bluuebunny/crossref_metadata_2025 huggingface dataset:
International Multicenter Evaluation of Autoantibodies to Ribosomal P Proteins
Authors: Mahler Michael , Kessenbrock Kai , Szmyrka Magdalena , Takasaki Yoshinari , Garcia-De La Torre Ignacio , Shoenfeld Yehuda , Hiepe Falk , Shun-le Chen , von Mühlen Carlos A. , Locht Henning , Höpfl Peter , Wiik Allan , Reeves Westley , Fritzler Marvin J.
Published: January 2006

Autoantibodies to the ribosomal phosphoproteins (Rib-P) are a serological feature of patients with systemic lupus erythematosus (SLE). The reported prevalence of anti-Rib-P antibodies in SLE ranges from 10 to 40%, being higher in Asian patients. The variation in the observed frequency may be related to a number of factors but is dependent in large part on the test system used to detect the autoantibodies. An association of anti-Rib-P with central nervous system involvement and neuropsychiatric manifestations of SLE has been controversial. In the present international multicenter study, we evaluated the clinical accuracy of a new sensitive Rib-P-specific enzyme-linked immunosorbent assay based on recombinant Rib-P polypeptides. The results showed that 21.3% of 947 SLE patients, but only 0.7% of 1,113 control patients, had a positive test result (
P
< 0.0001). The sensitivity, specificity, positive and negative predictive values, and diagnostic efficiency were determined to be 21.3%, 99.3%, 95.6%, 62.2%, and 65.3%, respectively. When evaluated in the context of participating centers, the prevalence of anti-Rib-P antibodies was found in descending frequency, as follows: China (35%) > Poland (34%) > Japan (28%) > United States (26%) > Germany (Freiburg; 23.3%) > Denmark (20.5%) > Germany (Berlin; 19%) > Mexico (15.7%) > Israel (11.7%) > Brazil (10%) > Canada (8%). The substantial data from this study indicate that the prevalence of anti-Rib-P antibodies may not be restricted to the genetic background of the patients or to the detection system but may depend on regional practice differences and patient selection. We confirm previously reported associations of antiribosomal antibodies with clinical symptoms and serological findings. Remarkably, we found a lower occurrence of serositis in Rib-P-positive lupus patients.
Detection of Immunoglobulin G Antibodies toNeospora caninumin Humans: High Seropositivity Rates in Patients Who Are Infected by Human Immunodeficiency Virus or Have Neurological Disorders
Authors: Lobato Janaína , Silva Deise A. O. , Mineo Tiago W. P. , Amaral Jodi D. H. F. , Segundo Gesmar R. Silva , Costa-Cruz Julia M. , Ferreira Marcelo S. , Borges Aércio S. , Mineo José R.
Published: January 2006

Considering that little is known about the epidemiology ofNeospora caninuminfection in humans, particularly in populations with highToxoplasma gondiiinfection rates, the present study aimed to investigate the presence of antibodies toN. caninuminT. gondii-seropositive and -seronegative individuals. A total of 256 serum samples divided into four groups (61 samples from human immunodeficiency virus [HIV]-positive patients, 50 samples from patients with neurological disorders, 91 samples from newborns, and 54 samples from healthy subjects) were assessed forN. caninumandT. gondiiserologies by indirect fluorescent-antibody test, enzyme-linked immunosorbent assay, and immunoblotting (IB). Immunoglobulin G antibodies toN. caninumwere predominantly detected in HIV-infected patients (38%) and patients with neurological disorders (18%), while newborns and healthy subjects showed lower seropositivity rates (5% and 6%, respectively). Seropositivity toN. caninumwas significantly associated with seropositivity toT. gondiiin both HIV-infected patients and patients with neurological disorders. Seroreactivity toN. caninumwas confirmed by IB, with positive sera predominantly recognizing the 29-kDa antigen ofN. caninum. The results of this study indicate the presence ofN. caninuminfection or exposure in humans, particularly in HIV-infected patients or patients with neurological disorders, who could have opportunistic and concurrent infections withT. gondii. These findings may bring a new concern for the unstable clinical health of HIV-infected patients and the actual role ofN. caninuminfection in immunocompromised patients.
Antigen Mining with Iterative Genome Screens Identifies Novel Diagnostics for the
Mycobacterium tuberculosis
Complex
Authors: Ewer Katie , Cockle Paul , Gordon Steve , Mansoor Huma , Govaerts Marc , Walravens Karl , Marché Sylvie , Hewinson Glyn , Vordermeier Martin
Published: January 2006

The definition of antigens for the diagnosis of human and bovine tuberculosis is a research priority. If diagnosis is to be used alongside
Mycobacterium bovis
BCG-based vaccination regimens, it will be necessary to have reagents that allow the discrimination of infected and vaccinated animals. A list of 42 potential
M. bovis-
specific antigens was prepared by comparative analysis of the genomes of
M. bovis
,
M. avium
subsp.
avium
,
M. avium
subsp.
paratuberculosis
, and
Streptomyces coelicolor
. Potential antigens were tested by applying them in a high-throughput peptide-based screening system to
M. bovis
-infected and BCG-vaccinated cattle and to cattle without prior exposure to
M. bovis
. A response hierarchy of antigens was established by comparing responses in infected animals. Three antigens (Mb2555, Mb2890, and Mb3895) were selected for further study, as they were strongly recognized in experimentally infected animals but with low or no frequency in BCG-vaccinated and naïve cows. Interestingly, all three antigens were recognized in animals vaccinated against Johne's disease, suggesting the presences of epitopes cross-reacting with
M. avium
subsp.
paratuberculosis
antigens. Eight peptides from the three antigens studied in detail were identified as immunodominant and were characterized in terms of major histocompatibility complex class II restriction element usage and shown to be restricted through both DR and DQ molecules. Reasons for antigenic cross-reactivity with
M. avium
subsp.
paratuberculosis
and refinement of the in silico strategy to predict such cross-reactivity from the primary protein sequence will be discussed. Evaluation of the peptides identified from the three dominant antigens by use of larger field studies is now a priority.
Development, inheritance, and linkage-group assignment of 60 novel microsatellite markers for the gray, short-tailed opossum Monodelphis domestica
Authors: Gouin Nicolas , Westenberger Scott J , Mahaney Susan M , Lindley Peter , VandeBerg John L , Samollow Paul B
Published: January 2006

Short-tandem-repeat (SSR) or microsatellite polymorphisms are some of the most extensively employed genetic markers in contemporary linkage mapping studies. To date, only a limited number of microsatellites have been isolated in the gray, short-tailed opossum Monodelphis domestica, a South American marsupial widely used for comparative biological and biomedical research. To increase the number of potentially useful mapping markers, we screened 2 microsatellite-enriched genomic libraries containing alternatively (CA)n or (GA)n repeats. A total of 184 clones were sequenced, from which 60 polymorphic microsatellite markers were successfully optimized. The efficiency of this enrichment protocol for M. domestica microsatellite isolation is discussed, and suggestions to improve the outcome are made. All 60 loci showed high allelic diversity, with allele numbers ranging from 2 to 10 in a subset of 33 unrelated animals. Normal Mendelian inheritance was confirmed for all loci by analyzing allelic segregation in 5 two-generation families. One microsatellite appeared to be X linked, and null alleles were found in 5 others. Two-point linkage analyses were implemented using the data on the 5 families, leading to the assignment of 59 of these loci to the existing linkage groups. The 60 novel microsatellites developed in this study will contribute significantly to the M. domestica linkage map, and further QTL mapping studies.Key words: Monodelphis domestica, marsupial, microsatellite, enriched libraries, genetic linkage analysis.
Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species
Authors: Kumpatla Siva P , Mukhopadhyay Snehasis
Published: January 2006

Simple sequence repeat (SSR) markers are widely used in many plant and animal genomes due to their abundance, hypervariability, and suitability for high-throughput analysis. Development of SSR markers using molecular methods is time consuming, laborious, and expensive. Use of computational approaches to mine ever-increasing sequences such as expressed sequence tags (ESTs) in public databases permits rapid and economical discovery of SSRs. Most of such efforts to date focused on mining SSRs from monocotyledonous ESTs. In this study, we have computationally mined and examined the abundance of SSRs in more than 1.54 million ESTs belonging to 55 dico tyledonous species. The frequency of ESTs containing SSRs among species ranged from 2.65% to 16.82%. Dinucleotide repeats were found to be the most abundant followed by tri- or mono-nucleotide repeats. The motifs A/T, AG/GA/CT/TC, and AAG/AGA/GAA/CTT/TTC/TCT were the predominant mono-, di-, and tri-nucleotide SSRs, respectively. Most of the mononucleotide SSRs contained 15–25 repeats, whereas the majority of the di- and tri-nucleotide SSRs contained 5–10 repeats. The comprehensive SSR survey data presented here demonstrates the potential of in silico mining of ESTs for rapid development of SSR markers for genetic analysis and applications in dicotyledonous crops.Key words: simple sequence repeats, expressed sequence tags, SSRs, ESTs, bioinformatics, mining, survey, dicotyledonous species, markers.
Molecular cytogenetic characterization ofAegilops biuncialisand its use for the identification of 5 derived wheat – Aegilops biuncialisdisomic addition lines
Authors: Schneider Annamária , Linc Gabriella , Molnár István , Molnár-Láng Márta
Published: January 2006

The aim of the experiments was to produce and identify different Triticum aestivum – Aegilops biuncialis disomic addition lines. To facilitate the exact identification of the Ae. biuncialis chromosomes in these Triticum aestivum – Ae. biuncialis disomic additions, it was necessary to analyze the fluorescence in situ hybridization (FISH) pattern of Ae. biuncialis (2n = 4x = 28, UbUbMbMb), comparing it with the diploid progenitors (Aegilops umbellulata, 2n = 2x = 14, UU and Aegilops comosa, 2n = 2x = 14, MM). To identify the Ae. biuncialis chromosomes, FISH was carried out using 2 DNA clones (pSc119.2 and pAs1) on Ae. biuncialis and its 2 diploid progenitor species. Differences in the hybridization patterns of all chromosomes were observed among the 4 Ae. umbellulata accessions, the 4 Ae. comosa accessions, and the 3 Ae. biuncialis accessions analyzed. The hybridization pattern of the M genome was more variable than that of the U genome. Five different wheat – Ae. biuncialis addition lines were produced from the wheat – Ae. biuncialis amphiploids produced earlier in Martonvásár. The 2M, 3M, 7M, 3U, and 5U chromosome pairs were identified with FISH using 3 repetitive DNA clones (pSc119.2, pAs1, and pTa71) in the disomic chromosome additions produced. Genomic in situ hybridization (GISH) was used to differentiate the Ae. biuncialis chromosomes from wheat, but no chromosome rearrangements between wheat and Ae. biuncialis were detected in the addition lines.Key words: Triticum aestivum, Aegilops biuncialis, fluorescence in situ hybridization, genomic in situ hybridization, wheat – Aegilops biuncialis addition lines.
Codling moth cytogenetics: karyotype, chromosomal location of rDNA, and molecular differentiation of sex chromosomes
Authors: Fuková Iva , Nguyen Petr , Marec Frantiek
Published: January 2006

We performed a detailed karyotype analysis in the codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), the key pest of pome fruit in the temperate regions of the world. The codling moth karyotype consisted of 2n = 56 chromosomes of a holokinetic type. The chromosomes were classified into 5 groups according to their sizes: extra large (3 pairs), large (3 pairs), medium (15 pairs), small (5 pairs), and dot-like (2 pairs). In pachytene nuclei of both sexes, a curious NOR (nucleolar organizer region) bivalent was observed. It carried 2 nucleoli, each associated with one end of the bivalent. FISH with an 18S ribosomal DNA probe confirmed the presence of 2 clusters of rRNA genes at the opposite ends of the bivalent. In accordance with this finding, 2 homologous NOR chromosomes were identified in mitotic metaphase, each showing hybridization signals at both ends. In highly polyploid somatic nuclei, females showed a large heterochromatin body, the so-called sex chromatin or W chromatin. The heterochromatin body was absent in male nuclei, indicating a WZ/ZZ (female/male) sex chromosome system. In keeping with the sex chromatin status, pachytene oocytes showed a sex chromosome bivalent (WZ) that was easily discernible by its heterochromatic W thread. To study molecular differentiation of the sex chromosomes, we employed genomic in situ hybridization (GISH) and comparative genomic hybridization (CGH). GISH detected the W chromosome by strong binding of the Cy3-labelled, female-derived DNA probe. With CGH, both the Cy3-labelled female-derived probe and Fluor-X labelled male-derived probe evenly bound to the W chromosome. This suggested that the W chromosome is predominantly composed of repetitive DNA sequences occurring scattered in other chromosomes but accumulated in the W chromosome. The demonstrated ways of W chromosome identification will facilitate the development of genetic sexing strains desirable for pest control using the sterile insect technique.Key words: CGH, codling moth, FISH, GISH, genomic hybridization, heterochromatin, holokinetic chromosomes, karyotype, NOR, rDNA, SIT, sex chromosomes.
Mapping of QTLs for androgenetic response based on a molecular genetic map of ×TriticosecaleWittmack
Authors: González Juan M , Muñiz Luis M , Jouve Nicolás
Published: January 2006

Quantitative trait loci (QTLs) for androgenetic response were mapped in a doubled haploid (DH) population derived from the F1hybrid of 2 unrelated varieties of triticale, 'Torote' and 'Presto'. A molecular marker linkage map of this cross was previously constructed using 73 DH lines. This map contains 356 markers (18 random amplified 5polymorphic DNA, 40 random amplified microsatellite polymorphics, 276 amplified fragment length polymorphisms, and 22 simple sequence repeats) and was used for QTL analysis. The genome was well covered, and of the markers analysed, 336 were located in 21 linkage groups (81.9%) identified using SSR markers. The map covered a total length of 2465.4 cM with an average of 1 marker for each 6.9 cM. The distribution of the markers was not homogeneous across the 3 genomes, with 50.7% detected in the R genome. Several QTLs were found for the following variables related to the androgenetic response: number of embryos/100 anthers; plants regenerated from 100 embryos; number of green plants/total number of plants; and number of green plants/1000 anthers. Two were detected on chromosome 6B and 4R, which together had a 30% total influence on the induction of embryos. Another was found on 6B and on the unidentified LG1; these influenced the production of total plants from haploid embryo cultures. One QTL on chromosome 3R determined the photosynthetic viability of the haploid plantlets regenerated from microspores. Other QTLs were found on chromosomes 1B, 1R, 4R, and 7R, which helped the control of the final androgenetic response (the number of plantlets obtained for every 1000 anthers cultured).Key words: triticale, genetic map, AFLP, RAMP, RAPD, SSR, QTL, androgenesis.
Toward the development of highly homozygous diploid potato lines using the self-compatibility controllingSligene
Authors: Phumichai Chalermpol , Mori Motoyuki , Kobayashi Akira , Kamijima Osamu , Hosaka Kazuyoshi
Published: January 2006

Cultivated diploid potatoes (2n = 2x = 24) are self-incompatible, but can be altered to become self-compatible using the Sli gene. Previously, a diploid clone 97H32–6 was selfed up to S3using the Sli gene. To explore the usefulness of the Sli gene for the production of highly homozygous diploid potatoes, 2 S4families from the above 97H32-6 derived S3lines (inbred series A) and 3 S5families by continuous selfings from a different F1(= S0) plant (inbred series B) were developed. The level of heterozygosity and the location of heterozygous loci on the genetic map were investigated using RFLP and AFLP markers. The average heterozygosity levels of the originally heterozygous loci decreased from 100% in S0to 10.7% in S4and 8.6% in S5(inbred series A and B, respectively). The average rate of reduction in heterozygosity per generation (38.4% and 38.5% for inbred series A and B, respectively) was lower than the theoretically expected rate (50%). However, none of the loci or chromosome sections was exclusively heterozygous in the advanced self-progeny. Thus, highly homozygous and seed-propagated diploid potatoes could be obtained by repeated selfing using the Sli gene.Key words: Selfing, heterozygosity, diploid potato, Sli gene, Solanum.
Relationships among 3Kochiaspecies based on PCR-generated molecular sequences and molecular cytogenetics
Authors: Lee B S , Kim M Y , Wang R R.-C , Waldron B L
Published: January 2006

Forage kochia (Kochia prostrata ssp. virescens 'Immigrant' is native to the arid and semiarid regions of central Eurasia. It was introduced into the United States in 1966 as PI 314929 and released as a perennial forage shrub in 1984. Kochia americana is a perennial native to the United States, whereas Kochia scorparia is an introduced annual species that became a weed. To assess both the breeding potential and the possibility of genetic contamination, relationships among the 3 Kochia species were analyzed using random amplified polymorphic DNA (RAPD) markers, sequence tagged site (STS) marker sequences of the chloroplast NADH dehydrogenase gene (ndhF), genomic in situ hybridization (GISH), and multicolor fluorescence in situ hybridization (MC-FISH). Seventy decamer random primers yielded 458 polymorphic bands from 9 plants of K. americana, 20 plants of K. prostrata, and 7 plants of K. scoparia. Fifty-four and 55 species-specific RAPD markers were identified for K. americana and K. prostrata, whereas 80 RAPD markers were specific to K. scoparia. Based on the presence or absence of informative RAPD markers, the 3 species always grouped into 3 distinct clusters in a NTSYSpc2.01b-generated dendrogram. The same relationships were found among the 3 Kochia species based on ndhF DNA sequence divergence. Using a set of 7 STS markers that can identify each Kochia species, we did not find a single interspecific hybrid from artificial hybridizations among the 3 Kochia species. In GISH studies, chromosomes of 1 species fluoresced in green only when they were probed by genomic DNA of the same species. Cross-hybridization by genomic DNA of another species was not observed. In FISH studies using pTa71 (for 18S–5.8S–26S rDNAs) and pScT7 (for 5S rDNA) as probes, there were 1, 1 and 3 pTa71 sites and 2, 1, and 1 pScT7 sites in each haplome of K. prostrata, K. americana, and K. scoparia, respectively. It is concluded that these 3 Kochia species are so genomically distinct that gene introgression among them would be extremely rare.Key words: RAPD, STS, ndhF, GISH, FISH, mixoploidy, forage kochia.
Comparative genomic analyses in Asparagus
Authors: Kuhl Joseph C , Havey Michael J , Martin William J , Cheung Foo , Yuan Qiaoping , Landherr Lena , Hu Yi , Leebens-Mack James , Town Christopher D , Sink Kenneth C
Published: January 2006

Garden asparagus (Asparagus officinalis L.) belongs to the monocot family Asparagaceae in the order Asparagales. Onion (Allium cepa L.) and Asparagus officinalis are 2 of the most economically important plants of the core Asparagales, a well supported monophyletic group within the Asparagales. Coding regions in onion have lower GC contents than the grasses. We compared the GC content of 3374 unique expressed sequence tags (ESTs) from A. officinalis with Lycoris longituba and onion (both members of the core Asparagales), Acorus americanus (sister to all other monocots), the grasses, and Arabidopsis. Although ESTs in A. officinalis and Acorus had a higher average GC content than Arabidopsis, Lycoris, and onion, all were clearly lower than the grasses. The Asparagaceae have the smallest nuclear genomes among all plants in the core Asparagales, which typically have huge genomes. Within the Asparagaceae, European Asparagus species have approximately twice the nuclear DNA of that of southern African Asparagus species. We cloned and sequenced 20 genomic amplicons from European A. officinalis and the southern African species Asparagus plumosus and observed no clear evidence for a recent genome doubling in A. officinalis relative to A. plumosus. These results indicate that members of the genus Asparagus with smaller genomes may be useful genomic models for plants in the core Asparagales.Key words: asparagus, GC content, duplication.
5S rDNA and U2 snRNA are linked in the genome of Crassostrea angulata and Crassostrea gigas oysters: does the (CT)n·(GA)n microsatellite stabilize this novel linkage of large tandem arrays?
Authors: Cross I , Rebordinos L
Published: January 2006

The 5S rRNA genes from 2 species of the Ostreidae family, Crassostrea angulata and Crassostrea gigas, were molecularly characterized. The genes were amplified, cloned, and sequenced. The results revealed a 5S rDNA tandem array with a nucleotide sequence in an inverted position within the nontranscribed spacer region that corresponded to the U2 small nuclear RNA (snRNA) gene. The sequence analysis indicated that both genes could be functionally active. The presence of the microsatellite (CT)n·(GA)n at the 3′ end of both genes and the possible involvement of concerted evolution are discussed.Key words: Crassostrea angulata, Crassostrea gigas, 5S rDNA, U2 snRNA, microsatellite, concerted evolution.
Mitochondrial DNA variation in the grasshopper Sinipta dalmani: application of long-PCR to the development of a homologous probe
Authors: Pensel S M , Vilardi J C , Remis M I
Published: January 2006

RFLP analysis of mtDNA in natural populations is a valuable tool for phylogeographic and population genetic studies. The amplification of long DNA fragments using universal primers may contribute to the development of novel homologous probes in species for which no previous genomic information is available. Here we report how we obtained the complete mtDNA genome of Sinipta dalmani (Orthoptera) in 2 fragments (7 and 9 kb) using primers of conserved regions. The specificity of the PCR reactions was ultimately confirmed by several lines of evidence. These fragments were used as a probe for a mtDNA RFLP study in S. dalmani that analyzed the pattern of haplotype distribution and nucleotide diversity within and among chromosomally differentiated natural populations. Our results suggest that the restriction in gene flow detected at the molecular level may explain the chromosome differentiation detected previously and the maintenance of chromosome polymorphism in some areas of S. dalmani geographic distribution.Key words: long-PCR, mitochondrial DNA, universal primers, RFLP, grasshopper.
Population dynamics of the 2 major mitochondrial DNA haplotypes in experimental populations ofDrosophila subobscura
Authors: Oliver Pedro , Balanyà Joan , Ramon Maria Misericòrdia , Picornell Antònia , Serra Lluis , Moya Andrés , Castro José A
Published: January 2006

The evolution of Drosophila subobscura mitochondrial DNA has been studied in experimental populations, founded with flies from a natural population from Calvià (Majorca, Balearic Islands, Spain). This population, like others founded in Europe, is characterized by the presence of 2 very common (>95%) mitochondrial haplotypes (named I and II) and rare and endemic haplotypes that appear at very low frequencies. Four experimental populations were established with flies having a heterogeneous nuclear genetic background, which was representative of the composition of the natural population. The populations were started with haplotypes I and II at an initial frequency of 50% each. After 33 generations, the 2 haplotypes coexisted. Random drift could be rejected as the only force responsible for the observed changes in haplotype frequencies. A slight but significant linear trend favouring a mtDNA (haploid) fitness effect has been detected, with a nonlinear deviation that could be due to a nuclear component. An analysis of chromosomal arrangements was made before the foundations of the cages and at generation 23. Our results indicated that the hypothesis that the maintenance of the frequencies of haplotypes I and II in natural populations could be due to their association with chromosomal arrangements remains controversial.Key words: natural selection, random drift, cytonuclear interactions, chromosomal arrangements, mtDNA haplotypes, Drosophila subobscura.
Construction of a hexaploid wheat (Triticum aestivumL.) bacterial artificial chromosome library for cloning genes for stripe rust resistance
Authors: Ling P , Chen X M
Published: January 2006

A hexaploid wheat (Triticum aestivum L.) bacterial artificial chromosome (BAC) library was constructed for cloning Yr5 and other genes conferring resistance to stripe rust (Puccinia striiformis f. sp. tritici). Intact nuclei from a Yr5 near-isogenic line were used to isolate high molecular weight DNA, which was partially cleaved with HindIII and cloned into pECBAC1 and pIndigoBAC-5 vectors. The wheat BAC library consisted of 422 400 clones arrayed in 1100 micro-titer plates (each plate with 384 wells). Random sampling of 300 BAC clones indicated an average insert size of 140 kb, with a size range from 25 to 365 kb. Ninety percent of the clones in the library had an insert size greater than 100 kb and fewer than 5% of the clones did not contain inserts. Based on an estimated genome size of 15 966 Mb for hexaploid wheat, the BAC library was estimated to have a total coverage of 3.58× wheat genome equivalents, giving approximately 96% probability of identifying a clone representing any given wheat DNA sequence. Twelve BAC clones containing an Yr5 locus-specific marker (Yr5STS7/8) were successfully selected by PCR screening of 3-dimensional BAC pools. The results demonstrated that the T. aestivum BAC library is a valuable genomic resource for positional cloning of Yr5. The library also should be useful in cloning other genes for stripe rust resistance and other traits of interest in hexaploid wheat.Key words: BAC library, BAC pools, hexaploid wheat, Puccinia striiformis f. sp. tritici, resistance gene, stripe rust, Triticum aestivum.
The efficacy of Cot-based gene enrichment in wheat (Triticum aestivum L.)
Authors: Lamoureux Didier , Peterson Daniel G , Li Wanlong , Fellers John P , Gill Bikram S
Published: January 2006

We report the results of a study on the effectiveness of Cot filtration (CF) in the characterization of the gene space of bread wheat (Triticum aestivum L.), a large genome species (1C = 16 700 Mb) of tremendous agronomic importance. Using published Cot data as a guide, 2 genomic libraries for hexaploid wheat were constructed from the single-stranded DNA collected at Cot values > 1188 and 1639 M·s. Compared with sequences from a whole genome shotgun library from Aegilops tauschii (the D genome donor of bread wheat), the CF libraries exhibited 13.7-fold enrichment in genes, 5.8-fold enrichment in unknown low-copy sequences, and a 3-fold reduction in repetitive DNA. CF is twice as efficient as methylation filtration at enriching wheat genes. This research suggests that, with improvements, CF will be a highly useful tool in sequencing the gene space of wheat.Key words: gene enrichment, renaturation kinetics, gene-rich regions, bread wheat.
The inheritance of organelle genes and genomes: patterns and mechanisms
Authors: Xu Jianping
Published: January 2006

Unlike nuclear genes and genomes, the inheritance of organelle genes and genomes does not follow Mendel's laws. In this mini-review, I summarize recent research progress on the patterns and mechanisms of the inheritance of organelle genes and genomes. While most sexual eukaryotes show uniparental inheritance of organelle genes and genomes in some progeny at least part of the time, increasing evidence indicates that strictly uniparental inheritance is rare and that organelle inheritance patterns are very diverse and complex. In contrast with the predominance of uniparental inheritance in multicellular organisms, organelle genes in eukaryotic microorganisms, such as protists, algae, and fungi, typically show a greater diversity of inheritance patterns, with sex-determining loci playing significant roles. The diverse patterns of inheritance are matched by the rich variety of potential mechanisms. Indeed, many factors, both deterministic and stochastic, can influence observed patterns of organelle inheritance. Interestingly, in multicellular organisms, progeny from interspecific crosses seem to exhibit more frequent paternal leakage and biparental organelle genome inheritance than those from intraspecific crosses. The recent observation of a sex-determining gene in the basidiomycete yeast Cryptococcus neoformans, which controls mitochondrial DNA inheritance, has opened up potentially exciting research opportunities for identifying specific molecular genetic pathways that control organelle inheritance, as well as for testing evolutionary hypotheses regarding the prevalence of uniparental inheritance of organelle genes and genomes.Key words: isogamy, anisogamy, paternal leakage, mating type, quantitative organelle inheritance.
Experimental backwater analysis around bridge waterways
Authors: Seckin Galip , Atabay Serter
Published: January 2006

A series of five experiments was performed in a two-stage compound channel including various roughness conditions and different types of bridge models, namely, single-opening semi-circular arch bridge model (ASOSC), multiple-opening semi-circular arch bridge model (AMOSC), single-opening elliptic arch bridge model (ASOE), and single-opening straight-deck bridge model with and without piers (DECK) including different span widths. The performances of six different methods for computing backwater around bridge waterways were compared using the experimental data carefully taken on many combinations of cases. The results of the energy method, momentum method, WSPRO method, Yarnell's method, USBPR method, and arch bridge method were compared with experimental results. The results showed that energy method was able to simulate more accurately the measured backwater values than the other methods. The backwater differences between the experimental values and computed values by the energy method are generally within –3.2% and 0.8% in terms of flow depth. A simple generalized function for estimating bridge backwater is also proposed.Key words: bridge backwater, hydraulic model testing, flood control, compound channel flow, one-dimensional methods.
Assessment of horizontal curves of an existing road using reliability concepts
Authors: Echaveguren Tomás , Bustos Marcelo , de Solminihac Hernán
Published: January 2006

Horizontal curves on road are commonly analyzed under design speed point of view, where it is assumed that the maximum speed of a vehicle in a curve is the design speed. The empirical evidence has demonstrated that when the design speed is low, the operating speed tends to be higher. This happens because of an available remaining lateral (or transverse) friction for speeds over design speed. This condition is determined by a speed limit, obtained from the demand and supply equilibrium of friction of a pavement. The difference between operating and design speeds is usually considered as the margin of safety of a horizontal curve on a road. In this study, a methodology to determine the margin of safety of an existing curve is proposed. The methodology is based on the reliability theory by which reliability of operational conditions can be analyzed by using a reliability index as a margin of safety. A case study for light vehicles is evaluated to determine high impact variables over reliability, such as, macrotexture, skid resistance, curve radius, and superelevation. The results obtained in this study demonstrated that curve radius, skid resistance, and macrotexture are variables with high impact over failure probability. In constrast, superelevation has little effect on the failure probability.Key words: reliability, horizontal curves, operating speed, skid resistance, pavement texture.
Large model test of prestressed carbon fibre reinforced polymer ground anchors
Authors: Zhang Burong , Benmokrane Brahim
Published: January 2006

This paper presents a full-scale prestressed ground anchor model test with carbon fibre reinforced polymer (CFRP) 9-bar tendons. The main objectives of this laboratory study were to evaluate the serviceability of the developed bond-type anchorage for post-tensioning applications with CFRP multibar tendons and to study load transfer mechanism of CFRP multibar tendons to surrounding rock mass. A cement-based mortar-filled steel tube was used to simulate a rock mass environment. Extensive instrumentation including resistance strain gauges, fibre optic sensors, embedded strain gauges, and linear variable displacement transducers (LVDTs) were used to monitor the behaviour of the anchor. The test results show that the tested CFRP 9-bar anchor presents an acceptable tensile behaviour under a load of 0.6fpu in accordance with existing codes. The CFRP multibar anchor presents a similar strain distribution profile as that for conventional steel anchors, except giving a shorter load transfer length. It is expected that CFRP 9-bar anchors require a minimum anchor bonded length of 2000 mm with plain cement grouts.Key words: anchor, anchorage, FRP, tendon, slip.
Evaluation of an approximate method for incorporating floating docks in harbor wave prediction models
Authors: Li Dongcheng , Panchang Vijay , Tang Zhaoxiang , Demirbilek Zeki , Ramsden Jerry
Published: January 2006

Computer models based on the two-dimensional (2-D) elliptic mild-slope equation are nowadays routinely used in harbor engineering applications. However, structures like floating breakwaters and docks, which are often encountered in the modeling domain, render the problem for locally three-dimensional model and hence are problematic to incorporate in a 2-D model. Tsay and Liu (Applied Ocean Research. 1983. Vol 5(1): 30–37) proposed a highly simplified but approximate approach that does not violate the overall two dimensionality of the problem. The validity of their approach is examined in detail, and it is found that although their approximation provides results with the correct trend, the actual solutions deviate considerably from the theoretical solutions. We have developed correction factors that may be used to produce more reliable results using the framework of Tsay and Liu. Application of the resulting method to a harbor in Alaska shows that docks in the harbor distort the wave field considerably and create a reflective pattern that has the potential to affect navigation safety in some areas. A by-product of this paper consists of plots of transmission coefficients for waves propagating past rectangular and cylindrical floating objects of infinite extent for a wide range of conditions encountered in practice. Such transmission coefficients are at present readily available in the published literature for selected cases only.Key words: wave, model, mild slope, equation, floating breakwater, dock, marina, harbor.
Comparing life cycle implications of building retrofit and replacement options
Authors: Dong Bonnie , Kennedy Christopher , Pressnail Kim
Published: January 2006

When is it better to retrofit a building as opposed to demolishing and rebuilding it? Life cycle environmental and economic analyses are used to address this question through the study of a typical four bedroom detached house in Toronto. Three vintages of the reference house are used: 1930s solid masonry; 1960s wood frame; and post oil crisis, 1980s wood frame. Retrofit studies considered include insulating the attic and basement walls and air leakage sealing. Over a 40-year life cycle, the rebuild option has lower life cycle energy, global warming potential, and air pollution, which are predominantly associated with building operation. But the retrofit options have lower water pollution, solid waste generation, and weighted resource use, associated with material flows. The retrofit options also have lower life cycle economic costs than rebuilding. In this respect, the preferred options are basement plus air leakage sealing retrofit for the 1930s house, basement retrofit for the 1960s house, and no change for 1980s house. There are ways to overcome the trade-off in negative environmental impacts between retrofitting and rebuilding, such as use of renewable energy sources or re-use and recycling of deconstruction and demolition materials in new construction.Key words: life cycle assessment, life cycle costing, building retrofits, sustainable development.
Correlation of strength, rubber content, and water to cement ratio in rubberized concrete
Authors: Ghaly Ashraf M , Cahill IV James D
Published: January 2006

Waste rubber tires that cannot be processed for useful applications are numbered in the millions around the world. The build up of old rubber tires in landfills is commonly considered a major threat to the environment, and it is unquestionably a burden on landfill space. This research project was an investigation into the possibility of using fine rubber particles in concrete mixtures. The experimental testing program was designed to study the effect of the addition of crumb rubber, as replacement of a portion of fine aggregates (sand), on the strength of concrete. Rubber was added to concrete in quantities of 5%, 10%, and 15% by volume of the mixture. Three different water/cement ratios were used: 0.47, 0.54, and 0.61. A total of 180 concrete cubes were made. The cubes were tested in compression at 1, 7, 14, 21, and 28 d with the load continuously and automatically measured until failure. The load values were used to calculate compressive stress as related to different rubber contents and water/cement ratios. Compression test results were used to develop several plots relating rubber content and water/cement ratio to compressive stress of concrete. Test results gathered in this research project indicated that the addition of crumb rubber to concrete results in a reduced strength as compared with that of conventional concrete. Based on the experimental results, correlations have been developed to estimate the reduction in concrete strength as a function of the rubber content in the mix.Key words: compressive strength, concrete, crumb rubber, rubberized concrete.
Impact resonance method for fatigue damage detection in reinforced concrete beams with carbon fibre reinforced polymer
Authors: Gheorghiu Catalin , Rhazi Jamal Eddine , Labossière Pierre
Published: January 2006

This paper reports on the potential of using the impact resonance method (IRM) for detecting fatigue damage in strengthened reinforced concrete (RC) beams. In this experimental program, 1.2 m long RC beams strengthened with a carbon fibre reinforced polymer (CFRP) plate have been employed. The specimens were subjected to fatigue loading under four-point bending for up to 2 × 106 cycles at 3 Hz. The load amplitude was varying from 15% to 75% of the cycles yielding load of the beam. Throughout fatigue testing, the cycling was stopped for IRM measurements to be taken. The obtained data provided information about changes in modal properties, such as, fundamental frequencies and damping ratios. Moreover, the results have shown that the IRM technique was successfully employed in laboratory for detecting fatigue damage in concrete beams strengthened with CFRP laminates.Key words: impact resonance method, modal properties, RC beam, FRP-strengthening, fatigue test, cracking.
Shear resistance of self-consolidating concrete beams — experimental investigations
Authors: Lachemi M , Hossain K M.A , Lambros V
Published: January 2006

Self-consolidating concrete (SCC) is a new generation of high performance concrete known for its excellent deformability and high resistance to segregation and bleeding. Lack of information regarding in situ properties and structural performance of SCC is one of the main barriers to its acceptance in the construction industry. There is some concern among researchers and designers that SCC may not be strong enough in shear because of some uncertainties in mechanisms resisting shear — notably the aggregate interlock mechanism. Because of the presence of comparatively smaller amount of coarse aggregates in SCC, the fracture planes are relatively smooth as compared with normal concrete (NC) that may reduce the shear resistance of concrete by reducing the aggregate interlock between the fracture surfaces. The paper compares the shear resistance of SCC and NC based on the results of an experimental investigation on 18 flexurally reinforced beams without shear reinforcements. The test parameters include concrete type, maximum size of coarse aggregate, coarse aggregate content, and beam shear span-to-depth ratio. Shear strength, shear ductility, crack patterns, and failure modes of all experimental beams are compared to analyze the shear resistance mechanisms of SCC and NC beams in both pre- and post-cracking stages. The recommendations of this paper can be of special interest to designers considering the use of SCC in structural applications.Key words: self-consolidating concrete, shear resistance, shear resistance factor, aggregate interlock, dowel action.
Photodegradation test of asphalt binder using pressed thin film samples
Authors: Yamaguchi Katsuyuki , Sasaki Iwao , Meiarashi Seishi
Published: January 2006

The photodegradation behavior of a straight asphalt was investigated using a new method "photodegradation test of asphalt binder using pressed thin film samples". Although the photodegradation caused by outdoor exposure is limited to the near surface, the results confirmed that the degree of degradation during 1 to 2 months is more severe than that by the pressure aging vessel (PAV) test, which is designed to simulate the degradation that will occur in the asphalt pavement over 5 to 10 service years.Key words: asphalt binder, aging, photodegradation, thin film, DSR, FTIR.
Use of tree ring reconstructed streamflows to assess drought
Authors: Bonin David V , Burn Donald H
Published: January 2006

The reconstruction of past streamflow events is of great interest to the water resources engineer to obtain the best possible estimates of extreme flow conditions for investment, decision making, and design. The tree ring data offer a unique way of addressing this problem. The pattern of growth rings of a tree reflects the environmental conditions experienced during each year. Tree rings are produced annually and can be precisely and reliably linked to climatic variations, which makes them ideal for correlation with annual climatic records. This paper demonstrates the utility of using the methods of dendroclimatology, the study of climate through tree rings, to extend streamflow records. The techniques developed were applied to the Athabasca River at Athabasca. The results reveal considerable benefits from the reconstruction through more precise, and more extreme, estimates of drought quantiles.Key words: drought, tree ring data, reconstruction, extreme flow quantiles, frequency analysis.
Ductility of concrete walls: the Canadian seismic design provisions 1984 to 2004
Authors: Adebar Perry , Mutrie James , DeVall Ronald
Published: January 2006

The National Building Code of Canada (NBCC) references Canadian Standards Association (CSA) standard A23.3 for the design of concrete structures. The seismic design provisions in the 2004 edition of CSA A23.3, which ensure concrete walls without confinement reinforcement have adequate flexural displacement capacity (ductility), have been completely revised from the provisions in the 1994 edition of CSA A23.3 standard, which are similar to the provisions in the 1984 edition. The new provisions require an estimate of the displacement demand of the seismic force resisting system due to the design earthquake. For ductile walls that are part of a system with good displacement control, the new provisions are less restrictive than the old provisions, while for moderately (nominally) ductile walls, the new provisions are considerably more restrictive than the old provisions. A comprehensive review of the 1984 and 1994 provisions and the background to the 2004 provisions are presented, and it is explained why the seismic design provisions required significant changes.Key words: building codes, concrete walls, displacement-based design, ductility, seismic design.
Analysis of concrete beams prestressed and post-tensioned with externally unbonded carbon fiber reinforced polymer tendons
Authors: Aziz Mohamad Abdel , Abdel-Sayed George , Ghrib Faouzi , Grace Nabil F , Madugula Murty K.S
Published: January 2006

Fiber reinforced polymer (FRP) tendons are being increasingly used nowadays in prestressing and (or) post-tensioning concrete structures. However, designers are faced with lack of practical analysis procedure that leads to proper evaluation of their structural performance, especially when bonded prestressing is combined with unbonded post-tensioning. This paper presents an analytical procedure for these beams. It examines the load–defelction characteristics and proceeds to estimate the ultimate load carrying capacity by taking into consideration the change of stress that occurs in the externally unbonded tendons during different stages of loading. The analytical procedure uses the concept of effective moment of inertia of concrete beams. The equations used are developed by ACI Committee 440, the Intelligent Sensing for Innovative Structures (ISIS) Canada Research Network, and the Comité Euro-International du Béton - Fédération International de la Précontrainte (CEB-FIP), for calculating the deflection of beams reinforced with carbon fiber reinforced polymer (CFRP) tendons. Finite element analyses have been conducted to verify the proposed analytical method. Two experimental programs were used to validate the proposed analytical method. The experimental findings of two box beams reinforced with bonded and unbonded external tendons are compared with finite element analyses and the analytical results. A full-scale test for an internally and externally prestressed double-T beam was undertaken at Construction Technology Laboratories Inc., Skokie, Illinois. The results from this experimental work were used to validate the analytical procedure.Key words: bonded CFRP tendons, concrete, post-tensioning, unbonded CFRP tendons.
Estimation des débits sous glace dans le sud du Québec : comparaison de modèles neuronal et déterministe
Authors: Turcotte Richard , Favre Anne-Catherine , Lacombe Pierre , Poirier Charles , Villeneuve Jean-Pierre
Published: January 2006

Real-time assessments of stream flows under ice cover, using two distinct objective approaches, were compared over a 5-year period. Approaches based on artificial neural networks, defining mathematical relationships between stream flow, water level, and air temperature, and on a deterministic hydrological model were applied at eight gauged sites located in southern Quebec. Good results were obtained using both approaches, when no snowmelt contributes to the rise of the inflows. In the other hydrological situations, the neural network results were the best, but results of both approaches were sensibly poorer. Nevertheless, the potential for increasing the skills of the deterministic model seems high. Otherwise, a preliminary analysis showed that both approaches lead to stream-flow estimations that are not radically worse than the ones performed by the team of experts.Key words: discharge measurement, hydrology, ice-affected stream flow, hydrological modeling, neural network.