bluuebunny/crossref_metadata_2025 huggingface dataset:
Object-oriented music representation
Authors: TRAVIS POPE STEPHEN
Published: July 2002

There is a rich literature on the design of formal languages for music representation on computers. Over the last thirty years, several generations of software technology have been applied to this problem, including structured software engineering, artificial intelligence, and object-oriented (O-O) software technology. This article introduces the basic notions of O-O software technology, and investigates how these might be useful for music representation. In particular, the author's Smalltalk music object kernel (Smoke) music representation language is described and examples given that illustrate the most important of Smoke's features.
DETECTION AND MODELING OF REGRESSION PARAMETER VARIATION ACROSS FREQUENCIES
Authors: Tan Hui Boon , Ashley Richard
Published: July 2002

A simple technique for directly testing the parameters of a
time-series regression
model for instability across frequencies is
presented. The method can be implemented easily in the time domain, so that
parameter instability across frequency bands can be conveniently detected
and modeled in conjunction with other econometric features
of the problem at
hand, such as simultaneity, cointegration, missing observations, and
cross-equation restrictions. The usefulness of the new
technique is illustrated with an application to a cointegrated
consumption-income regression model, yielding a straightforward
test of the permanent income hypothesis.
Identification and characterization of yUAP/Sub2p, a yeast homolog of the essential human pre-mRNA splicing factor hUAP56
Authors: Zhang Meng , Green Michael R.
Published: July 2002

The human 56-kD U2AF65-associated protein (hUAP56), a member of the DExD/H box protein family of RNA-dependent ATPases, is required for the stable binding of U2 snRNP to the pre-mRNA branchpoint. Here we identify a highly conserved Saccharomyces cerevisiae homolog of hUAP56, yUAP/Sub2p. yUAP/Sub2p can be functionally substituted for by hUAP56 and, like its human counterpart, is an essential pre-mRNA splicing factor. yUAP/Sub2p is required for formation of the commitment complex, the precursor for U2 snRNP addition. In conjunction with previous studies, we conclude that at least two DExD/H box proteins, Prp5p and yUAP/Sub2p, mediate the U2 snRNP-branchpoint interaction.
Putative telomere-independent mechanisms of replicative aging reflect inadequate growth conditions
Authors: Ramirez Ruben D. , Morales Carmela P. , Herbert Brittney-Shea , Rohde Jeffrey M. , Passons Christina , Shay Jerry W. , Wright Woodring E.
Published: July 2002

Telomere shortening is the mechanism underlying replicative aging in fibroblasts. A variety of reports now claim that inactivation of the p16INK4a/pRB pathway is required in addition to telomere maintenance for the immortalization of cells such as skin keratinocytes and breast epithelial cells. We here show that the premature growth arrest of these cell types can be explained by an inadequate culture environment. Providing mesenchymal/epithelial interactions by cultivating the telomerase-expressing cells on feeder layers avoids the growth arrest associated with increased p16INK4a. These results do not support a telomere-independent mechanism of replicative aging.
Developmental regulation of transcription by a tissue-specific TAF homolog
Authors: Hiller Mark A. , Lin Ting-Yi , Wood Cricket , Fuller Margaret T.
Published: July 2002

Alternate forms of the general transcription machinery have been described in several tissues or cell types. However, the role of tissue-specific TBP-associated factors (TAFIIs) and other tissue-specific transcription components in regulating differential gene expression during development was not clear. Here we show that thecannonballgene ofDrosophilaencodes a cell type-specific homolog of a more ubiquitously expressed component of the general transcription factor TFIID.cannonballis required in vivo for high level transcription of a set of stage- and tissue-specific target genes during male gametogenesis. Regulation of transcription bycannonballis absolutely required for spermatogenesis, as null mutations block meiotic cell cycle progression and result in a complete failure of spermatid differentiation. Our results demonstrate that cell type-specific TAFIIs play an important role in developmental regulation of gene expression.
Asf1 links Rad53 to control of chromatin assembly
Authors: Hu Fenghua , Alcasabas Annette A. , Elledge Stephen J.
Published: July 2002

Yeast defective in the checkpoint kinase Rad53 fail to recover from transient DNA replication blocks and synthesize intact chromosomes. The effectors of Rad53 relevant to this recovery process are unknown. Here we report that overproduction of the chromatin assembly factor Asf1 can suppress the Ts phenotype of mrc1rad53double mutants and the HU sensitivity of rad53 mutants. Eliminating silencing also suppresses this lethality, further implicating chromatin structure in checkpoint function. We find that Asf1 and Rad53 exist in a dynamic complex that dissociates in response to replication blocks and DNA damage. Thus, checkpoint pathways directly regulate chromatin assembly to promote survival in response to DNA damage and replication blocks.
Tcf3 and Lef1 regulate lineage differentiation of multipotent stem cells in skin
Authors: Merrill Bradley J. , Gat Uri , DasGupta Ramanuj , Fuchs Elaine
Published: July 2002

In skin, multipotent stem cells generate the keratinocytes of the epidermis, sebaceous gland, and hair follicles. In this paper, we show that Tcf3 and Lef1 control these differentiation lineages. In contrast to Lef1, which requires Wnt signaling and stabilized β-catenin to express the hair-specific keratin genes and control hair differentiation, Tcf3 can act independently of its β-catenin interacting domain to suppress features of epidermal terminal differentiation, in which Tcf3 is normally shut off, and promote features of the follicle outer root sheath (ORS) and multipotent stem cells (bulge), the compartments which naturally express Tcf3. These aspects of Tcf3's action are dependent on its DNA binding and Groucho repressor-binding domains. In the absence of its β-catenin interacting domain, Lef1's behavior (ΔNLef1) seems to be markedly distinct from that of ΔNTcf3. ΔNLef1 does not suppress epidermal differentiation and promote ORS/bulge differentiation, but rather suppresses hair differentiation and gives rise to sebocyte differentiation. Taken together, these findings provide powerful evidence that the status of Tcf3/Lef complexes has a key role in controlling cell fate lineages in multipotent skin stem cells.
High-Throughput SNP Allele-Frequency Determination in Pooled DNA Samples by Kinetic PCR
Authors: Germer Søren , Holland Michael J. , Higuchi Russell
Published: July 2002

We have developed an accurate, yet inexpensive and high-throughput, method for determining the allele frequency of biallelic polymorphisms in pools of DNA samples. The assay combines kinetic (real-time quantitative) PCR with allele-specific amplification and requires no post-PCR processing. The relative amounts of each allele in a sample are quantified. This is performed by dividing equal aliquots of the pooled DNA between two separate PCR reactions, each of which contains a primer pair specific to one or the other allelic SNP variant. For pools with equal amounts of the two alleles, the two amplifications should reach a detectable level of fluorescence at the same cycle number. For pools that contain unequal ratios of the two alleles, the difference in cycle number between the two amplification reactions can be used to calculate the relative allele amounts. We demonstrate the accuracy and reliability of the assay on samples with known predetermined SNP allele frequencies from 5% to 95%, including pools of both human and mouse DNAs using eight different SNPs altogether. The accuracy of measuring known allele frequencies is very high, with the strength of correlation between measured and known frequencies having anr2 = 0.997. The loss of sensitivity as a result of measurement error is typically minimal, compared with that due to sampling error alone, for population samples up to 1000. We believe that by providing a means for SNP genotyping up to thousands of samples simultaneously, inexpensively, and reproducibly, this method is a powerful strategy for detecting meaningful polymorphic differences in candidate gene association studies and genome-wide linkage disequilibrium scans.
Drosophila Genomic Sequence Annotation Using the BLOCKS+ Database
Authors: Henikoff Jorja G. , Henikoff Steven
Published: July 2002

A simple and general homology-based method for gene finding was applied to the 2.9-Mb Drosophila melanogaster Adh region, the target sequence of the Genome Annotation Assessment Project (GASP). Each strand of the entire sequence was used as query of theBLOCKS+ database of conserved regions of proteins. This led to functional assignments for more than one-third of the genes and two-thirds of the transposons. Considering the enormous size of the query, the fact that only two false-positive matches were reported emphasizes the high selectivity of protein family-based methods for gene finding. We used the search results to improveBLOCKS+ by identifying compositionally biased blocks. Our results confirm that protein family databases can be used effectively in automated sequence annotation efforts.
Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays
Authors: Fan Jian-Bing , Chen Xiaoqiong , Halushka Marc K. , Berno Anthony , Huang Xiaohua , Ryder Thomas , Lipshutz Robert J. , Lockhart David J. , Chakravarti Aravinda
Published: July 2002

Large scale human genetic studies require technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. We describe a highly parallel method for genotyping single nucleotide polymorphisms (SNPs), using generic high-density oligonucleotide arrays that contain thousands of preselected 20-mer oligonucleotide tags. First, marker-specific primers are used in PCR amplifications of genomic regions containing SNPs. Second, the amplification products are used as templates in single base extension (SBE) reactions using chimeric primers with 3' complementarity to the specific SNP loci and 5' complementarity to specific probes, or tags, synthesized on the array. The SBE primers, terminating one base before the polymorphic site, are extended in the presence of labeled dideoxy NTPs, using a different label for each of the two SNP alleles, and hybridized to the tag array. Third, genotypes are deduced from the fluorescence intensity ratio of the two colors. This approach takes advantage of multiplexed sample preparation, hybridization, and analysis at each stage. We illustrate and test this method by genotyping 44 individuals for 142 human SNPs identified previously in 62 candidate hypertension genes. Because the hybridization results are quantitative, this method can also be used for allele-frequency estimation in pooled DNA samples.
From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins
Authors: Grishin Nick V. , Wolf Yuri I. , Koonin Eugene V.
Published: July 2002

Accumulation of complete genome sequences of diverse organisms creates new possibilities for evolutionary inferences from whole-genome comparisons. In the present study, we analyze the distributions of substitution rates among proteins encoded in 19 complete genomes (the interprotein rate distribution). To estimate these rates, it is necessary to employ another fundamental distribution, that of the substitution rates among sites in proteins (the intraprotein distribution). Using two independent approaches, we show that intraprotein substitution rate variability appears to be significantly greater than generally accepted. This yields more realistic estimates of evolutionary distances from amino-acid sequences, which is critical for evolutionary-tree construction. We demonstrate that the interprotein rate distributions inferred from the genome-to-genome comparisons are similar to each other and can be approximated by a single distribution with a long exponential shoulder. This suggests that a generalized version of the molecular clock hypothesis may be valid on genome scale. We also use the scaling parameter of the obtained interprotein rate distribution to construct a rooted whole-genome phylogeny. The topology of the resulting tree is largely compatible with those of global rRNA-based trees and trees produced by other approaches to genome-wide comparison.
An Assessment of Gene Prediction Accuracy in Large DNA Sequences
Authors: Guigó Roderic , Agarwal Pankaj , Abril Josep F. , Burset Moisés , Fickett James W.
Published: July 2002

One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of both methods and accuracy evaluation measures, most of the sequence sets in which the programs are tested are short genomic sequences, and there is concern that these accuracy measures may not extrapolate well to larger, more challenging data sets. Given the absence of experimentally verified large genomic data sets, we constructed a semiartificial test set comprising a number of short single-gene genomic sequences with randomly generated intergenic regions. This test set, which should still present an easier problem than real human genomic sequence, mimics the ∼200kb long BACs being sequenced. In our experiments with these longer genomic sequences, the accuracy ofGENSCAN, one of the most accurate ab initio gene prediction programs, dropped significantly, although its sensitivity remained high. Conversely, the accuracy of similarity-based programs, such as GENEWISE,PROCRUSTES, andBLASTX, was not affected significantly by the presence of random intergenic sequence, but depended on the strength of the similarity to the protein homolog. As expected, the accuracy dropped if the models were built using more distant homologs, and we were able to quantitatively estimate this decline. However, the specificities of these techniques are still rather good even when the similarity is weak, which is a desirable characteristic for driving expensive follow-up experiments. Our experiments suggest that though gene prediction will improve with every new protein that is discovered and through improvements in the current set of tools, we still have a long way to go before we can decipher the precise exonic structure of every gene in the human genome using purely computational methodology.
Long-Range Comparison of Human and Mouse SCL Loci: Localized Regions of Sensitivity to Restriction Endonucleases Correspond Precisely with Peaks of Conserved Noncoding Sequences
Authors: Göttgens Berthold , Gilbert James G.R. , Barton Linda M. , Grafham Darren , Rogers Jane , Bentley David R. , Green Anthony R.
Published: July 2002

Long-range comparative sequence analysis provides a powerful strategy for identifying conserved regulatory elements. The stem cell leukemia (SCL) gene encodes a bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis, and it displays a highly conserved expression pattern. We present here a detailed sequence comparison of 193 kb of the human SCL locus to 234 kb of the mouse SCL locus. Four new genes have been identified together with an ancient mitochondrial insertion in the human locus. The SCL gene is flanked upstream by theSIL gene and downstream by the MAP17 gene in both species, but the gene order is not collinear downstream fromMAP17. To facilitate rapid identification of candidate regulatory elements, we have developed a new sequence analysis tool (SynPlot) that automates the graphical display of large-scale sequence alignments. Unlike existing programs, SynPlot can display the locus features of more than one sequence, thereby indicating the position of homology peaks relative to the structure of all sequences in the alignment. In addition, high-resolution analysis of the chromatin structure of the mouse SCL gene permitted the accurate positioning of localized zones accessible to restriction endonucleases. Zones known to be associated with functional regulatory regions were found to correspond precisely with peaks of human/mouse homology, thus demonstrating that long-range human/mouse sequence comparisons allow accurate prediction of the extent of accessible DNA associated with active regulatory regions.
Prediction of the Archaeal Exosome and Its Connections with the Proteasome and the Translation and Transcription Machineries by a Comparative-Genomic Approach
Authors: Koonin Eugene V. , Wolf Yuri I. , Aravind L.
Published: July 2002

By comparing the gene order in the completely sequenced archaeal genomes complemented by sequence profile analysis, we predict the existence and protein composition of the archaeal counterpart of the eukaryotic exosome, a complex of RNAses, RNA-binding proteins, and helicases that mediates processing and 3′->5′ degradation of a variety of RNA species. The majority of the predicted archaeal exosome subunits are encoded in what appears to be a previously undetected superoperon. In Methanobacterium thermoautotrophicum, this predicted superoperon consists of 15 genes; in the Crenarchaea, Sulfolobus solfataricus andAeropyrum pernix, one and two of the genes from the superoperon, respectively, are relocated in the genome, whereas in other Euryarchaeota, the superoperon is split into a variable number of predicted operons and solitary genes. Methanococcus jannaschiipartially retains the superoperon, but lacks the three core exosome subunits, and in Halobacterium sp., the superoperon is divided into two predicted operons, with the same three exosome subunits missing. This suggests concerted gene loss and an alteration of the structure and function of the predicted exosome in theMethanococcus and Halobacterium lineages. Additional potential components of the exosome are encoded by partially conserved predicted small operons. Along with the orthologs of eukaryotic exosome subunits, namely an RNase PH and two RNA-binding proteins, the predicted archaeal exosomal superoperon also encodes orthologs of two protein subunits of RNase P. This suggests a functional and possibly a physical interaction between RNase P and the postulated archaeal exosome, a connection that has not been reported in eukaryotes. In a pattern of apparent gene loss complementary to that seen inMethanococcus and Halobacterium, Thermoplasma acidophilum lacks the RNase P subunits. Unexpectedly, the identified exosomal superoperon, in addition to the predicted exosome components, encodes the catalytic subunits of the archaeal proteasome, two ribosomal proteins and a DNA-directed RNA polymerase subunit. These observations suggest that in archaea, a tight functional coupling exists between translation, RNA processing and degradation, (apparently mediated by the predicted exosome) and protein degradation (mediated by the proteasome), and may have implications for cross-talk between these processes in eukaryotes.
A Combinatorial Partitioning Method to Identify Multilocus Genotypic Partitions That Predict Quantitative Trait Variation
Authors: Nelson M.R. , Kardia S.L.R. , Ferrell R.E. , Sing C.F.
Published: July 2002

Recent advances in genome research have accelerated the process of locating candidate genes and the variable sites within them and have simplified the task of genotype measurement. The development of statistical and computational strategies to utilize information on hundreds — soon thousands — of variable loci to investigate the relationships between genome variation and phenotypic variation has not kept pace, particularly for quantitative traits that do not follow simple Mendelian patterns of inheritance. We present here the combinatorial partitioning method (CPM) that examines multiple genes, each containing multiple variable loci, to identify partitions of multilocus genotypes that predict interindividual variation in quantitative trait levels. We illustrate this method with an application to plasma triglyceride levels collected on 188 males, ages 20–60 yr, ascertained without regard to health status, from Rochester, Minnesota. Genotype information included measurements at 18 diallelic loci in six coronary heart disease–candidate susceptibility gene regions: APOA1-C3-A4, APOB, APOE,LDLR, LPL, and PON1. To illustrate the CPM, we evaluated all possible partitions of two-locus genotypes into two to nine partitions (∼106 evaluations). We found that many combinations of loci are involved in sets of genotypic partitions that predict triglyceride variability and that the most predictive sets show nonadditivity. These results suggest that traditional methods of building multilocus models that rely on statistically significant marginal, single-locus effects, may fail to identify combinations of loci that best predict trait variability. The CPM offers a strategy for exploring the high-dimensional genotype state space so as to predict the quantitative trait variation in the population at large that does not require the conditioning of the analysis on a prespecified genetic model.
Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification
Authors: Dean Frank B. , Nelson John R. , Giesler Theresa L. , Lasken Roger S.
Published: July 2002

We describe a simple method of using rolling circle amplification to amplify vector DNA such as M13 or plasmid DNA from single colonies or plaques. Using random primers and φ29 DNA polymerase, circular DNA templates can be amplified 10,000-fold in a few hours. This procedure removes the need for lengthy growth periods and traditional DNA isolation methods. Reaction products can be used directly for DNA sequencing after phosphatase treatment to inactivate unincorporated nucleotides. Amplified products can also be used for in vitro cloning, library construction, and other molecular biology applications.
Chronic, Severe Hypertension Does Not Impair Spatial Learning and Memory in Sprague-Dawley Rats
Authors: Kadish Inga , van Groen Thomas , Wyss J. Michael
Published: July 2002

This study tested the hypothesis that long-term hypertension impairs spatial learning and memory in rats. In 6-wk-old Sprague-Dawley rats, chronic hypertension was induced by placing one of three sizes of stainless steel clips around the descending aorta (above the renal artery), resulting in a 20–80-mm Hg increase of arterial pressure in all arteries above the clip, that is, the upper trunk and head. Ten months later, the rats were tested for 5 d in a repeated-acquisition water maze task, and on the fifth day, they were tested in a probe trial; that is, there was no escape platform present. At the end of the testing period, the nonsurgical and sham control groups had similar final escape latencies (16 ± 4 sec and 23 ± 9 sec, respectively) that were not significantly different from those of the three hypertensive groups. Rats with mild hypertension (140–160 mm Hg) had a final escape latency of 25 ± 6 sec, whereas severely hypertensive rats (170–199 mm Hg) had a final escape latency of 21 ± 7 sec and extremely hypertensive rats (>200 Hg) had a final escape latency of 19 ± 5 sec. All five groups also displayed a similar preference for the correct quadrant in the probe trial. Together, these data suggest that sustained, severe hypertension for over 10 mo is not sufficient to impair spatial learning and memory deficits in otherwise normal rats.
A Nitric Oxide-Independent and β-Adrenergic Receptor-Sensitive Form of Metaplasticity Limits θ-Frequency Stimulation-Induced LTP in the Hippocampal CA1 Region
Authors: Moody Teena D. , Carlisle Holly J. , O'Dell Thomas J.
Published: July 2002

The induction of long-term potentiation (LTP) and long-term depression (LTD) at excitatory synapses in the hippocampus can be strongly modulated by patterns of synaptic stimulation that otherwise have no direct effect on synaptic strength. Likewise, patterns of synaptic stimulation that induce LTP or LTD not only modify synaptic strength but can also induce lasting changes that regulate how synapses will respond to subsequent trains of stimulation. Collectively known as metaplasticity, these activity-dependent processes that regulate LTP and LTD induction allow the recent history of synaptic activity to influence the induction of activity-dependent changes in synaptic strength and may thus have an important role in information storage during memory formation. To explore the cellular and molecular mechanisms underlying metaplasticity, we investigated the role of metaplasticity in the induction of LTP by υ-frequency (5-Hz) synaptic stimulation in the hippocampal CA1 region. Our results show that brief trains of υ-frequency stimulation not only induce LTP but also activate a process that inhibits the induction of additional LTP at potentiated synapses. Unlike other forms of metaplasticity, the inhibition of LTP induction at potentiated synapses does not appear to arise from activity-dependent changes in NMDA receptor function, does not require nitric oxide signaling, and is strongly modulated by β-adrenergic receptor activation. Together with previous findings, our results indicate that mechanistically distinct forms of metaplasticity regulate LTP induction and suggest that one way modulatory transmitters may act to regulate synaptic plasticity is by modulating metaplasticity.
Visual Input Regulates Circuit Configuration in Courtship Conditioning of Drosophila melanogaster
Authors: Joiner Mei-ling A. , Griffith Leslie C.
Published: July 2002

Courtship and courtship conditioning are behaviors that are regulated by multiple sensory inputs, including chemosensation and vision. Globally inhibiting CaMKII activity inDrosophila disrupts courtship plasticity while leaving visual and chemosensory perception intact. Light has been shown to modulate CaMKII-dependent memory formation in this paradigm and the circuitry for the nonvisual version of this behavior has been investigated. In this paradigm, volatile and tactile pheromones provide the primary driving force for courtship, and memory formation is dependent upon intact mushroom bodies and parts of the central complex. In the present study, we use the GAL4/UAS binary expression system to define areas of the brain that require CaMKII for modulation of courtship conditioning in the presence of visual, as well as chemosensory, information. Visual input suppressed the ability of mushroom body- and central complex-specific CaMKII inhibition to disrupt memory formation, indicating that the cellular circuitry underlying this behavior can be remodeled by changing the driving sensory modality. These findings suggest that the potential for plasticity in courtship behavior is distributed among multiple biochemically and anatomically distinct cellular circuits.
Differential Transcription of Phycobiliprotein Components in Rhodella violacea (Light and Nitrogen Effects on the 33-Kilodalton Phycoerythrin Rod Linker Polypeptide, Phycocyanin, and Phycoerythrin Transcripts)
Authors: Lichtle C. , Garnier F. , Bernard C. , Zabulon G. , Spilar A. , Thomas J. C. , Etienne A. L.
Published: July 2002

In Rhodella violacea phycoerythrin (PE) has two transcripts, a premessenger and a mature messenger (the gene contains an intron). Phycocyanin, which is plastid-encoded, and the 33-kD PE rod linker polypeptide, which is nuclear-encoded, have only one transcript. The PE premessenger had a rapid turnover; mature transcripts were stable in the light and more stable in the dark. In the presence of rifampicin, cells that shifted from dark to light exhibited an active translation of preexisting transcripts. There are indications of a modulation of the nuclear genome expression by the chloroplast; it may involve an unstable, plastid-encoded translational activator. All transcripts disappeared rapidly during nitrogen starvation. If nitrogen addition was carried out in the dark, active transcription and translation resumed as in light conditions, but ceased after 2 d. Both nitrogen and light were required for a total recovery after nitrogen starvation. Compared with the transcripts of phycobilisome components studied so far in cyanobacteria and Rhodophyceae, the mature transcripts of R. violacea are very stable when nitrogen is not limiting. The unstable PE premessenger is a good indicator of active transcription. This organism is therefore an interesting model to study the regulation of gene expression and the interactions between chloroplastic and nuclear genomes.
Induction of Phloem Unloading in Arabidopsis thaliana Roots by the Parasitic Nematode Heterodera schachtii
Authors: Bockenhoff A. , Prior DAM. , Grundler FMW. , Oparka K. J.
Published: July 2002

Phloem unloading of both the fluorescent probe carboxyfluorescein (CF) and 14C-labeled solutes was induced in Arabidopsis thaliana L. roots by the parasitic nematode Heterodera schachtii Schmidt. Confocal laser scanning microscopy demonstrated that anomalous unloading of CF from the sieve element companion cell complexes occurred specifically into the syncytium, the nematode- induced feeding structure located within the stele of the root. From this syncytial complex of modified root cells, both fluorescent and radioactive labels were withdrawn by feeding nematodes. Movement of CF was unidirectional from the phloem to the syncytium. A range of low-molecular-weight fluorescent probes (including CF) microinjected into the syncytium stayed in this structure, demonstrating that it is symplastically isolated from the surrounding root tissue. The mechanism of unloading in this host-pathogen relationship therefore appears to be apoplastic. Our results provide unequivocal evidence that sedentary cyst-forming nematodes have direct access to phloem-derived solutes.
Genetic and Developmental Control of Nuclear Accumulation of COP1, a Repressor of Photomorphogenesis in Arabidopsis
Authors: von Arnim A. G. , Osterlund M. T. , Kwok S. F. , Deng X. W.
Published: July 2002

Using a β-glucuronidase (GUS) reporter-COP1 fusion transgene, it was shown previously that Arabidopsis COP1 acts within the nucleus as a repressor of seedling photomorphogenic development and that light inactivation of COP1 was accompanied by a reduction of COP1 nuclear abundance (A.G. von Arnim, X.-W. Deng [1994] Cell 79: 1035–1045). Here we report that the GUS-COP1 fusion transgene can completely rescue the defect of cop1 mutations and thus is fully functional during seedling development. The kinetics of GUS-COP1 relocalization in a cop1 null mutant background during dark/light transitions imply that the regulation of the functional nuclear COP1 level plays a role in stably maintaining a committed seedling's developmental fate rather than in causing such a commitment. Analysis of GUS-COP1 cellular localization in mutant hypocotyls of all other pleiotropic COP/DET/FUS loci revealed that nuclear localization of GUS-COP1 was diminished under both dark and light conditions in all mutants tested, whereas nuclear localization was not affected in the less pleiotropic cop4 mutant. Using both the brassinosteroid-deficient mutant det2 and brassinosteroid treatment of wild-type seedlings, we have demonstrated that brassinosteroid does not control the hypocotyl cell elongation through regulating nuclear localization of COP1. The growth regulator cytokinin, which also dramatically reduced hypocotyl cell elongation in the absence of light, did not prevent GUS-COP1 nuclear localization in dark-grown seedlings. Our results suggest that all of the previously characterized pleiotropic COP/DET/FUS loci are required for the proper nuclear localization of the COP1 protein in the dark, whereas the less pleiotropic COP/DET loci or plant regulators tested are likely to act either downstream of COP1 or by independent pathways.
Osmotic Stress Induces Expression of Choline Monooxygenase in Sugar Beet and Amaranth1
Authors: Russell Brenda L. , Rathinasabapathi Bala , Hanson Andrew D.
Published: July 2002

Choline monooxygenase (CMO) catalyzes the committing step in the synthesis of glycine betaine, an osmoprotectant accumulated by many plants in response to salinity and drought. To investigate how these stresses affect CMO expression, a spinach (Spinacia oleracea L., Chenopodiaceae) probe was used to isolate CMO cDNAs from sugar beet (Beta vulgarisL., Chenopodiaceae), a salt- and drought-tolerant crop. The deduced beet CMO amino acid sequence comprised a transit peptide and a 381-residue mature peptide that was 84% identical (97% similar) to that of spinach and that showed the same consensus motif for coordinating a Rieske-type [2Fe-2S] cluster. A mononuclear Fe-binding motif was also present. When water was withheld, leaf relative water content declined to 59% and the levels of CMO mRNA, protein, and enzyme activity rose 3- to 5-fold; rewatering reversed these changes. After gradual salinization (NaCl:CaCl2 = 5.7:1, mol/mol), CMO mRNA, protein, and enzyme levels in leaves increased 3- to 7-fold at 400 mm salt, and returned to uninduced levels when salt was removed. Beet roots also expressed CMO, most strongly when salinized. Salt-inducible CMO mRNA, protein, and enzyme activity were readily detected in leaves of Amaranthus caudatus L. (Amaranthaceae). These data show that CMO most probably has a mononuclear Fe center, is inducibly expressed in roots as well as in leaves of Chenopodiaceae, and is not unique to this family.
Two Structurally Similar Maize Cytosolic Superoxide Dismutase Genes,Sod4andSod4A, Respond Differentially to Abscisic Acid and High Osmoticum1
Authors: Guan Lingqiang , Scandalios John G.
Published: July 2002

The maize (Zea mays) superoxide dismutase genes Sod4 and Sod4Aare highly similar in structure but each responds differentially to environmental signals. We examined the effects of the hormone abscisic acid (ABA) on the developmental response of Sod4 andSod4A. Although both Sod4 andSod4A transcripts accumulate during late embryogenesis, only Sod4 is up-regulated by ABA and osmotic stress. Accumulation of Sod4 transcript in response to osmotic stress is a consequence of increased endogenous ABA levels in developing embryos. Sod4 mRNA is up-regulated by ABA inviviparous-1 mutant embryos. Sod4transcript increases within 4 h with ABA not only in developing embryos but also in mature embryos and in young leaves.Sod4A transcript is up-regulated by ABA only in young leaves, but neither Sod4 nor Sod4Atranscripts changed in response to osmotic stress. Our data suggest that in leaves Sod4 and Sod4A may respond to ABA and osmotic stress via alternate pathways. Since theSod genes have a known function, we hypothesize that the increase in Sod mRNA in response to ABA is due in part to ABA-mediated metabolic changes leading to changes in oxygen free radical levels, which in turn lead to the induction of the antioxidant defense system.
Biosynthesis of the Monoterpenes Limonene and Carvone in the Fruit of Caraway1
Authors: Bouwmeester Harro J. , Gershenzon Jonathan , Konings Maurice C.J.M. , Croteau Rodney
Published: July 2002

The biosynthesis of the monoterpenes limonene and carvone in the fruit of caraway (Carum carvi L.) proceeds from geranyl diphosphate via a three-step pathway. First, geranyl diphosphate is cyclized to (+)-limonene by a monoterpene synthase. Second, this intermediate is stored in the essential oil ducts without further metabolism or is converted by limonene-6-hydroxylase to (+)-trans-carveol. Third, (+)-trans-carveol is oxidized by a dehydrogenase to (+)-carvone. To investigate the regulation of monoterpene formation in caraway, we measured the time course of limonene and carvone accumulation during fruit development and compared it with monoterpene biosynthesis from [U-14C]Suc and the changes in the activities of the three enzymes. The activities of the enzymes explain the profiles of monoterpene accumulation quite well, with limonene-6-hydroxylase playing a pivotal role in controlling the nature of the end product. In the youngest stages, when limonene-6-hydroxylase is undetectable, only limonene was accumulating in appreciable levels. The appearance of limonene-6-hydroxylase correlates closely with the onset of carvone accumulation. At later stages of fruit development, the activities of all three enzymes declined to low levels. Although this correlates closely with a decrease in monoterpene accumulation, the latter may also be the result of competition with other pathways for substrate.
A Functional Calvin Cycle Is Not Indispensable for the Light Activation of C4Phosphoenolpyruvate Carboxylase Kinase and Its Target Enzyme in the Maize Mutantbundle sheath defective2-mutable11
Authors: Smith Lucy H. , Langdale Jane A. , Chollet Raymond
Published: July 2002

We used a pale-green maize (Zea mays L.) mutant that fails to accumulate ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to test the working hypothesis that the regulatory phosphorylation of C4 phosphoenolpyruvate carboxylase (PEPC) by its Ca2+-insensitive protein-serine/threonine kinase (PEPC kinase) in the C4mesophyll cytosol depends on cross-talk with a functional Calvin cycle in the bundle sheath. Wild-type (W22) and bundle sheath defective2-mutable1 (bsd2-m1) seeds were grown in a controlled environment chamber at 100 to 130 μmol m−2 s−1 photosynthetic photon flux density, and leaf tissue was harvested 11 d after sowing, following exposure to various light intensities. Immunoblot analysis showed no major difference in the amount of polypeptide present for several mesophyll- and bundle-sheath-specific photosynthetic enzymes apart from Rubisco, which was either completely absent or very much reduced in the mutant. Similarly, leaf net CO2-exchange analysis and in vitro radiometric Rubisco assays showed that no appreciable carbon fixation was occurring in the mutant. In contrast, the sensitivity of PEPC to malate inhibition in bsd2-m1 leaves decreased significantly with an increase in light intensity, and there was a concomitant increase in PEPC kinase activity, similar to that seen in wild-type leaf tissue. Thus, although bsd2-m1 mutant plants lack an operative Calvin cycle, light activation of PEPC kinase and its target enzyme are not grossly perturbed.
Mannose Inhibits Arabidopsis Germination via a Hexokinase-Mediated Step1
Authors: Pego Jónatas V. , Weisbeek Peter J. , Smeekens Sjef C.M.
Published: July 2002

Low concentrations of the glucose (Glc) analog mannose (Man) inhibit germination of Arabidopsis seeds. Man is phosphorylated by hexokinase (HXK), but the absence of germination was not due to ATP or phosphate depletion. The addition of metabolizable sugars reversed the Man-mediated inhibition of germination. Carbohydrate-mediated regulation of gene expression involving a HXK-mediated pathway is known to be activated by Glc, Man, and other monosaccharides. Therefore, we investigated whether Man blocks germination through this system. By testing other Glc analogs, we found that 2-deoxyglucose, which, like Man, is phosphorylated by HXK, also blocked germination; no inhibition was observed with 6-deoxyglucose or 3-O-methylglucose, which are not substrates for HXK. Since these latter two sugars are taken up at a rate similar to that of Man, uptake is unlikely to be involved in the inhibition of germination. Furthermore, we show that mannoheptulose, a specific HXK inhibitor, restores germination of seeds grown in the presence of Man. We conclude that HXK is involved in the Man-mediated repression of germination of Arabidopsis seeds, possibly via energy depletion.
The Mechanism of Rhythmic Ethylene Production in Sorghum. The Role of Phytochrome B and Simulated Shading1
Authors: Finlayson Scott A. , Lee In-Jung , Mullet John E. , Morgan Page W.
Published: July 2002

Mutant sorghum (Sorghum bicolor [L.] Moench) deficient in functional phytochrome B exhibits reduced photoperiodic sensitivity and constitutively expresses a shade-avoidance phenotype. Under relatively bright, high red:far-red light, ethylene production by seedlings of wild-type and phytochrome B-mutant cultivars progresses through cycles in a circadian rhythm; however, the phytochrome B mutant produces ethylene peaks with approximately 10 times the amplitude of the wild type. Time-course northern blots show that the mutant's abundance of the 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase mRNA SbACO2 is cyclic and is commensurate with ethylene production, and that ACC oxidase activity follows the same pattern. Both SbACO2 abundance and ACC oxidase activity in the wild-type plant are very low under this regimen. ACC levels in the two cultivars did not demonstrate fluctuations coincident with the ethylene produced. Simulated shading caused the wild-type plant to mimic the phenotype of the mutant and to produce high amplitude rhythms of ethylene evolution. The circadian feature of the ethylene cycle is conditionally present in the mutant and absent in the wild-type plant under simulated shading. SbACO2 abundance in both cultivars demonstrates a high-amplitude diurnal cycle under these conditions; however, ACC oxidase activity, although elevated, does not exhibit a clear rhythm correlated with ethylene production. ACC levels in both cultivars show fluctuations corresponding to the ethylene rhythm previously observed. It appears that at least two separate mechanisms may be involved in generating high-amplitude ethylene rhythms in sorghum, one in response to the loss of phytochrome B function and another in response to shading.
Fluxes of Reserve-Derived and Currently Assimilated Carbon and Nitrogen in Perennial Ryegrass Recovering from Defoliation. The Regrowing Tiller and Its Component Functionally Distinct Zones1
Authors: Schnyder Hans , de Visser Ries
Published: July 2002

The quantitative significance of reserves and current assimilates in regrowing tillers of severely defoliated plants of perennial ryegrass (Lolium perenneL.) was assessed by a new approach, comprising13C/12C and 15N/14N steady-state labeling and separation of sink and source zones. The functionally distinct zones showed large differences in the kinetics of currently assimilated C and N. These are interpreted in terms of ”substrate” and ”tissue” flux among zones and C and N turnover within zones. Tillers refoliated rapidly, although C and N supply was initially decreased. Rapid refoliation was associated with (a) transient depletion of water-soluble carbohydrates and dilution of structural biomass in the immature zone of expanding leaves, (b) rapid transition to current assimilation-derived growth, and (c) rapid reestablishment of a balanced C:N ratio in growth substrate. This balance (C:N, approximately 8.9 [w/w] in new biomass) indicated coregulation of growth by C and N supply and resulted from complementary fluxes of reserve- and current assimilation-derived C and N. Reserves were the dominant N source until approximately 3 d after defoliation. Amino-C constituted approximately 60% of the net influx of reserve C during the first 2 d. Carbohydrate reserves were an insignificant source of C for tiller growth after d 1. We discuss the physiological mechanisms contributing to defoliation tolerance.
Mtsym6, a Gene ConditioningSinorhizobium Strain-Specific Nitrogen Fixation inMedicago truncatula
Authors: Tirichine Leı̈la , de Billy Françoise , Huguet Thierry
Published: July 2002

The availability of a wide range of independent lines for the annual medic Medicago truncatula led us to search for natural variants in the symbiotic association with Sinorhizobium meliloti. Two homozygous lines, Jemalong 6 and DZA315.16, originating from an Australian cultivar and a natural Algerian population, respectively, were inoculated with two wild-type strains ofS. meliloti, RCR2011 and A145. Both plant lines formed nitrogen-fixing (effective) nodules with the RCR2011 strain. However, the A145 strain revealed a nitrogen fixation polymorphism, establishing an effective symbiosis (Nod+Fix+) with DZA315.16, whereas only small, white, non-nitrogen fixing nodules (Nod+Fix−) were elicited on Jemalong 6. Cytological studies demonstrated that these non-fixing nodules are encircled by an endodermis at late stages of development, with no visible meristem, and contain hypertrophied and autofluorescent infection threads, suggesting the induction of plant defense reactions. The non-fixing phenotype is independent of growth conditions and determined by a single recessive allele (Mtsym6), which is located on linkage group 8.
Tissue-Specific and Developmental Pattern of Expression of the Rice sps1 Gene
Authors: Chávez-Bárcenas Ana T. , Valdez-Alarcón Juan J. , Martı́nez-Trujillo Miguel , Chen Lilly , Xoconostle-Cázares Beatriz , Lucas William J. , Herrera-Estrella Luis
Published: July 2002

Sucrose-phosphate synthase (SPS) is one of the key regulatory enzymes in carbon assimilation and partitioning in plants. SPS plays a central role in the production of sucrose in photosynthetic cells and in the conversion of starch or fatty acids into sucrose in germinating seeds. To explore the mechanisms that regulate the tissue-specific and developmental distribution of SPS, the expression pattern of rice (Oryza sativa) sps1 (GenBank accession no. U33175) was examined by in situ reverse transcriptase-polymerase chain reaction and the expression directed by the sps1promoter using the β-glucuronidase reporter gene. It was found that the expression of the rice sps1 gene is limited to mesophyll cells in leaves, the scutellum of germinating seedlings, and pollen of immature inflorescences. During leaf development, thesps1 promoter directs a basipetal pattern of expression that coincides with the distribution of SPS activity during the leaf sink-to-source transition. It was also found that during the vegetative part of the growth cycle, SPS expression and enzymatic activity are highest in the youngest fully expanded leaf. Additionally, it was observed that the expression of the sps1 promoter is regulated by light and dependent on plastid development in photosynthetic tissues, whereas expression in scutellum is independent of both light and plastid development.
Local and Systemic Induction of Two Defense-Related Subtilisin-Like Protease Promoters in Transgenic Arabidopsis Plants. Luciferin Induction of PR Gene Expression
Authors: Jordá Lucia , Vera Pablo
Published: July 2002

Following a pathogenic attack, plants are able to mount a defense response with the coordinated activation of a battery of defense-related genes. In this study we have characterized the mode of expression of the P69B and P69C genes from tomato (Lycopersicon esculentum Mill.), which encodes two closely related subtilisin-like proteases associated with the defense response. We have compared the mode of gene regulation in heterologous transgenic Arabidopsis plants harboring promoter-β-glucuronidase (GUS) and promoter-luciferase (LUC) gene fusions for these two genes. These studies revealed that the P69B and P69C promoters are induced by salicylic acid as well as during the course of both a compatible and an incompatible interaction with Pseudomonas syringae. Furthermore, P69B andP69C expression takes place in both the local and the distal (noninoculated) leaves upon inoculation with bacteria but following different and unique tissue-specific patterns of expression that are also different to that described for most other classicalPR genes. Also, we report that luciferin, the substrate for the reporter luciferase (LUC) gene, is able to activate expression of PR genes, and this may pose a problem when using this gene reporter system in studies related to plant defense.