bluuebunny/crossref_metadata_2025 huggingface dataset:
Construction of anEnterococcus faecalisTn917-Mediated-Gene-Disruption Library Offers Insight into Tn917Insertion Patterns
Authors: Garsin Danielle A. , Urbach Jonathan , Huguet-Tapia Jose C. , Peters Joseph E. , Ausubel Frederick M.
Published: October 2004

Sequencing the insertion sites of 8,865 Tn917insertions inEnterococcus faecalisstrain OG1RF identified a hot spot in the replication terminus region corresponding to 6% of the genome where 65% of the transposons had inserted. InE. faecalis, Tn917preferentially inserted at a 29-bp consensus sequence centered on TATAA, a 5-bp sequence that is duplicated during insertion. The regional insertion site preference at the chromosome terminus was not observed in another low-G+C gram-positive bacterium,Listeria monocytogenes, although the consensus insertion sequence was the same. The 8,865 Tn917insertion sites sequenced inE. faecaliscorresponded to only ∼610 different open reading frames, far fewer than the predicted number of 2,400, assuming random insertion. There was no significant preference in orientation of the Tn917insertions with either transcription or replication. Even though OG1RF has a smaller genome than strain V583 (2.8 Mb versus 3.2 Mb), the onlyE. faecalisstrain whose sequence is in the public domain, over 10% of the Tn917insertions appear to be in a OG1RF-specific sequence, suggesting that there are significant genomic differences amongE. faecalisstrains.
TouR-Mediated Effector-Independent Growth Phase-Dependent Activation of the σ54PtouPromoter ofPseudomonas stutzeriOX1
Authors: Solera Dafne , Arenghi Fabio L. G. , Woelk Tanja , Galli Enrica , Barbieri Paola
Published: October 2004

Transcription of the catabolictouABCDEFoperon, encoding the toluene-o-xylene monooxygenase ofPseudomonas stutzeriOX1, is driven by the σ54-dependent Ptoupromoter, whose activity is controlled by the phenol-responsive NtrC-like activator TouR. In this paper we describe for the first time a peculiar characteristic of this system, namely, that Ptoutranscription is activated in a growth phase-dependent manner in the absence of genuine effectors of the cognate TouR regulator. This phenomenon, which we named gratuitous activation, was observed in the native strainP. stutzeriOX1, as well as in aPseudomonas putidaPaW340 host harboring the reconstructedtouregulatory circuit. Regulator-promoter swapping experiments demonstrated that the presence of TouR is necessary and sufficient for imposing gratuitous activation on the Ptoupromoter, as well as on other σ54-dependent catabolic promoters, whereas the highly similar phenol-responsive activator DmpR is unable to activate the Ptoupromoter in the absence of effectors. We show that this phenomenon is specifically triggered by carbon source exhaustion but not by nitrogen starvation. An updated model of thetouregulatory circuit is presented.
Diversion of the Metabolic Flux from Pyruvate Dehydrogenase to Pyruvate Oxidase Decreases Oxidative Stress during Glucose Metabolism in Nongrowing
Escherichia coli
Cells Incubated under Aerobic, Phosphate Starvation Conditions
Authors: Moreau Patrice L.
Published: October 2004

Ongoing aerobic metabolism in nongrowing cells may generate oxidative stress. It is shown here that the levels of thiobarbituric acid-reactive substances (TBARSs), which measure fragmentation products of oxidized molecules, increased strongly at the onset of starvation for phosphate (P
i
). This increase in TBARS levels required the activity of the histone-like nucleoid-structuring (H-NS) protein. TBARS levels weakly increased further in Δ
ahpCF
mutants deficient in alkyl hydroperoxide reductase (AHP) activity during prolonged metabolism of glucose to acetate. Inactivation of pyruvate oxidase (PoxB) activity decreased the production of acetate by half and significantly increased the production of TBARS. Overall, these data suggest that during incubation under aerobic, P
i
starvation conditions, metabolic flux is diverted from the pyruvate dehydrogenase (PDH) complex (NAD dependent) to PoxB (NAD independent). This shift may decrease the production of NADH and in turn the adventitious production of H
2
O
2
by NADH dehydrogenase in the respiratory chain. The residual low levels of H
2
O
2
produced during prolonged incubation can be scavenged efficiently by AHP. However, high levels of H
2
O
2
may be reached transiently at the onset of stationary phase, primarily because H-NS may delay the metabolic shift from PDH to PoxB.
Analysis of Promoter Elements Involved in the Transcriptional Initiation of RpoS-DependentBorrelia burgdorferiGenes
Authors: Eggers Christian H. , Caimano Melissa J. , Radolf Justin D.
Published: October 2004

Borrelia burgdorferi, the causative agent of Lyme disease, encodes an RpoS ortholog (RpoSBb) that controls the temperature-inducible differential expression of at least some of the spirochete's lipoprotein genes, includingospCanddbpBA. To begin to dissect the determinants of RpoSBbrecognition of, and selectivity for, its dependent promoters, we linked a green fluorescent protein reporter to the promoter regions of severalB. burgdorferigenes with well-characterized expression patterns. Consistent with the expression patterns of the native genes/proteins inB. burgdorferistrain 297, we found that expression of theospC,dbpBA, andospFreporters in the spirochete was RpoSBbdependent, while theospEandflaBreporters were RpoSBbindependent. To compare promoter recognition by RpoSBbwith that of the prototype RpoS (RpoSEc), we also introduced our panel of constructs intoEscherichia coli. In this surrogate, maximal expression from theospC,dbpBA, andospFpromoters clearly required RpoS, although in the absence of RpoSEctheospFpromoter was weakly recognized by anotherE. colisigma factor. Furthermore, RpoSBbunder the control of an inducible promoter was able to complement anE. coli rpoSmutant, although RpoSEcand RpoSBbeach initiated greater activity from their own dependent promoters than they did from those of the heterologous sigma factor. Genetic analysis of theospCpromoter demonstrated that (i) the T(−14) in the presumptive −10 region plays an important role in sigma factor recognition in both organisms but is not as critical for transcriptional initiation by RpoSBbas it is for RpoSEc; (ii) the nucleotide at the −15 position determines RpoS or σ70selectivity inE. colibut does not serve the same function inB. burgdorferi; and (iii) the 110-bp region upstream of the core promoter is not required for RpoSEc- or RpoSBb-dependent activity inE. colibut is required for maximal expression from this promoter inB. burgdorferi. Taken together, the results of our studies suggest that theB. burgdorferiandE. coliRpoS proteins are able to catalyze transcription from RpoS-dependent promoters of either organism, but at least some of the nucleotide elements involved in transcriptional initiation and sigma factor selection inB. burgdorferiplay a different role than has been described forE. coli.
RpoS Proteolysis Is Regulated by a Mechanism That Does Not Require the SprE (RssB) Response Regulator Phosphorylation Site
Authors: Peterson Celeste N. , Ruiz Natividad , Silhavy Thomas J.
Published: October 2004

InEscherichia colithe response regulator SprE (RssB) facilitates degradation of the sigma factor RpoS by delivering it to the ClpXP protease. This process is regulated: RpoS is degraded in logarithmic phase but becomes stable upon carbon starvation, resulting in its accumulation. Because SprE contains a CheY domain with a conserved phosphorylation site (D58), the prevailing model posits that this control is mediated by phosphorylation. To test this model, we mutated the conserved response regulator phosphorylation site (D58A) of the chromosomal allele ofsprEand monitored RpoS levels in response to carbon starvation. Though phosphorylation contributed to the SprE basal activity, we found that RpoS proteolysis was still regulated upon carbon starvation. Furthermore, our results indicate that phosphorylation of wild-type SprE occurs by a mechanism that is independent of acetyl phosphate.
AplA, a Member of a New Class of Phycobiliproteins Lacking a Traditional Role in Photosynthetic Light Harvesting
Authors: Montgomery Beronda L. , Casey Elena Silva , Grossman Arthur R. , Kehoe David M.
Published: October 2004

All known phycobiliproteins have light-harvesting roles during photosynthesis and are found in water-soluble phycobilisomes, the light-harvesting complexes of cyanobacteria, cyanelles, and red algae. Phycobiliproteins are chromophore-bearing proteins that exist as heterodimers of α and β subunits, possess a number of highly conserved amino acid residues important for dimerization and chromophore binding, and are invariably 160 to 180 amino acids long. A new and unusual group of proteins that is most closely related to the allophycocyanin members of the phycobiliprotein superfamily has been identified. Each of these proteins, which have been named allophycocyanin-like (Apl) proteins, apparently contains a 28-amino-acid extension at its amino terminus relative to allophycocyanins. Apl family members possess the residues critical for chromophore interactions, but substitutions are present at positions implicated in maintaining the proper α-β subunit interactions and tertiary structure of phycobiliproteins, suggesting that Apl proteins are able to bind chromophores but fail to adopt typical allophycocyanin conformations. AplA isolated from the cyanobacterium
Fremyella diplosiphon
contained a covalently attached chromophore and, although present in the cell under a number of conditions, was not detected in phycobilisomes. Thus, Apl proteins are a new class of photoreceptors with a different cellular location and structure than any previously described members of the phycobiliprotein superfamily.
Biosynthesis of Cryptic Lipopolysaccharide Glycoforms in
Haemophilus influenzae
Involves a Mechanism Similar to That Required for O-Antigen Synthesis
Authors: Hood Derek W. , Randle Gaynor , Cox Andrew D. , Makepeace Katherine , Li Jianjun , Schweda Elke K. H. , Richards James C. , Moxon E. Richard
Published: October 2004

It is generally thought that mucosal bacterial pathogens of the genera
Haemophilus
,
Neisseria
, and
Moraxella
elaborate lipopolysaccharide (LPS) that is fundamentally different from that of enteric organisms that express O-specific polysaccharide side chains.
Haemophilus influenzae
elaborates short-chain LPS that has a role in the pathogenesis of
H. influenzae
infections. We show that the synthesis of LPS in this organism can no longer be as clearly distinguished from that in other gram-negative bacteria that express an O antigen. We provide evidence that a region of the
H. influenzae
genome, the
hmg
locus, is involved in the synthesis of glycoforms in which tetrasaccharide units are added en bloc, not stepwise, to the normal core glycoforms, similar to the biosynthesis of an O-antigen.
Increased Stability ofbmr3mRNA Results in a Multidrug-Resistant Phenotype inBacillus subtilis
Authors: Ohki Reiko , Tateno Kozue
Published: October 2004

A spontaneous mutant isolated in the presence of a high concentration of puromycin acquired a multidrug-resistant phenotype. Expression of thebmr3gene was dramatically increased. A base substitution, T to A at the +4 position, detected in the mutant resulted in the stabilization ofbmr3mRNA.
The Aer Protein of
Escherichia coli
Forms a Homodimer Independent of the Signaling Domain and Flavin Adenine Dinucleotide Binding
Authors: Ma Qinhong , Roy Francis , Herrmann Sarah , Taylor Barry L. , Johnson Mark S.
Published: October 2004

In vivo cross-linking between native cysteines in the Aer receptor of
Escherichia coli
showed dimer formation at the membrane anchor and in the putative HAMP domain. Dimers also formed in mutants that did not bind flavin adenine dinucleotide and in truncated peptides without a signaling domain and part of the HAMP domain.
Molecular Basis of the Indole-Negative Reaction in
Shigella
Strains: Extensive Damages to the
tna
Operon by Insertion Sequences
Authors: Rezwan Ferdousi , Lan Ruiting , Reeves Peter R.
Published: October 2004

The molecular basis of the loss of tryptophan utilization (indole-negative phenotype) of
Shigella
strains, in effect clones of
Escherichia coli
, was investigated. Analysis of the
tna
operon of 23
Shigella
strains representing each of the indole-negative serotypes revealed that insertion sequence-mediated insertion and/or deletions damaged the
tna
operon, leading to inability to convert tryptophan to indole. These events differ for cluster 1, cluster 3, and the outlier
Shigella
strains, confirming our previous observation of independent origins of these lineages from within
E. coli
. Parallel loss of the trait and prevalence of indole-negative strains suggest that the trait is deleterious in
Shigella
strains and advantages those without it.
Influence of shrub encroachment on aboveground net primary productivity and carbon and nitrogen pools in a mesic grassland
Authors: Lett Michelle S , Knapp Alan K , Briggs John M , Blair John M
Published: October 2004

The clonal shrub Cornus drummondii C.A. Mey. is rapidly increasing in cover and displacing mesic grassland species in the central USA as a consequence of fire suppression. We assessed the impact of C. drummondii on carbon (C) and nitrogen (N) pools and C fluxes in a tallgrass prairie in eastern Kansas, USA, through a comparison of both burned and unburned C. drummondii islands with open grassland areas. Allometric equations relating C. drum mondii foliage and wood biomass to basal stem diameter were developed to estimate aboveground biomass and net primary productivity (ANPP) of C. drummondii. Within C. drummondii islands, ANPP was 496 ± 45 g C·m2·year1, nearly three times that within open grassland (167 ± 13 g C·m2·year1). As a result of greater aboveground biomass, aboveground C and N storage within shrub islands (3270 ± 466 g C·m2, 37.9 ± 5.3 g N·m2) was substantially greater than that within open grassland (241 ± 33 g C·m2, 6.1 ± 0.8 g N·m2). No change in soil organic C or total N to 10-cm depth was evident; however, soil CO2flux was significantly reduced in C. drummondii islands relative to the open grassland. The storage of C in aboveground biomass of C. drummondii represents a significant short-term increase in C storage relative to open grassland. However, potential alterations in belowground processes must be quantified before the long-term net effect of shrub encroachment on C and N pools within this mesic grassland can be determined.Key words: aboveground biomass, Cornus drummondii, net primary productivity, shrub encroachment, tallgrass prairie.
A probable late Neoproterozoic age for the Kennedy Channel and Ella Bay formations, northeastern Ellesmere Island and its implications for passive margin history of the Canadian Arctic
Authors: Dewing Keith , Harrison J C , Pratt Brian R , Mayr Ulrich
Published: October 2004

The Kennedy Channel and Ella Bay formations are the two oldest stratigraphic units exposed in the Franklinian margin sedimentary sequence in the Canadian Arctic Islands. An Early Cambrian age had previously been accepted by the occurrence of trilobites and small shelly fossils in the type section of the Kennedy Channel Formation. Reinvestigation of the area around the type section shows that several large strike-slip faults cut the succession and that the olenelloid trilobites are from an infaulted slice of a younger unit, the Lower Cambrian Kane Basin Formation. Thus, there is no unambiguous paleontological evidence for the age of either the Kennedy Channel or Ella Bay formations. However, the abundance of stromatolites, absence of trace fossils, and separation from overlying Lower Cambrian clastics by a regional angular unconformity indicate a probable late Neoproterozoic age for these two formations. The Ella Bay Formation likely correlates with the Portfjeld Formation in North Greenland, the Spiral Creek Formation in East Greenland, and the Risky Formation of the Mackenzie Mountains in northwestern Canada. The passive margin that existed in northern Laurentia during the early Paleozoic was, therefore, established in the late Neoproterozoic, and the onset of rifting must have preceded this, rather than occurring in the Early Cambrian as some authors have suggested.
GISHGenomic in situ hybridization reveals cryptic genetic differences between maize and its putative wild progenitorZea mayssubsp.parviglumis
Authors: Gonzalez G , Confalonieri V , Comas C , Naranjo C A , Poggio L
Published: October 2004

The aim of this paper is to test with genomic in situ hybridization the genomic affinities between maize and its putative progenitor Zea mays subsp. parviglumis. Blocking procedures were applied for the purpose of improving discrimination among chromosome regions. Unlabeled genomic DNA from Z. mays subsp. parviglumis as a blocking agent and labeled genomic DNA from maize were hybridized on maize chromosomes. On the other hand, mitotic metaphases from Z. mays subsp. parviglumis were blocked with unlabeled genomic DNA of maize and hybridized with labeled genomic DNA from Z. mays subsp. parviglumis. Both experiments showed that either maize or Z. mays subsp. parviglumis chromosomes have their own unique sequences. This means an unexpected degree of divergence if Z. mays subsp. parviglumis is the only progenitor of maize, a result that is discussed in relation to our previous genomic in situ hybridization observations and to the different scenarios proposed about the origin of maize.Key words: evolutionary relationships, Zea mays subsp. mays, teosinte, Tripsacum, molecular cytogenetics, genomic in situ hybridization (GISH).
Genome-wide analysis ofKluyveromyces lactisin wild-type andrag2 mutant strains
Authors: Becerra Manuel , Tarrío Nuria , González-Siso M Isabel , Cerdán M Esperanza
Published: October 2004

The use of heterologous DNA arrays from Saccharomyces cerevisiae has been tested and revealed as a suitable tool to compare the transcriptomes of S. cerevisiae and Kluyveromyces lactis, two yeasts with notable differences in their respirofermentative metabolism. The arrays have also been applied to study the changes in the K. lactis transcriptome owing to mutation in the RAG2 gene coding for the glycolytic enzyme phosphoglucose isomerase. Comparison of the rag2 mutant growing in 2% glucose versus 2% fructose has been used as a model to elucidate the importance of transcriptional regulation of metabolic routes, which may be used to reoxidize the NADPH produced in the pentose phosphate pathway. At this transcriptional level, routes related to the oxidative stress response become an interesting alternative for NADPH use.Key words: Kluyveromyces lactis, transcription, phosphoglucose isomerase, carbohydrate use.
Mining EST databases to resolve evolutionary events in major crop species
Authors: Schlueter Jessica A , Dixon Phillip , Granger Cheryl , Grant David , Clark Lynn , Doyle Jeff J , Shoemaker Randy C
Published: October 2004

Using plant EST collections, we obtained 1392 potential gene duplicates across 8 plant species: Zea mays, Oryza sativa, Sorghum bicolor, Hordeum vulgare, Solanum tuberosum, Lycopersicon esculentum, Medicago truncatula, and Glycine max. We estimated the synonymous and nonsynonymous distances between each gene pair and identified two to three mixtures of normal distributions corresponding to one to three rounds of genome duplication in each species. Within the Poaceae, we found a conserved duplication event among all four species that occurred approximately 50–60 million years ago (Mya); an event that probably occurred before the major radiation of the grasses. In the Solanaceae, we found evidence for a conserved duplication event approximately 50–52 Mya. A duplication in soybean occurred approximately 44 Mya and a duplication in Medicago about 58 Mya. Comparing synonymous and nonsynonymous distances allowed us to determine that most duplicate gene pairs are under purifying, negative selection. We calculated Pearson's correlation coefficients to provide us with a measure of how gene expression patterns have changed between duplicate pairs, and compared this across evolutionary distances. This analysis showed that some duplicates seemed to retain expression patterns between pairs, whereas others showed uncorrelated expression.Key words: genome evolution, polyploidy, genome duplication, expressed sequence tag.
Structural and transcriptional features ofBombus terrestrissatellite DNA and their potential involvement in the differentiation process
Authors: Rouleux-Bonnin Florence , Bigot Sylvie , Bigot Yves
Published: October 2004

A unique satellite DNA family was characterized in the genome of the bumble bee, Bombus terrestris. Sequence analysis revealed that it contains two wide palindromes of about 160 and 190 bp, respectively, that span 75% of the repeated unit. One feature of this satellite DNA is that it accounts for different amounts of genomic DNA in males and females. The DNA curvature and bendability were determined by migration on PAGE and by computer analysis. It has been correlated with the presence of dA/dT stretches repeated in phase with the helix turn and with the presence of the deformable dinucleotide CA–TG embedded in some of these A–T-rich regions. Transcription of the satellite DNA was also analyzed by Northern blot hybridization and RT-PCR. Multimeric transcripts spanning several satellite DNA units were found in RNA samples from males, workers, and queens. These transcripts resulted from a specific transcription occurring on one DNA strand in the embryos or on both DNA strands in imagoes. The involvement of DNA curvature in the organization of the satellite DNA and the function of the satellite transcripts is discussed.Key words: Satellite DNA, transcription, curvature, bendability, Hymenoptera.
Microsatellite variability among wild and cultivated hops (HumuluslupulusL.)
Authors: Jakse Jernej , Satovic Zlatko , Javornik Branka
Published: October 2004

Hop (Humulus lupulus L.) is a dioecious perennial plant native to the northern hemisphere cultivated for its use in the brewing industry. To investigate the genetic diversity present in wild hop accessions in comparison with cultivated hops, microsatellite marker variation was assessed at four loci in 124 accessions of wild (from Europe, Asia and from North America) and cultivated (varieties and breeding lines) hops. A total of 63 alleles were identified, with an average of 15.7 alleles per locus and an average PIC of 0.64 over four loci. The average number of alleles per locus in groups of accessions ranged from 5.75 to 8.30, with the highest number detected in groups of wild hops either of European (EU) or North American (NA) origin. Accessions from NA revealed the highest number of unique alleles indicating the high diversity present in this gene pool. Cluster analysis based on the DDor Dswdistance matrix divided accessions into 10 different clusters, which reflect the relationship among geographically diverse wild accessions and hop cultivars. The highest genetic differences were found between NA wild accessions, forming one distant cluster, and all the other accessions. The differentiation between European wild and cultivated accessions was revealed by PCoA based on the DDdistance matrix and by AMOVA results. Cultivated hops differ significantly from wild ones, although most of the variability was found within groups. The molecular variances within groups of cultivated and wild hops were homogeneous, suggesting that a similar level of molecular variability is found in both groups of accessions. The analysis of allele polymorphism and of allele sequences showed that hop germplasm can be differentiated to NA and EU geographic types according to the differences of allele sizes at three loci or by the specific microsatellite repeat type at one locus. The analysis also indicates the different evolutionary dynamics and complex mutations of microsatellite sequences within loci that can be followed in the two biogeographically separated germplasms.Key words: Humulus lupulus L., genetic diversity, germplasm, microsatellites, allele sequence variation.
Effect of distance from road intersection on developed traffic noise levels
Authors: Abo-Qudais Saad , Alhiary Arwa
Published: October 2004

The main objective of this study was to evaluate the variation in traffic equivalent noise levels as distance from the road intersection increases. To achieve this objective, traffic volume and equivalent noise level were monitored at 40 signalized intersections in Amman, the capital of Jordan. An integrated sound level meter (ISLM) was used to measure 1 min equivalent noise level along all approaches of the evaluated intersections. A total of 3326 noise measurements were performed. The collected data were analyzed to evaluate the variation of noise levels as distance from the intersection increases. The results indicated that equivalent noise levels were significantly affected by distance from the signal stop line. The equivalent noise levels at distances 50 and 100 m from the intersection were found to be 1.5 to 2.0 dB less than those at 0 m. While at 200, 250, and 300 m from the intersection, the monitored equivalent noise levels were found to be 3.8 to 4 dB higher than that at 0 m. At distances farther than 250 m, the measured equivalent noise levels tend to keep constant value of equivalent noise level as distance increased.Key words: noise, traffic, intersection, environment, pollution.
Ratio between peak inelastic and elastic responses with uncertain structural properties
Authors: Hong H P , Jiang J
Published: October 2004

A systematical assessment of the impact of the uncertainty in the natural vibration period and damping ratio on the peak displacement of linear elastic and elastoplastic single-degree-of-freedom systems is carried out using more than 200 strong ground-motion records. The assessment is based on the ratio of the peak inelastic displacement with uncertain structural properties to the peak linear elastic displacement and, the ratio of the peak linear elastic displacement to the yield displacement. Statistical analysis for the ratios obtained is presented. The analysis results indicate that the impact of the uncertainty in the damping ratio on these ratios is less significant than that of the uncertainty in the natural vibration period. The results also show that the consideration of uncertainty in the natural vibration period slightly alters the average peak displacement of the linear or elastoplastic systems. However, the coefficients of variation of these ratios change significantly, especially, if the mean of the natural vibration period is less than about 0.1 s. Simple to use empirical equations, based on the results obtained, are suggested in evaluating the mean and the coefficient of variation of the ratios considering the uncertainty in structural properties. Key words: seismic excitation, uncertainty, peak elastic displacement, peak inelastic displacement.
Flow regimes and energy loss on chutes with upward inclined steps
Authors: Chinnarasri Chaiyuth , Wongwises Somchai
Published: October 2004

This paper presents new experimental data on water flow on stepped chutes with upward inclined steps. The slopes of the chutes are 30°, 45°, and 60° whereas the upward angles of the inclined steps are 10°, 20°, and 30°, respectively. Classifications of flow patterns by empirical correlations are presented. Based on dimensional analysis, the important parameters are analyzed, and the relevant dimensionless parameters are established. The energy loss and outlet velocity are strongly influenced by the Drop number and the slope of the stepped chutes. As the Drop number increases, the energy loss ratio decreases. At identical Drop numbers the energy loss ratio on the more moderate slope is greater than on the steeper. The adverse slope of the inclined steps increases the energy loss ratio and decreases the outlet velocity by less than 10%. To estimate the kinetic energy ratio, an empirical equation is proposed.Key words: stepped chutes, inclined step, energy dissipation, skimming flow, spillways.
A comparison of one-dimensional methods for estimating discharge capacity of straight compound channels
Authors: Seckin Galip
Published: October 2004

A series of experiments was carried out in a two-stage flume having a smooth main channel and smooth or rough floodplains to investigate the reliability and performance of four different one-dimensional methods for computing the discharge capacity of compound channels, namely, the single-channel method (SCM), the divided-channel method (DCM), the exchange discharge method (EDM), and the Ackers method (AM). Additional data from fixed- and mobile-bed compound laboratory channels with smooth and roughened floodplains and of a prototype compound river channel were also used in the computations. The boundary roughness and scale effects associated with the performance of the four methods are also examined. The results show that the EDM and the AM are able to simulate the measured discharge values more accurately than those of the traditional methods, namely, the DCM and the SCM. Although the error in discharge estimation produced by both the AM and the EDM was generally lower than 10% for both smooth and fixed boundaries, it increased up to 20% for mobile boundaries. Overall, the average relative error in discharge estimations using the AM and the EDM was about 5.4% and 7.1%, respectively, with a standard deviation of 6.7% and 6.8%, respectively. Key words: compound channel flow, stage-discharge relationship, one-dimensional methods.
Erosion behaviour of fine sediment deposits
Authors: Krishnappan Bommanna G
Published: October 2004

Erosion characteristics of fine sediment deposits were studied experimentally using a rotating circular flume in the laboratory. The influence of the rate of application of bed shear stress and the structure of sediment beds was investigated. When the shear stress was applied suddenly on a bed formed by placing a thick slurry of kaolin in the flume, the concentration of the eroded sediment first increased to reach a maximum value, and then it started to decrease and finally attained a steady state value that was significantly lower than the maximum concentration (the steady state concentration value was one third of the maximum concentration value). When the shear stress was applied gradually, the behaviour was similar, but the difference between the values of the maximum concentration and steady state concentration was very small (<10%). When the shear stress was applied gradually on a bed formed by depositing a dilute suspension, the concentration increased monotonically and reached the steady state concentration without exhibiting the hump. Such a behaviour was attributed to the sorting of flocs in the settling of dilute suspension in which stronger flocs deposit first followed by weaker flocs in succession.Key words: kaolin, erosion rate, bed shear stress, bed structure, rotating circular flume, flocculation, size distribution.
Role of Serine 286 in cosubstrate binding and catalysis of a flavonolO-methyltransferase
Authors: Kornblatt Jack , Muzac Ingrid , Lim Yoongho , Ahn Joong Hoon , Ibrahim Ragai K
Published: October 2004

O-Methyltransferases catalyze the transfer of the methyl groups of S-adenosyl-L-methionine to specific hydroxyl groups of several classes of flavonoid compounds. Of the several cDNA clones isolated from a Chrysosplenium americanum library, FOMT3′ encodes the 3′/5′-O-methylation of partially methylated flavonols. The recombinant protein of another clone, FOMTx which differs from FOMT3′ by a single amino acid residue (Ser286Arg) exhibits no enzymatic activity towards any of the flavonoid substrates tested. Replacement of Ser 286 in FOMT3′ with either Ala, Leu, Lys or Thr, almost abolished O-methyltransferase activity. In contrast with FOMT3′, no photoaffinity labeling could be achieved using [14CH3]AdoMet with the mutant recombinant proteins indicating that Ser 286 is also required for cosubstrate binding. These results are corroborated by isothermal titration microcalorimetry measurements. Circular dichroism spectra ruled out any significant conformational differences in the secondary structures of both FOMT3′ and Ser286Arg. Modeling FOMT3′ on the structure of chalcone methyltransferase indicates that serine 286 is greater than 10 Å from any of the residues of the active site or the AdoMet binding site of FOMT3′. At the same time, residues 282 to 290 are conserved in most of the Chrysosplenium americanum OMTs. These residues form a large part of the subunit interface, and at least five of these residues are within 4 Å of the opposing subunit. It would appear, therefore, that mutations in Ser286 exert their influence by altering the contacts between the subunits and that these contacts are necessary for maintaining the integrety of the AdoMet binding site and active site of this group of enzymes. Key words: flavonoids, O-methyltransferase, photoaffinity labeling.
Two-dimensional isotropic harmonic oscillator approach to classical and quantum Stokes parameters
Authors: Mota R D , Xicoténcatl M A , Granados V D
Published: October 2004

We show that the well-known Stokes operators, defined as elements of the JordanSchwinger map with the Pauli matrices of two independent bosons, are equal to the constants of motion of the two-dimensional isotropic harmonic oscillator. Taking the expectation value of the Stokes operators in a two-mode coherent state, we obtain the corresponding classical Stokes parameters. We show that this classical limit of the Stokes operators, the 2 × 2 unit matrix and the Pauli matrices may be used to expand the polarization matrix. Finally, by means of the constants of motion of the classical two-dimensional isotropic harmonic oscillator, we describe the geometric properties of the polarization ellipse. Our study is restricted to the case of a monochromatic quantized-plane electromagnetic wave that propagates along the z axis.PACS Nos.: 42.50.p, 42.25.Ja, 11.30.j
Electrochemical cementation of offshore calcareous soil
Authors: Shang J Q , Mohamedelhassan E , Ismail M
Published: October 2004

The electrochemical stabilization processes are studied in a calcareous soil recovered from the Western Australia coast and on the interface of calcareous soil and steel foundation. A series of experiments are performed to study the effects of two chemical agents used in electrochemical stabilization tests. The strengthening effects of electro kinetics and electrochemical treatments on the calcareous soil are investigated first. Significant increases in the undrained shear strength and effective cohesion are obtained after all tests, and the most significant improvement is found after the electrochemical treatment using a 15% CaCl2 solution as the stabilization agent. Subsequently, an electrochemical test is carried out on the calcareous soil with an embedded steel plate to simulate a part of a caisson foundation, using CaCl2 as the stabilization agent. In this test, the practical considerations for later large-scale tests and ultimately for field implementation are taken into account in the design, including factors such as the attachment of electrodes to the foundation, injection of the stabilization agent via perforated pipe electrodes, and distributions of voltage and electrical current in the soil. The result of this test reveals a 700% increase in the steel plate axial load capacity after 7 days of treatment with an applied voltage of 4 V. The main features of the approach are that it generates virtually no disturbance to the soil and the treatment is targeted at the soilstructure interface. With further development, the electrochemical treatment may be applied in offshore engineering for stabilization of foundations installed in weak calcareous soils.Key words: calcareous soil, offshore foundations, soil improvement, chemical stabilization, electrokinetics.
Design and laboratory verification of a physical model of sloping capillary barrier
Authors: Tami Denny , Rahardjo Harianto , Leong Eng-Choon , Fredlund Delwyn G
Published: October 2004

A physical model was designed and constructed to study the mechanisms associated with capillary barriers for slope stabilization purposes. Prior to construction of the model, various numerical analyses were conducted to determine the optimum dimensions and appropriate soil types for the materials of the capillary barrier model. This paper is divided into three sections: the first two sections are related to the design of the model and are to obtain the optimum dimensions of the model and to investigate the range of soil properties that are most suitable for experimental studies in the laboratory; and the last section is laboratory verification of the numerical analysis where the numerical simulation results are compared with the experimental data. Based on the numerical simulation results, the physical capillary barrier model was constructed using two different combinations of soils, namely silty sand over gravelly sand and fine sand over gravelly sand. From the comparison of the numerical results and experimental data, it was found that the numerical analysis was able to simulate the experiment on the physical capillary barrier model reasonably well.Key words: physical capillary barrier model, unsaturated water flow, numerical simulation, pore-water pressure, volumetric water content, slope stability, infiltration.
NUCLEAR MATTER AND PROTON HALO NUCLEI IN A CHIRAL HADRONIC MODEL
Authors: GUO HUA , LIANG YINHUA , LI XIGUO , LIU YUXIN , LIU BO
Published: October 2004

The results for the nuclear-matter properties in a chiral hadronic model have been compared with those in the nonlinear Walecka model. It has been found that the scalar and the vector potentials and binding energies per nucleon for nuclear matter in the chiral hadronic model are very close to those of the RBHF. Two-proton halo in 27 S and one-proton halo in 26 P are predicted when the chiral hadronic model is extended to study proton halos in light proton-rich nuclei. Comparison between the results obtained in the chiral hadronic model and in the nonlinear Walecka model has been made, it has been shown that the chiral hadronic model can also be used to describe the properties of light proton-rich nuclei.
TWO-DIMENSIONAL INTERACTIONS BETWEEN A BF-TYPE THEORY AND A COLLECTION OF VECTOR FIELDS
Authors: CIOROIANU E. M. , SĂRARU S. C.
Published: October 2004

Consistent interactions that can be added to a two-dimensional, free Abelian gauge theory comprising a special class of BF-type models and a collection of vector fields are constructed from the deformation of the solution to the master equation based on specific cohomological techniques. The deformation procedure modifies the Lagrangian action, the gauge transformations, as well as the accompanying algebra of the interacting model.
ANTICIPATING AND LAG SYNCHRONIZATION IN CHAOTIC LASER SYSTEM
Authors: ZHU SHIQUN , WU LIANG
Published: October 2004

The chaotic synchronization between two unidirectionally coupled single-mode semiconductor lasers is investigated when the lasers are subjected to external feedback. The dynamics of lasers is described by Lang–Kobayashi equation. Through numerical simulations, it is found that the lag and anticipating synchronization coexist in the system, and the transition occurs between two kinds of synchronization. Further discussion shows that the coexistence and transition process is based on the continuous similarity relation in bifilar helix structure.
VAN DER WAALS INTERACTION OF TWO ATOMS NEAR A METALLIC PLANE
Authors: TOPOR NADIA , PIATEK SLAWOMIR
Published: October 2004

We have made the first calculation of the retarded van der Waals potential for two identical, neutral atoms near a perfectly conducting plane. As the distance between the atoms and the plane becomes large, compared to atomic dimensions, our results reduce to the Casimir–Polder potential. We have shown that one of the effects determined by the boundary is either an attractive or a repulsive force between the atoms and the plane.
INFLUENCE OF THE COUNTER-ROTATING TERMS ON THE RABI OSCILLATIONS AND SQUEEZING IN THE POLYATOMIC JAYNES-CUMMINGS MODEL WITH CAVITY LOSSES FOR INITIAL COHERENT FIELDS
Authors: SEKE J.
Published: October 2004

The influence of the counter-rotating terms in the polyatomic Jaynes-Cummings model with cavity losses is investigated. Numerical results for the time evolution of the atomic population inversion, dipole moment, mean-photon number and atomic and field squeezing parameters for an initial coherent field are presented for different cavity dampings. As a consequence of the counter-rotating terms, the appearance of new steady states for the population inversion and the mean-photon number is pointed out.
FERMIONIC FOUR-LEVEL SYSTEM IN THE PRESENCE OF A TIME-DEPENDENT MAGNETIC FIELD
Authors: THOMAZ M.T.
Published: October 2004

The exact fermionic four-level system is studied in the presence of time-dependent magnetic field. The system is considered under two initial conditions: general initial vector state, and, at thermal equilibrium. The exact time evolution of one-particle operators is derived.
EFFECTIVE FIELD THEORY OF IDEAL-FLUID HYDRODYNAMICS
Authors: SCHAKEL ADRIAAN M.J.
Published: October 2004

Starting from a standard description of an ideal, isentropic fluid, we derive the effective theory governing a gapless non-relativistic mode — the sound mode. The theory, which is dictated by the requirement of Galilei invariance, entails the entire set of hydrodynamic equations. The gaplessness of the sound mode is explained by identifying it as the Goldstone mode associated with the spontaneous breakdown of Galilei invariance. Differences with a superfluid are pointed out.
RELAXATIONAL HEAT CAPACITY AND UNIVERSALITY IN LINEAR POLYMER CHAINS
Authors: DE HARO M. LÓPEZ , GONÇALVES L. L. , TAGÜEÑA-MARTÍNEZ J.
Published: October 2004

The relaxational heat capacity of an infinite linear polymer chain is computed. The result is derived within a kinetic Ising-like model previously introduced to provide for a dynamical generalization of the Gibbs-di Marzio lattice model. The questions of universality of the dynamic responses of the chain and of the existence of more than one relaxation time if one considers different probes are discussed.
GOOD NEWS: PARTITIONING A SIMPLE POLYGON BY COMPASS DIRECTIONS
Authors: VAN KREVELD MARC , REINBACHER IRIS
Published: October 2004

Motivated by geographic information retrieval, we study the problem of partitioning a simple polygon into four parts that can be considered as the North, East, West, and South. We list criteria for such partitionings, propose formalizations into geometric problems, and give efficient algorithms. An implementation and tests on country outlines show the results for three different partitionings.
ESTIMATING SURFACE NORMALS IN NOISY POINT CLOUD DATA
Authors: MITRA NILOY J. , NGUYEN AN , GUIBAS LEONIDAS
Published: October 2004

In this paper we describe and analyze a method based on local least square fitting for estimating the normals at all sample points of a point cloud data (PCD) set, in the presence of noise. We study the effects of neighborhood size, curvature, sampling density, and noise on the normal estimation when the PCD is sampled from a smooth curve in ℝ2or a smooth surface in ℝ3, and noise is added. The analysis allows us to find the optimal neighborhood size using other local information from the PCD. Experimental results are also provided.
CONTROLLED PERTURBATION FOR ARRANGEMENTS OF CIRCLES
Authors: HALPERIN DAN , LEISEROWITZ ERAN
Published: October 2004

Given a collection [Formula: see text] of circles in the plane, we wish to construct the arrangement [Formula: see text] (namely the subdivision of the plane into vertices, edges and faces induced by [Formula: see text]) using floating point arithmetic. We present an efficient scheme, controlled perturbation, that perturbs the circles in [Formula: see text] slightly to form a collection [Formula: see text], so that all the predicates that arise in the construction of [Formula: see text] are computed accurately and [Formula: see text] is degeneracy free.

We introduced controlled perturbation several years ago, and already applied it to certain types of arrangements. The major contribution of the current work is the derivation of a good (small) resolution bound, that is, a bound on the minimum separation of features of the arrangement that is required to guarantee that the predicates involved in the construction can be safely computed with the given (limited) precision arithmetic. A smaller resolution bound leads to smaller perturbation of the original input.

We present the scheme, describe how the resolution bound is determined and how it effects the perturbation magnitude. We implemented the perturbation scheme and the construction of the arrangement and we report on experimental results.
GEOMETRIC ALGORITHMS FOR STATIC LEAF SEQUENCING PROBLEMS IN RADIATION THERAPY
Authors: CHEN DANNY Z. , HU XIAOBO S. , LUAN SHUANG (SEAN) , WANG CHAO , WU XIAODONG
Published: October 2004

The static leaf sequencing (SLS) problem arises in radiation therapy for cancer treatments, aiming to accomplish the delivery of a radiation prescription to a target tumor in the minimum amount of delivery time. Geometrically, the SLS problem can be formulated as a 3-D partition problem for which the 2-D problem of partitioning a polygonal domain (possibly with holes) into a minimum set of monotone polygons is a special case. In this paper, we present new geometric algorithms for a basic case of the 3-D SLS problem (which is also of clinical value) and for the general 3-D SLS problem. Our basic 3-D SLS algorithm, based on new geometric observations, produces guaranteed optimal quality solutions using O(1) Steiner points in polynomial time; the previously best known basic 3-D SLS algorithm gives optimal outputs only for the case without considering any Steiner points, and its time bound involves a multiplicative factor of a factorial function of the input. Our general 3-D SLS algorithm is based on our basic 3-D SLS algorithm and a polynomial time algorithm for partitioning a polygonal domain (possibly with holes) into a minimum set of x-monotone polygons, and has a fast running time. Experiments of our SLS algorithms and software in clinical settings have shown substantial improvements over the current most popular commercial treatment planning system and the most well-known SLS algorithm in medical literature. The radiotherapy plans produced by our software not only take significantly shorter delivery times, but also have a much better treatment quality. This proves the feasibility of our software and has led to its clinical applications at the Department of Radiation Oncology at the University of Maryland Medical Center. Some of our techniques and geometric procedures (e.g., for partitioning a polygonal domain into a minimum set of x-monotone polygons) are interesting in their own right.
LOW-SPIN STATES OF 76Se EXCITED IN 76Br(β++EC)76Se DECAY
Authors: LI YAN , SHEN SHUIFA , HUANG WENDA , SHI SHUANGHUI , GU JIAHUI , LIU JINGYI , XU HUI
Published: October 2004

The decay of bromine-76 was studied using high resolution HpGe detectors in singles and coincidence mode. Bromine-76 was produced via two reactions: 75 As (α,3 n )76 Br and 76 Se ( p , n )76 Br . The results of these experiments verified the previously reported levels of 76 Se . In addition to the previously described transitions and levels, 37 new γ-rays and 15 new energy levels were found for the first time.
VARIATION IN HUMAN MEIOTIC RECOMBINATION
Authors: Lynn Audrey , Ashley Terry , Hassold Terry
Published: October 2004

▪ Abstract  As recently as 20 years ago, there was relatively little information about the number and distribution of recombinational events in human meiosis, and we knew virtually nothing about factors affecting patterns of recombination. However, the generation of a variety of linkage-based genetic mapping tools and, more recently, cytological approaches that enable us to directly visualize the recombinational process in meiocytes, have led to an increased understanding of human meiosis. In this review, we discuss the different approaches used to study meiotic recombination in humans, our understanding of factors that affect the number and location of recombinational events, and clinical consequences of variation in the recombinational process.