bluuebunny/crossref_metadata_2025 huggingface dataset:
Influences of central metal ions on the electroluminescene and transport properties of tris-(8-hydroxyquinoline) metal chelates
Authors: Chen B. J. , Sun X. W. , Li Y. K.
Published: May 2003

A series of tris-(8-hydroxyquinoline) metal chelates with central metal ions of Al3+, Ga3+, and In3+ was synthesized, characterized, and used in organic electroluminescent devices. The ionization potential and optical band gap of the three chelates were measured by ultraviolet photoelectron spectroscopy and ultraviolet-visible spectrum, respectively. Two types of devices, with configurations of indium tin oxide (ITO)/N,N′-diphenyl-N,N′-(3-methylphenyl)-1,1′-biphenyl-4,4′-diamine (TPD) (80 nm)/Mq3 (80 nm)/Mg:Ag (200 nm) and ITO/TPD (60 nm)/TPD:rubrene (3%) (20 nm)/Mq3 (80 nm)/Mg:Ag (200 nm) (M=Al, Ga, or In), were fabricated and characterized based on these metal chelates. In the first type of configuration, the metal chelates were used as both the emitter and the electron-transporting layer. In the second type of configuration, the metal chelates were believed to only act as electron-transporting layer. As the central ion changed, both the luminescence and the carrier transport properties of the metal chelates were changed. By comparing the performance of the two types of devices, we found that as the size of the metal ion increased, the luminance efficiency decreased and the electron mobility increased.
Identification of hexagonal polycrystal in epitaxially grown InN by synchrotron x-ray diffraction and near-edge x-ray absorption fine structure spectroscopy
Authors: Lee Ik Jae , Shin Hyun-Joon , Chang Suk Sang , Lee Min Kyu , Kim Hyung-Kook
Published: May 2003

The structures and crystallographic orientations of indium nitride films of varying thicknesses on sapphire(0001) were investigated using high-resolution synchrotron x-ray scattering and angle-dependent near-edge x-ray absorption fine structure (NEXAFS) spectroscopy with linearly polarized x rays. The x-ray scattering data showed that epitaxially grown InN films have a polycrystalline structure when their thickness is greater than 3000 Å. The N 1s NEXAFS spectra of thin films have a strong polarization-dependent spectral feature resulting from the preferred c-axis orientation. This polarization dependence decreases as the film thickness increases and is not present in the spectra of films that are more than 3000 Å thick. These results indicate that the c axis has a preferred orientation in thin films, but that this orientation is random in thick films, which have a polycrystalline hexagonal structure.
Adhesins encoded by the gingipain genes of Porphyromonas gingivalis are responsible for co-aggregation with Prevotella intermedia
Authors: Kamaguchi Arihide , Ohyama Tohru , Sakai Eiko , Nakamura Reiko , Watanabe Toshihiro , Baba Hisae , Nakayama Koji
Published: May 2003

Co-aggregation among bacterial cells caused by the adherence of one bacterial species to another is a potential colonization mechanism. Several putative aggregation factors for co-aggregation betweenPorphyromonas(Por.)gingivalisandPrevotella(Pre.)intermediawere partially purified fromPor. gingivalisvesicles by gel filtration and affinity chromatography. Antisera against the aggregation factors were made. Analysis using these antisera revealed that 18 and 44 kDa proteins might be responsible forPor. gingivalisvesicle-mediated aggregation ofPre. intermedia. Using antiserum against the 18 kDa protein, the DNA region encoding it was cloned fromPor. gingivalisgenomic DNA. Sequence analysis revealed that the DNA region was located within thergpAandkgpgenes, encoding Arg-gingipain (Rgp) and Lys-gingipain (Kgp), respectively, and it encoded non-catalytic adhesin domain regions, namely a C-terminal portion of HGP15, the entire HGP17 sequence and an N-terminal portion of HGP27. A portion of the DNA sequence was also found in the haemagglutinin A (hagA) gene. A recombinant glutathioneS-transferase (GST)–HGP17 fusion protein reacted to antiserum against the 18 kDa protein andPre. intermediacells could adhere to GST–HGP17-conjugated Sepharose 4B beads, indicating that the HGP17 domain protein is responsible forPor. gingivalisvesicle-mediated aggregation ofPre. intermedia.
Synergistic inhibition of APC/C by glucose and activated Ras proteins can be mediated by each of the Tpk1–3 proteins in Saccharomyces cerevisiae
Authors: Bolte Melanie , Dieckhoff Patrick , Krause Cindy , Braus Gerhard H. , Irniger Stefan
Published: May 2003

Proteolysis triggered by the anaphase-promoting complex/cyclosome (APC/C) is essential for the progression through mitosis. APC/C is a highly conserved ubiquitin ligase whose activity is regulated during the cell cycle by various factors, including spindle checkpoint components and protein kinases. The cAMP-dependent protein kinase (PKA) was identified as negative regulator of APC/C in yeast and mammalian cells. In the yeastSaccharomyces cerevisiae, PKA activity is induced upon glucose addition or by activated Ras proteins. This study shows that glucose and the activated Ras2Val19protein synergistically inhibit APC/C function via the cAMP/PKA pathway in yeast. Remarkably, Ras2 proteins defective in the interaction with adenylate cyclase fail to influence APC/C, implying that its function is regulated exclusively by PKA, but not by alternative Ras pathways. Furthermore, it is shown that the three PKAs in yeast, Tpk1, Tpk2 and Tpk3, have redundant functions in regulating APC/C in response to glucose medium. Single or double deletions ofTPKgenes did not prevent inhibition of APC/C, suggesting that each of the Tpk proteins can take over this function. However, Tpk2 seems to inhibit APC/C function more efficiently than Tpk1 and Tpk3. Finally, evidence is provided that Cdc20 is involved in APC/C regulation by the cAMP/PKA pathway.
Modification of the signal sequence cleavage site of listeriolysin O does not affect protein secretion but impairs the virulence of Listeria monocytogenes
Authors: Lety Marie-Annick , Frehel Claude , Beretti Jean-luc , Berche Patrick , Charbit Alain
Published: May 2003

Listeriolysin O (LLO, hly-encoded), a major virulence factor secreted by the bacterial pathogen Listeria monocytogenes, is synthesized as a precursor of 529 residues. To impair LLO secretion, the four residues of the predicted signal sequence cleavage site (EA-KD) were deleted and the mutant LLO protein was expressed in a hly-negative derivative of L. monocytogenes. Unexpectedly, the mutant protein was secreted in normal amounts in the culture supernatant and was fully haemolytic. N-terminal sequencing of the secreted LLO molecule revealed that N-terminal processing of the preprotein occurred three residues downstream of the natural cleavage site. L. monocytogenes expressing this truncated LLO showed a reduced capacity to disrupt the phagosomal membranes of bone marrow macrophages and of hepatocytes; and the mutant strain showed a 100-fold decrease in virulence in the mouse model. These results suggest that the first N-terminal residues of mature LLO participate directly in phagosomal escape and bacterial infection.
Calcium release from Synechocystis cells induced by depolarization of the plasma membrane: MscL as an outward Ca2+ channel
Authors: Nazarenko Lyudmila V. , Andreev Igor M. , Lyukevich Alexander A. , Pisareva Tatiana V. , Los Dmitry A.
Published: May 2003

Cells of the cyanobacteriumSynechocystissp. PCC 6803 are equipped with a mechanosensitive ion channel MscL that is located in their plasma membrane. However, the exact function of the channel in this freshwater cyanobacterium is unknown. This study shows that cells ofSynechocystisare capable of releasing Ca2+in response to depolarization of the plasma membrane by the K+ionophore valinomycin in the presence of K+or by tetraphenylphosphonium (TPP+). A fluorescent dye, diS-C3-(5), sensitive to membrane potential and the metallochromic Ca2+indicator arsenazo III were used to follow the plasma membrane depolarization and the Ca2+release, respectively. The Ca2+release from wild-type cells was temperature-dependent and it was strongly inhibited by the Ca2+channel blocker verapamil and by the mechanosensitive channel blocker amiloride. In MscL-deficient cells, Ca2+release was about 50 % of that from the wild-type cells. The mutant cells had lost temperature sensitivity of Ca2+release completely. However, verapamil and amiloride inhibited Ca2+release from these cells in same manner as in the wild-type cells. This suggests the existence of additional Ca2+transporters inSynechocystis, probably of a mechanosensitive nature. Evidence for the putative presence of intracellular Ca2+stores in the cells was obtained by following the increase in fluorescence intensity of the Ca2+indicator chlortetracycline. These results suggest that the MscL ofSynechocystismight operate as a verapamil/amiloride-sensitive outward Ca2+channel that is involved in the plasma-membrane depolarization-induced Ca2+release from the cells under temperature stress conditions.
Limited regions of homology between linear and circular plasmids encoding methylenomycin biosynthesis in two independently isolated streptomycetes
Authors: Yamasaki Masayuki , Ikuto Yasuhiro , Ohira Akiyo , Chater Keith , Kinashi Haruyasu
Published: May 2003

pSV1 is a plasmid in Streptomyces violaceoruber SANK95570 that carries the methylenomycin biosynthetic (mmy) gene cluster. An ordered cosmid map and an EcoRI map have been constructed for pSV1, confirming that pSV1 is a 163 kb circular plasmid. The mmy gene cluster has been found on three different replicon structures; the circular plasmid pSV1, the 356 kb linear plasmid SCP1 and, via SCP1 integration, the linear chromosome of Streptomyces coelicolor A3(2). Comparison of pSV1 and SCP1 sequences revealed that the two plasmids have homology to each other only around the mmy and parAB regions, eliminating models in which pSV1 was generated by circularization of SCP1 or vice versa. It is likely that the mmy gene cluster was horizontally transferred as a set together with the parAB region in the comparatively recent evolutionary past.
Genetic relatedness and phenotypic characteristics of Treponema associated with human periodontal tissues and ruminant foot disease
Authors: Edwards Andrew M. , Dymock David , Woodward Martin J. , Jenkinson Howard F.
Published: May 2003

Treponemahave been implicated recently in the pathogenesis of digital dermatitis (DD) and contagious ovine digital dermatitis (CODD) that are infectious diseases of bovine and ovine foot tissues, respectively. Previous analyses of treponemal 16S rDNA sequences, PCR-amplified directly from DD or CODD lesions, have suggested relatedness of animalTreponemato some human oralTreponemaspecies isolated from periodontal tissues. In this study a range of adhesion and virulence-related properties of three animalTreponemaisolates have been compared with representative human oral strains ofTreponema denticolaandTreponema vincentii. In adhesion assays using biotinylated treponemal cells,T. denticolacells bound in consistently higher numbers to fibronectin, laminin, collagen type I, gelatin, keratin and lactoferrin than didT. vincentiior animalTreponemaisolates. However, animal DD strains adhered to fibrinogen at equivalent or greater levels thanT. denticola. AllTreponemastrains bound to the amino-terminal heparin I/fibrin I domain of fibronectin. 16S rDNA sequence analyses placed ovine strain UB1090 and bovine strain UB1467 within a cluster that was phylogenetically related toT. vincentii, while ovine strain UB1466 appeared more closely related toT. denticola. These observations correlated with phenotypic properties. Thus,T. denticolaATCC 35405, GM-1, andTreponemaUB1466 had similar outer-membrane protein profiles, produced chymotrypsin-like protease (CTLP), trypsin-like protease and high levels of proline iminopeptidase, and co-aggregated with human oral bacteriaPorphyromonas gingivalisandStreptococcus crista. Conversely,T. vincentiiATCC 35580, D2A-2, and animal strains UB1090 and UB1467 did not express CTLP or trypsin-like protease and did not co-aggregate withP. gingivalisorS. crista. Taken collectively, these results suggest that human oral-relatedTreponemahave broad host specificity and that similar control or preventive strategies might be developed for human and animalTreponema-associated infections.
Limitations of the widely used GAM42a and BET42a probes targeting bacteria in the Gammaproteobacteria radiation
Authors: Yeates Christine , Saunders Aaron M. , Crocetti Gregory R. , Blackall Linda L.
Published: May 2003

The 23S rRNA-targeted probes GAM42a and BET42a provided equivocal results with the uncultured gammaproteobacterium ‘Candidatus Competibacter phosphatis' where some cells bound GAM42a and other cells bound BET42a in fluorescence in situ hybridization (FISH) experiments. Probes GAM42a and BET42a span positions 1027–1043 in the 23S rRNA and differ from each other by one nucleotide at position 1033. Clone libraries were prepared from PCR products spanning the 16S rRNA genes, intergenic spacer region and 23S rRNA genes from two mixed cultures enriched in ‘Candidatus C. phosphatis’. With individual clone inserts, the 16S rDNA portion was used to confirm the source organism as ‘Candidatus C. phosphatis' and the 23S rDNA portion was used to determine the sequence of the GAM42a/BET42a probe target region. Of the 19 clones sequenced, 8 had the GAM42a probe target (T at position 1033) and 11 had G at position 1033, the only mismatch with GAM42a. However, none of the clones had the BET42a probe target (A at 1033). Non-canonical base-pairing between the 23S rRNA of ‘Candidatus C. phosphatis' with G at position 1033 and GAM42a (G–A) or BET42a (G–T) is likely to explain the probing anomalies. A probe (GAM42_C1033) was optimized for use in FISH, targeting cells with G at position 1033, and was found to highlight not only some ‘Candidatus C. phosphatis' cells, but also other bacteria. This demonstrates that there are bacteria in addition to ‘Candidatus C. phosphatis' with the GAM42_C1033 probe target and not the BET42a or GAM42a probe target.
Detection and analysis of transpositionally active head-to-tail dimers in three additional Escherichia coli IS elements
Authors: Szeverényi Ildikó , Nagy Zita , Farkas Tibor , Olasz Ferenc , Kiss János
Published: May 2003

This study demonstrates thatEscherichia coliinsertion elements IS3, IS150and IS186are able to form transpositionally active head-to-tail dimers which show similar structure and transpositional activity to the dimers of IS2, IS21and IS30. These structures arise by joining of the left and right inverted repeats (IRs) of two elements. The resulting junction includes a spacer region (SR) of a few base pairs derived from the flanking sequence of one of the reacting IRs. Head-to-tail dimers of IS3, IS150and IS186are unstable due to their transpositional activity. They can be resolved in two ways that seem to form a general rule for those elements reported to form dimers. One way is a site-specific process (dimer dissolution) which is accompanied by the loss of one IS copy along with the SR. The other is ‘classical’ transposition where the joined ends integrate into the target DNA. In intramolecular transposition this often gives rise to deletion formation, whereas in intermolecular transposition it gives rise to replicon fusion. The results presented for IS3, IS150and IS186are in accordance with the IS dimer model, which is in turn consistent with models based on covalently closed minicircles.
Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes
Authors: Cooper Gregory M. , Brudno Michael , Program NISC Comparative Sequencing , Green Eric D. , Batzoglou Serafim , Sidow Arend
Published: May 2003

Comparative sequence analyses on a collection of carefully chosen mammalian genomes could facilitate identification of functional elements within the human genome and allow quantification of evolutionary constraint at the single nucleotide level. High-resolution quantification would be informative for determining the distribution of important positions within functional elements and for evaluating the relative importance of nucleotide sites that carry single nucleotide polymorphisms (SNPs). Because the level of resolution in comparative sequence analyses is a direct function of sequence diversity, we propose that the information content of a candidate mammalian genome be defined as the sequence divergence it would add relative to already-sequenced genomes. We show that reliable estimates of genomic sequence divergence can be obtained from small genomic regions. On the basis of a multiple sequence alignment of ∼1.4 megabases each from eight mammals, we generate such estimates for five unsequenced mammals. Estimates of the neutral divergence in these data suggest that a small number of diverse mammalian genomes in addition to human, mouse, and rat would allow single nucleotide resolution in comparative sequence analyses.

[The multiple sequence alignment of theCFTR region and a spreadsheet with the calculations performed, will be available as supplementary information online atwww.genome.org.]
Predicting Gene Function From Patterns of Annotation
Authors: King Oliver D. , Foulger Rebecca E. , Dwight Selina S. , White James V. , Roth Frederick P.
Published: May 2003

The Gene Ontology (GO) Consortium has produced a controlled vocabulary for annotation of gene function that is used in many organism-specific gene annotation databases. This allows the prediction of gene function based on patterns of annotation. For example, if annotations for two attributes tend to occur together in a database, then a gene holding one attribute is likely to hold the other as well. We modeled the relationships among GO attributes with decision trees and Bayesian networks, using the annotations in theSaccharomycesGenome Database (SGD) and in FlyBase as training data. We tested the models using cross-validation, and we manually assessed 100 gene–attribute associations that were predicted by the models but that were not present in the SGD or FlyBase databases. Of the 100 manually assessed associations, 41 were judged to be true, and another 42 were judged to be plausible.

[Detailed lists of hypotheses including the curators' comments on each hypothesis, are available athttp://llama.med.harvard.edu/∼king/predictions.html.]
Predicting Human Minisatellite Polymorphism
Authors: Denoeud France , Vergnaud Gilles , Benson Gary
Published: May 2003

We seek to define sequence-based predictive criteria to identify polymorphic and hypermutable minisatellites in the human genome. Polymorphism of a representative pool of minisatellites, selected from human chromosomes 21 and 22, was experimentally measured by PCR typing in a population of unrelated individuals. Two predictive approaches were tested. One uses simple repeat characteristics (e.g., unit length, copy number, nucleotide bias) and a more complex measure, termed HistoryR, based on the presence of variant motifs in the tandem array. We find that HistoryR and percentage of GC are strongly correlated with polymorphism and, as predictive criteria, reduce by half the number of repeats to type while enriching the proportion with heterozygosity ≥0.5, from a background level of 43% to 59%. The second approach uses length differences between minisatellites in the two releases of the human genome sequence (from the public consortium and Celera). As a predictor, this similarly enriches the number of polymorphic minisatellites, but fails to identify an unexpectedly large number of these. Finally, typing of the highly polymorphic minisatellites in large families identified one new hypermutable minisatellite, located in a predicted coding sequence. This may represent the first coding human hypermutable minisatellite.

[Supplemental material is available online at www.genome.org.]
Comparing Bacterial Genomes Through Conservation Profiles
Authors: Martı́n Maria J. , Herrero Javier , Mateos Alvaro , Dopazo Joaquin
Published: May 2003

We constructed two-dimensional representations of profiles of gene conservation across different genomes using the genome ofEscherichia colias a model. These profiles permit both the visualization at the genome level of different traits in the organism studied and, at the same time, reveal features related to the genomes analyzed (such as defective genomes or genomes that lack a particular system). Conserved genes are not uniformly distributed along theE. coligenome but tend to cluster together. The study of gene distribution patterns across genomes is important for the understanding of how sets of genes seem to be dependent on each other, probably having some functional link. This provides additional evidence that can be used for the elucidation of the function of unannotated genes. Clustering these patterns produces families of genes which can be arranged in a hierarchy of closeness. In this way, functions can be defined at different levels of generality depending on the level of the hierarchy that is studied. The combined study of conservation and phenotypic traits opens up the possibility of defining phenotype/genotype associations, and ultimately inferring the gene or genes responsible for a particular trait.
Analysis of 5′-End Sequences of Chimpanzee cDNAs
Authors: Sakate Ryuichi , Osada Naoki , Hida Munetomo , Sugano Sumio , Hayasaka Ikuo , Shimohira Naoko , Yanagi Shinsuke , Suto Yumiko , Hashimoto Katsuyuki , Hirai Momoki
Published: May 2003

We constructed full-length enriched cDNA libraries from chimpanzee brain, skin, and liver tissues by the oligo-capping method to establish a database of sequences of chimpanzee genes. Randomly selected clones from the libraries were subjected to one-pass sequencing from their 5′-ends. As a result, we collected 6813 chimpanzee cDNA sequences longer than 400 bp. Homology search against human mRNA sequences (RefSeq mRNAs) revealed that our collection included sequences of 1652 putative chimpanzee genes. In order to calculate the sequence identity between human and chimpanzee homologs, we constructed 5′-end consensus sequences of 226 chimpanzee genes by aligning at least three sequences for individual genes. Sequence identity was estimated by comparing these consensus sequences and the corresponding sequences of their human homologs. The average sequence identity of the 5′-end cDNAs was 99.30%. Those of the 5′-UTRs and CDSs were 98.79% and 99.42%, respectively. The results confirmed that human and chimpanzee genes are highly conserved at the nucleotide level. As for amino acids, the average sequence identity was 99.44%. The average synonymous (KS) and nonsynonymous (KA) divergences were estimated to be 1.33% and 0.28%, respectively.

[Supplemental material is available online atwww.genome.org. All of the 1947 sequences used for constructing the consensus sequences of 226 chimpanzee genes have been submitted to DDBJ under accession nos. AU296732–AU298678. Two hundred twenty-six consensus sequences and their detailed annotation descriptions are available at our Web site http://www.prigen.org/.]
DASH-2: Flexible, Low-Cost, and High-Throughput SNP Genotyping by Dynamic Allele-Specific Hybridization on Membrane Arrays
Authors: Jobs Magnus , Howell W. Mathias , Strömqvist Linda , Mayr Torsten , Brookes Anthony J.
Published: May 2003

Genotyping technologies need to be continually improved in terms of their flexibility, cost-efficiency, and throughput, to push forward genome variation analysis. To this end, we have leveraged the inherent simplicity of dynamic allele-specific hybridization (DASH) and coupled it to recent innovations of centrifugal arrays and iFRET. We have thereby created a new genotyping platform we term DASH-2, which we demonstrate and evaluate in this report. The system is highly flexible in many ways (any plate format, PCR multiplexing, serial and parallel array processing, spectral-multiplexing of hybridization probes), thus supporting a wide range of application scales and objectives. Precision is demonstrated to be in the range 99.8–100%, and assay costs are 0.05 USD or less per genotype assignment. DASH-2 thus provides a powerful new alternative for genotyping practice, which can be used without the need for expensive robotics support.
The Organization and Rate of Evolution of Wheat Genomes Are Correlated With Recombination Rates Along Chromosome Arms
Authors: Akhunov Eduard D. , Goodyear Andrew W. , Geng Shu , Qi Li-Li , Echalier Benjamin , Gill Bikram S. , Miftahudin  , Gustafson J. Perry , Lazo Gerard , Chao Shiaoman , Anderson Olin D. , Linkiewicz Anna M. , Dubcovsky Jorge , Rota Mauricio La , Sorrells Mark E. , Zhang Deshui , Nguyen Henry T. , Kalavacharla Venugopal , Hossain Khwaja , Kianian Shahryar F. , Peng Junhua , Lapitan Nora L.V. , Gonzalez-Hernandez Jose L. , Anderson James A. , Choi Dong-Woog , Close Timothy J. , Dilbirligi Muharrem , Gill Kulvinder S. , Walker-Simmons M. Kay , Steber Camille , McGuire Patrick E. , Qualset Calvin O. , Dvorak Jan
Published: May 2003

Genes detected by wheat expressed sequence tags (ESTs) were mapped into chromosome bins delineated by breakpoints of 159 overlapping deletions. These data were used to assess the organizational and evolutionary aspects of wheat genomes. Relative gene density and recombination rate increased with the relative distance of a bin from the centromere. Single-gene loci present once in the wheat genomes were found predominantly in the proximal, low-recombination regions, while multigene loci tended to be more frequent in distal, high-recombination regions. One-quarter of all gene motifs within wheat genomes were represented by two or more duplicated loci (paralogous sets). For 40 such sets, ancestral loci and loci derived from them by duplication were identified. Loci derived by duplication were most frequently located in distal, high-recombination chromosome regions whereas ancestral loci were most frequently located proximal to them. It is suggested that recombination has played a central role in the evolution of wheat genome structure and that gradients of recombination rates along chromosome arms promote more rapid rates of genome evolution in distal, high-recombination regions than in proximal, low-recombination regions.
Fidelity of the Methylation Pattern and Its Variation in the Genome
Authors: Ushijima Toshikazu , Watanabe Naoko , Okochi Eriko , Kaneda Atsushi , Sugimura Takashi , Miyamoto Kazuaki
Published: May 2003

The methylated or unmethylated status of a CpG site is copied faithfully from parental DNA to daughter DNA, and functions as a cellular memory. However, no information is available for the fidelity of methylation pattern in unmethylated CpG islands (CGIs) or its variation in the genome. Here, we determined the methylation status of each CpG site on each DNA molecule obtained from clonal populations of normal human mammary epithelial cells. Methylation pattern error rates (MPERs) were calculated based upon the deviation from the methylation patterns that should be obtained if the cells had 100% fidelity in replicating the methylation pattern. Unmethylated CGIs in the promoter regions of five genes showed MPERs of 0.018–0.032 errors/site/21.6 generations, and the fidelity of methylation pattern was calculated as 99.85%–99.92%/site/generation. In contrast, unmethylated CGIs outside the promoter regions showed MPERs more than twice as high (P < 0.01). Methylated regions, including a CGI in theMAGE-A3 promoter and DMR of the H19 gene, showed much lower MPERs than unmethylated CGIs. These showed that errors in methylation pattern were mainly due to de novo methylations in unmethylated regions. The differential MPERs even among unmethylated CGIs indicated that a promoter-specific protection mechanism(s) from de novo methylation was present.

[Supplemental material is available online at www.genome.org.]
DNA Analysis by Fluorescence Quenching Detection
Authors: Xiao Ming , Kwok Pui-Yan
Published: May 2003

The analysis of human genetic variations such as single nucleotide polymorphisms (SNPs) has great applications in genome-wide association studies of complex genetic traits. We have developed an SNP genotyping method based on the primer extension assay with fluorescence quenching as the detection. The template-directed dye-terminator incorporation with fluorescence quenching detection (FQ-TDI) assay is based on the observation that the intensity of fluorescent dye R110- and R6G-labeled acycloterminators is universally quenched once they are incorporated onto a DNA oligonucleotide primer. By comparing the rate of fluorescence quenching of the two allelic dyes in real time, we have extended this method for allele frequency estimation of SNPs in pooled DNA samples. The kinetic FQ-TDI assay is highly accurate and reproducible both in genotyping and in allele frequency estimation. Allele frequencies estimated by the kinetic FQ-TDI assay correlated well with known allele frequencies, with an r2 value of 0.993. Applying this strategy to large-scale studies will greatly reduce the time and cost for genotyping hundreds and thousands of SNP markers between affected and control populations.
Conserved Noncoding Sequences among Cultivated Cereal Genomes Identify Candidate Regulatory Sequence Elements and Patterns of Promoter Evolution[W]
Authors: Guo Hena , Moose Stephen P.
Published: May 2003

Surveys for conserved noncoding sequences (CNS) among genes from monocot cereal species were conducted to assess the general properties of CNS in grass genomes and their correlation with known promoter regulatory elements. Initial comparisons of 11 orthologous maize-rice gene pairs found that previously defined regulatory motifs could be identified within short CNS but could not be distinguished reliably from random sequence matches. Among the different phylogenetic footprinting algorithms tested, the VISTA tool yielded the most informative alignments of noncoding sequence. VISTA was used to survey for CNS among all publicly available genomic sequences from maize, rice, wheat, barley, and sorghum, representing >300 gene comparisons. Comparisons of orthologous maize-rice and maize-sorghum gene pairs identified 20 bp as a minimal length criterion for a significant CNS among grass genes, with few such CNS found to be conserved across rice, maize, sorghum, and barley. The frequency and length of cereal CNS as well as nucleotide substitution rates within CNS were consistent with the known phylogenetic distances among the species compared. The implications of these findings for the evolution of cereal gene promoter sequences and the utility of using the nearly completed rice genome sequence to predict candidate regulatory elements in other cereal genes by phylogenetic footprinting are discussed.
Direct numerical simulation of turbulent heat transfer in an axially rotating pipe flow
Authors: Satake Shin‐ichi , Kunugi Tomoaki
Published: May 2003

A direct numerical simulation with turbulent transport of a scalar quantity has been carried out to grasp and understand a laminarization phenomena caused by a pipe rotation. In this study, the Reynolds number, which is based on a bulk velocity and a pipe diameter, was set to be constant; Reb=5283, and the rotating ratios of a wall velocity to a bulk velocity were set to be 0.5, 1.0, 2.0 and 3.0. A uniform heat‐flux was applied to the wall as a thermal boundary condition. Prandtl number of the working fluid was assumed to be 0.71. The number of computational grids used in this study was 256×128×128 in the z‐, r‐ and ϕ‐ directions, respectively. The turbulent quantities such as the mean flow, temperature fluctuations, turbulent stresses and pressure distribution and the turbulent statistics were obtained. Moreover, the Reynolds stress and the scalar flux budgets were also obtained for each rotating ratio. The turbulent drag decreases with the rotating ratio increase. The reason of this drag reduction can be considered that the additional rotational production terms appear in the azimuthal turbulence component. The contributions of convection and production terms to the radial scalar flux budget and also to the balance with temperature‐pressure gradient term are significant. The dissipation and viscous diffusion terms are negligible in higher rotating ratio.
Numerical Analysis of Unsteady Exhaust Gas Flow and Its Application for Lambda Control Improvement
Authors: Yoshizawa K. , Mori K. , Arai K. , Iiyama A.
Published: May 2003

A multidimensional computational fluid dynamics (CFD) tool has been applied to analyze the exhaust system of a gasoline engine. Since gas flow in the exhaust manifold is affected by exhaust pulsations, prediction methods based on steady flow are not able to predict gas flow precisely enough. Therefore, a new multidimensional calculation method, called pulsation flow calculation, has been developed. A one-dimensional gas exchange simulation and a three-dimensional exhaust gas flow calculation are combined to simulate gas flow pulsations caused by the gas exchange process. Predicted gas flow in the exhaust manifold agreed with the experimental data. With the aim of reducing emissions, the pulsation flow calculation method has been applied to improve lambda feedback control using an oxygen sensor. The factors governing sensor sensitivity to the exhaust gas from each cylinder were clarified. The possibility of selecting the oxygen sensor location in the exhaust manifold on the basis of calculations was proved. The effect of an exhaust manifold with equal-length cylinder runners on achieving uniform sensor sensitivities was made clear. In addition, a new lambda feedback control method for an exhaust manifold with different-length cylinder runners is proposed.
Development of Micro-Diesel Injector Nozzles via Microelectromechanical Systems Technology and Effects on Spray Characteristics
Authors: Baik S. , Blanchard J. P. , Corradini M. L.
Published: May 2003

Micromachined planar orifice nozzles have been developed using MEMS (micro-electro-mechanical systems) technology and tested with commercially produced diesel injection systems. Such a system, properly designed, may have the capability to improve the spray characteristics in DI diesel engines due to improved atomization and fuel-air mixing. To demonstrate this process, 14 microplanar orifice nozzles were fabricated with deep X-ray lithography and electroplating (LIGA) technology. The circular orifice diameters were varied from 40 to 260 microns and the number of orifices varied from one to 169. Three plates with noncircular orifices were also fabricated to examine the effect of orifice shape on spray characteristics. These nozzles were then attached to commercial diesel injectors and the associated injection systems were used in the study of drop sizes. The experiments were carried out at two different injection pressures (around 25 MPa and 80 MPa). Local drop sizes were measured by a laser diffraction technique, and the average drop sizes of the whole sprays were measured by a light extinction technique. The drop sizes were found to depend primarily on the total mass flow area. Coalescence droplet collisions among adjacent sprays were apparent for the multiple orifice nozzles. Nonplanar configurations are under development and may show improved performance.
Investigation of a Large High- Speed Diesel Engine Transient Behavior Including Compressor Surging and Emergency Shutdown
Authors: Theotokatos G. , Kyrtatos N. P.
Published: May 2003

The operation of a large high-speed engine under transient loading conditions was investigated, using a detailed simulation code in conjunction with a model capable of predicting compressor surging. Engine loadings were applied, which were considered dangerous for initiating compressor surging and cases where compressor surging could occur were identified. A means of avoiding compressor surging by opening a bypass valve connected between the compressor outlet and turbine inlet was examined. Finally, the case of engine abrupt stopping by rapidly closing the engine emergency shutdown valve, located downstream of the compressor, was also investigated.
Exhaust Particulate Matter Emission Factors and Deterioration Rate for In-Use Motor Vehicles
Authors: Ubanwa B. , Burnette A. , Kishan S. , Fritz, S. G.
Published: May 2003

Recent measurements and modeling of primary exhaust particulate matter (PM) emissions from both gasoline and diesel-powered motor vehicles suggest that many vehicles produce PM at rates substantially higher than assumed in the current EPA PM emission factor model, known as “PART5.” The discrepancy between actual versus modeled PM emissions is generally attributed to inadequate emissions data and outdated assumptions in the PART5 model. This paper presents a study with the objective of developing an in-house tool (a modified PART5 model) for the Texas Natural Resource Conservation Commission (TNRCC) to use for estimating motor vehicle exhaust PM emissions in Texas. The work included chassis dynamometer emissions testing on several heavy-duty diesel vehicles at the Southwest Research Institute (SwRI), analysis of the exhaust PM emissions and other regulated pollutants (i.e., HC,CO,NOx), review of related studies and exhaust PM emission data obtained from literature of similar types of light and heavy-duty vehicle tests, a review of the current PART5 model, and analysis of the associated emission deterioration rates. Exhaust PM emissions data obtained from the vehicle testing at SwRI and other similar studies (covering a relatively large number and wide range of vehicles) were merged, and finally, used to modify the PART5 model. The modified model, which was named PART5-TX1, was then used to estimate new exhaust PM emission factors for in-use motor vehicles. Modifications to the model are briefly described, along with emissions test results from the heavy-duty diesel-powered vehicles tested at SwRI. Readers interested in a detailed understanding of the techniques used to modify the PART5 model are referred to the final project report to TNRCC (Eastern Research Group 2000).
Knock Rating of Gaseous Fuels
Authors: Attar A. A. , Karim G. A.
Published: May 2003

The knock tendency in spark ignition engines of binary mixtures of hydrogen, ethane, propane and n-butane is examined in a CFR engine for a range of mixture composition, compression ratio, spark timing, and equivalence ratio. It is shown that changes in the knock characteristics of binary mixtures of hydrogen with methane are sufficiently different from those of the binary mixtures of the other gaseous fuels with methane that renders the use of the methane number of limited utility. However, binary mixtures of n-butane with methane may offer a better alternative. Small changes in the concentration of butane produce almost linearly significant changes in both the values of the knock limited compression ratio for fixed spark timing and the knock limited spark timing for a fixed compression ratio.
Knocking Cylinder Pressure Data Characteristics in a Spark-Ignition Engine
Authors: Syrimis M. , Assanis D. N.
Published: May 2003

An experimental study of the knock initiation and development period was conducted in a single-cylinder research engine. Cylinder pressure was recorded at two locations in the combustion chamber using a high sampling frequency, thus allowing the identification of spatial and temporal pressure characteristics introduced by knock. It was found that substantial local pressure differences exist inside the chamber during the initiation of autoignition. In most cases, knock-induced pressure waves are of acoustic nature, but they can become weak shock waves in heavily knocking cycles. Waves appear first in the pressure trace of the transducer closer to the site of autoignition, and are subsequently detected by the other transducer. The results show evidence of multiple sites of autoignition, and indicate changes in the nature and the direction of propagation of pressure waves. Cylinder pressure signals sampled at locations closer to the center of the chamber show significantly smaller amplitude of pressure fluctuation, making them more suitable for further mathematical processing.
Experimental and Analytical Examination of the Development of Inhomogeneities and Autoignition During Rapid Compression of Hydrogen-Oxygen-Argon Mixtures
Authors: Chen K. , Karim G. A. , Watson H. C.
Published: May 2003

The reliable prediction of the processes leading to autoignition during the rapid compression of an initially homogeneous mixture of fuel and air requires the coupled modeling of multidimensional fluid dynamics and heat transfer together with a sufficiently detailed description of the chemical kinetics of the oxidation reactions. To satisfy fully such requirements tends at present to be unmanageable. The paper describes an improvised approach that combines multidimensional fluid dynamics modeling (CFD KIVA-3) with derived variable effective global chemical kinetic data. These were generated through a fitting procedure of the corresponding results obtained while using a detailed chemical kinetic scheme; albeit with uniform properties, at constant volume and an initial state similar to that existing during the ignition delay. It is shown while using such an approach that spatially nonuniform properties develop rapidly within the initially homogeneous charge due to piston motion, heat transfer and any preignition energy release activity. This leads autoignition to take place first within the hottest region and a reaction front progresses at a finite rate to consume the rest of the mixture. The present contribution examines the compression ignition of hydrogen-oxygen mixtures in the presence of argon as a diluent. Validation of the predicted results is made using a range of corresponding experimental values obtained in a single-shot pneumatically driven rapid compression apparatus. It is to be shown that the simulation which indicates the build up of temperature gradients during the compression stroke, predicts earlier autoignition than that obtained with a single-zone simulation. Good agreement between predicted and experimental results is achieved, especially for lean and stoichiometric mixtures under high compression ratio conditions. The CFD-based simulation results are found to be closer to the corresponding experimental results than those obtained with an assumed reactive system of uniform properties and using detailed reaction kinetics.
Reduction of NOx and Particulate Emissions by Using Oxygen-Enriched Combustion Air in a Locomotive Diesel Engine
Authors: Poola R. B. , Sekar R.
Published: May 2003

This paper discusses operational and emissions results obtained with a locomotive (two-cylinder, EMD 567B) research diesel engine when oxygen-enriched combustion air is used. An operating regime was identified in which particulates and NOx could be reduced simultaneously when the concentration of intake air oxygen, fueling rate, and injection timing were optimized. Using oxygen from an external source, particulates were reduced by approximately 60% and NOx emissions were reduced by 15–20% with the optimal operating strategy. Higher gross power, lower peak cylinder pressures, and lower brake-specific fuel consumption were also observed. Gross power was increased by about 15–20% at base peak combustion pressure, and gross brake-specific fuel consumption was decreased by 2–10% with load. The effect of achieving oxygen enrichment by means of an air separation membrane is beyond the scope of the current study.
A Predictive Ignition Delay Correlation Under Steady-State and Transient Operation of a Direct Injection Diesel Engine
Authors: Assanis D. N. , Filipi Z. S. , Fiveland S. B. , Syrimis M.
Published: May 2003

Available correlations for the ignition delay in pulsating, turbulent, two-phase, reacting mixtures found in a diesel engine often have limited predictive ability, especially under transient conditions. This study focuses on the development of an ignition delay correlation, based on engine data, which is suitable for predictions under both steady-state and transient conditions. Ignition delay measurements were taken on a heavy-duty diesel engine across the engine speed/load spectrum, under steady-state and transient operation. The dynamic start of injection was calculated by using a skip-fire technique to determine the dynamic needle lift pressure from a measured injection pressure profile. The dynamic start of combustion was determined from the second derivative of measured cylinder pressure. The inferred ignition delay measurements were correlated using a modified Arrhenius expression to account for variations in fuel/air composition during transients. The correlation has been compared against a number of available correlations under steady-state conditions. In addition, comparisons between measurements and predictions under transient conditions are made using the extended thermodynamic simulation framework of Assanis and Heywood. It is concluded that the proposed correlation provides better predictive capability under both steady-state and transient operation.
The Use of Neural Nets for Matching Fixed or Variable Geometry Compressors With Diesel Engines
Authors: Nelson S. A. , Filipi Z. S. , Assanis D. N.
Published: May 2003

A technique which uses trained neural nets to model the compressor in the context of a turbocharged diesel engine simulation is introduced. This technique replaces the usual interpolation of compressor maps with the evaluation of a smooth mathematical function. Following presentation of the methodology, the proposed neural net technique is validated against data from a truck type, 6-cylinder 14-liter diesel engine. Furthermore, with the introduction of an additional parameter, the proposed neural net can be trained to simulate an entire family of compressors. As a demonstration, a family of compressors of different sizes is represented with a single neural net model which is subsequently used for matching calculations with intercooled and nonintercooled engine configurations at different speeds. This novel approach readily allows for evaluation of various options within a wide range of possible compressor configurations prior to prototype production. It can also be used to represent the variable geometry machine regardless of the method used to vary compressor characteristics. Hence, it is a powerful design tool for selection of the best compressor for a given diesel engine system and for broader system optimization studies.
Homogeneous Charge Compression Ignition Engine: A Simulation Study on the Effects of Inhomogeneities
Authors: Maigaard P. , Mauss F. , Kraft M.
Published: May 2003

A stochastic model for the HCCI engine is presented. The model is based on the PaSPFR-IEM model and accounts for inhomogeneities in the combustion chamber while including a detailed chemical model for natural gas combustion, consisting of 53 chemical species and 590 elementary chemical reactions. The model is able to take any type of inhomogeneities in the initial gas composition into account, such as inhomogeneities in the temperature field, in the air-fuel ratio or in the concentration of the recirculated exhaust gas. With this model the effect of temperature differences caused by the thermal boundary layer and crevices in the cylinder for a particular engine speed and fuel to air ratio is studied. The boundary layer is divided into a viscous sublayer and a turbulent buffer zone. There are also colder zones due to crevices. All zones are modeled by a characteristic temperature distribution. The simulation results are compared with experiments and a previous numerical study employing a PFR model. In all cases the PaSPFR-IEM model leads to a better agreement between simulations and experiment for temperature and pressure. In addition a sensitivity study on the effect of different intensities of turbulent mixing on the combustion is performed. This study reveals that the ignition delay is a function of turbulent mixing of the hot bulk and the colder boundary layer.