bv viciae.
Characterization of DNA-Binding Proteins from Pea Mitochondria1
Authors: Hatzack Frank , Dombrowski Saskia , Brennicke Axel , Binder Stefan 
Published: July 2002

Abstract
We studied transcription initiation in the mitochondria of higher plants, with particular respect to promoter structures. Conserved elements of these promoters have been successfully identified by in vitro transcription systems in different species, whereas the involved protein components are still unknown. Proteins binding to double-stranded oligonucleotides representing different parts of the pea (Pisum sativum) mitochondrial atp9were analyzed by denaturation-renaturation chromatography and mobility-shift experiments. Two DNA-protein complexes were detected, which appeared to be sequence specific in competition experiments. Purification by hydroxyapatite, phosphocellulose, and reversed-phase high-pressure liquid chromatography separated two polypeptides with apparent molecular masses of 32 and 44 kD. Both proteins bound to conserved structures of the pea atp9 and the heterologous Oenothera berterianaatp1promoters and to sequences just upstream. Possible functions of these proteins in mitochondrial promoter recognition are discussed.