bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular mapping of resistance to Leptosphaeria maculans in Australian cultivars of Brassica napus
Authors: Mayerhofer R. , Good A. G. , Bansal V. K. , Thiagarajah M. R. , Stringam G. R.
Published: May 2008

Doubled haploid (DH) lines together with a cotyledon bioassay were employed for the molecular analysis of resistance to the blackleg fungus Leptosphaeria maculans in the Australian Brassica napus cultivars Shiralee and Maluka. We used bulked segregant analysis to identify 13 RAPD and two RFLP markers linked to the resistance phenotype and mapped these markers in the segregating DH population. Our data suggest the presence of a single major locus controlling resistance in the cultivar Shiralee, confirming our previous results obtained from Mendelian genetic analyses. In addition, preliminary mapping data for the cultivar Maluka also support a single locus model for resistance and indicate that the resistance genes from 'Shiralee' and 'Maluka' are either linked or possibly identical. The molecular markers identified in this study should be a useful tool for breeding blackleg resistant varieties using marker-assisted selection, and are the essential first step towards the map-based cloning of this resistance gene.Key words: blackleg, Leptosphaeria maculans, Brassica napus, DNA mapping, disease resistance.
Relationships of wildBrassicaspecies with chromosome number 2n = 18, based on RFLP studies
Authors: Lannér C. , Bryngelsson T. , Gustafsson M.
Published: May 2008

An array of 10 wild Brassica species with chromosome number 2n = 18 represented by 34 populations was analyzed for genome similarity using genomic and cDNA clones. Species studied included B. bourgeaui (Webb) O. Kuntze, B. cretica Lam., B. hilarionis G.E. Post, B. incana Ten., B. insularis Moris, B. macrocarpa (Guss.) Caruel, B. montana Pourret, B. oleracea L., B. rupestris Rafin., and B. villosa Biv. The RFLP data were used to calculate similarities between populations that were subsequently treated in a cluster analysis. Most populations of a species were grouped together and were separate from populations of other species. The previously identified B. incana – B. rupestris – B. villosa complex was verified, and genetic similarity between the species B. montana and B. oleracea was evident. An interesting association between B. insularis and B. macrocarpa was observed. The UPGMA analysis showed that the species tended to cluster according to geographic region: B. cretica and B. hilarionis comprise a cluster that could be called Eastern Mediterranean; B. oleracea, B. bourgeaui, and B. montana define an Atlantic – Western Mediterranean cluster; B. incana, B. rupestris, and B. villosa form an Italian group; and a B. insularis – B. macrocarpa association may be called Central Mediterranean.Key words: wild Brassica species, wild kales, RFLP, genetic similarity, phenogram.
Sex and meiosis in autotetraploid Pacific oyster, Crassostrea gigas (Thunberg)
Authors: Guo Ximing , Allen Jr. Standish K.
Published: May 2008

Sex and meiosis were studied in induced autotetraploids of the Pacific oyster (Crassostrea gigas Thunberg) and were compared with sex and meiosis in autotriploids and normal diploids. Tetraploid oysters reached sexual maturity at 1 year of age in an approximately 1:1 sex ratio. In contrast with the abnormally high frequency of hermaphrodites among triploids, tetraploids had about the same level of hermaphrodites as normal diploids. Fecundity of tetraploids was comparable to that of normal diploids, differing from the greatly reduced fecundity of triploids. Homologous chromosomes synapsed predominantly as trivalents in eggs from triploids and as quadrivalents in eggs from tetraploids. After fertilization, eggs from tetraploids and triploids went through two meiotic divisions, as normal eggs did. The average gamete chromosome number was 10.0 for diploids and 19.9 for tetraploids. The distribution of gamete chromosome numbers from triploids suggested that the extra chromosome in the trivalent segregated randomly during anaphase I. In tetraploids, however, the two extra chromosomes in the quadrivalents did not segregate independently and, instead, they preferentially cosegregated to opposite poles producing balanced gametes. These results suggest that mechanisms may exist to weigh, balance, and equally distribute quadrivalents, possibly through mitotic force and tension. Errors in chromosome balancing in normal meiosis may result in nondisjunction, which is the primary cause of human aneuploidy.Key words: sex, meiosis, multivalent segregation, polyploidy, aneuploidy, Crassostrea gigas.
Discriminating between barley genotypes using microsatellite markers
Authors: Russell Joanne , Fuller John , Young George , Thomas Bill , Macaulay Malcolm , Waugh Robbie , Powell Wayne , Taramino Graziana
Published: May 2008

Eleven microsatellite loci were used to survey 24 barley genotypes representing 23 cultivars and a breeding line in official trials. Three separate combinations of four microsatellites had overall probabilities of identity of less than 1 in 1000 and could distinguish between all 24 barley genotypes. It is shown that the microsatellites could distinguish genotypes with the same pedigree and also that patterns of discrimination were different from those obtained from botanical descriptors. The stability of microsatellites across different generations was demonstrated by a retrospective analysis of the pedigree of Golden Promise. One of the parents of Maythorpe, the immediate ancestor of Golden Promise, was shown to be Irish Goldthorpe rather than Goldthorpe, thereby resolving conflicting published pedigrees.Key words: barley, microsatellites, cultivar identification, stability, Golden Promise.
Three novelT-box genes inCaenorhabditis elegans
Authors: Agulnik Sergei I. , Ruvinsky Ilya , Silver Lee M.
Published: May 2008

The T-box gene family consists of members that share a unique DNA binding domain. The best characterized T-box gene, Brachyury or T, encodes a transcription factor that plays an important role in early vertebrate development. Seven other recently described mouse T-box genes are also expressed during development. In the nematode Caenorhabditis elegans, four T-box genes have been characterized to date. In this study, we describe three new C. elegans T-box genes, named Ce-tbx-11, Ce-tbx-12, and Ce-tbx-17. Ce-tbx-11 and Ce-tbx-17 were uncovered through the sequencing efforts of the C. elegans Genome Project. Ce-tbx-12 was uncovered through degenerate PCR analysis of C. elegans genomic DNA. Ce-tbx-11 and Ce-tbx-17 are located in close proximity to the four other previously described T-box genes in the central region of chromosome III. In contrast, Ce-tbx-12 maps alone to chromosome II. Phylogenetic analysis of all known T-box domain sequences provides evidence of an ancient origin for this gene family.Key words: transcription factor, T-box genes, evolution, Brachyury.
A complex arrangement of genes at a starch branching enzyme I locus in the D-genome donor of wheat
Authors: Rahman S. , Morell M. , Appels R. , Abrahams S. , Abbott D. , Samuel M. , Mukai Y.
Published: May 2008

Genomic DNA fragments from Triticum tauschii (D-genome donor to wheat) carrying starch branching enzyme I (SBE I) type genes have been characterized. One fragment contains one complete gene and two partial genes in 16 kb of DNA. One of the partial genes is oriented in the opposite strand to the other two. The gene that is complete was sequenced. Its structure corresponds closely to that of rice in that exons 3–8 are retained at similar sizes and spacings. A cDNA closely corresponding to the complete gene was isolated and characterized; it codes for a putative protein that represents a novel type of SBE I, as it is shorter at the 3′ end than the forms reported so far in other plants. A second genomic fragment contains a different SBE I gene. There appear to be approximately 10 copies of SBE I type genes in wheat (approximately 5 in T. tauschii) and most of them have been assigned to group 7 chromosomes. In situ hybridization indicates that a major locus for the genes is located at the distal end of the short arm of chromosome 7D.Key words: starch, branching enzyme genes, wheat, Triticum tauschii, in situ hybridization.
FISH of a maizesh2-selected sorghum BAC to chromosomes ofSorghum bicolor
Authors: Gómez Martha I. , Islam-Faridi M. Nurul , Woo Sung-Sick , Czeschin Jr. Don , Zwick Michael S. , Stelly David M. , Price H. James , Schertz Keith F. , Wing Rod A.
Published: May 2008

Fluorescence in situ hybridization (FISH) of a 205 kb Sorghum bicolor bacterial artificial chromosome (BAC) containing a sequence complementary to maize sh2 cDNA produced a large pair of FISH signals at one end of a midsize metacentric chromosome of S. bicolor. Three pairs of signals were observed in metaphase spreads of chromosomes of a sorghum plant containing an extra copy of one arm of the sorghum chromosome arbitrarily designated with the letter D. Therefore, the sequence cloned in this BAC must reside in the arm of chromosome D represented by this monotelosome. This demonstrates a novel procedure for physically mapping cloned genes or other single-copy sequences by FISH, sh2 in this case, by using BACs containing their complementary sequences. The results reported herein suggest homology, at least in part, between one arm of chromosome D in sorghum and the long arm of chromosome 3 in maize.Key words: sorghum, maize, shrunken locus, physical mapping, fluorescence in situ hybridization, bacterial artificial chromosomes.
Conserved patterns of chromosome pairing and recombination inBrassica napuscrosses
Authors: Parkin I. A. P. , Lydiate D. J.
Published: May 2008

The patterns of chromosome pairing and recombination in two contrasting Brassica napus F1hybrids were deduced. One hybrid was from a winter oilseed rape (WOSR) × spring oilseed rape cross, the other from a resynthesized B. napus × WOSR cross. Segregation at 211 equivalent loci assayed in the population derived from each hybrid produced two collinear genetic maps. Alignment of the maps indicated that B. napus chromosomes behaved reproducibly as 19 homologous pairs and that the 19 distinct chromosomes of B. napus each recombined with unique chromosomes from the interspecific hybrid between Brassica rapa and Brassica oleracea. This result indicated that the genomes of the diploid progenitors of amphidiploid B. napus have remained essentially unaltered since the formation of the species and that the progenitor genomes were similar to those of modern-day B. rapa and B. oleracea. The frequency and distribution of crossovers were almost indistinguishable in the two populations, suggesting that the recombination machinery of B. napus could cope easily with different degrees of genetic divergence between homologous chromosomes. Efficient recombination in wide crosses will facilitate the introgression of novel alleles into oilseed rape from B. rapa and B. oleracea (via resynthesized B. napus) and reduce linkage drag.Key words: integrating genetic maps, microspore culture, segregation distortion, recombination frequency, locus distribution.
Genome analysis of South AmericanElymus(Triticeae) andLeymus(Triticeae) species based on variation in repeated nucleotide sequences
Authors: Dubcovsky Jorge , Schlatter A. R. , Echaide M.
Published: May 2008

Variation in repeated nucleotide sequences (RNSs) at the level of entire families assayed by Southern blot hybridization is remarkably low within species and is a powerful tool for scrutinizing the origin of allopolyploid taxa. Thirty-one clones from RNSs isolated from different Triticeae genera were used to investigate the genome constitution of South American Elymus. One of these clones, pHch2, preferentially hybridized with the diploid H genome Hordeum species. Hybridization of this clone with a worldwide collection of Elymus species with known genome formulas showed that pHch2 clearly discriminates Elymus species with the H genome (StH, StHH, StStH, and StHY) from those with other genome combinations (StY, StStY, StPY, and StP). Hybridization with pHch2 indicates the presence of the H genome in all South American Elymus species except Elymus erianthus and Elymus mendocinus. Hybridization with additional clones that revealed differential restriction fragments (marker bands) for the H genome confirmed the absence of the H genome in these species. Differential restriction fragments for the Nsgenome of Psathyrostachys were detected in E. erianthus and E. mendocinus and three species of Leymus. Based on genome constitution, morphology, and habitat, E. erianthus and E. mendocinus were transferred to the genus Leymus.Key words: Triticeae, Elymus, Leymus, repeated sequences.
A novel RNA species from the turtle mitochondrial genome: induction and regulation of transcription and processing under anoxic and freezing stresses
Authors: Cai Qinyin , Storey Kenneth B.
Published: May 2008

The present study identifies a previously cloned cDNA, pBTaR914, as homologous to the mitochondrial WANCY (tryptophan, alanine, asparagine, cysteine, and tyrosine) tRNA gene cluster. This cDNA clone has a 304-bp sequence and its homologue, pBTaR09, has a 158-bp sequence with a long poly(A)+tail (more than 60 adenosines). RNA blotting analysis using pBTaR914 probe against the total RNA from the tissues of adult and hatchling turtles revealed five bands: 540, 1800, 2200, 3200, and 3900 nucleotides (nt). The 540-nt transcript is considered to be an intact mtRNA unit from a novel mtDNA gene designated WANCYHPthat overlaps the WANCY tRNA gene cluster region. This transcript was highly induced by both anoxic and freezing stresses in turtle heart. The other transcripts are considered to be the processed intermediates of mtRNA transcripts with WANCYHPsequence. All these transcripts were differentially regulated by anoxia and freezing in different organs. The data suggest that mtRNA processing is sensitive to regulation by external stresses, oxygen deprivation, and freezing. Furthermore, the fact that the WANCYHPtranscript is highly induced during anoxic exposure suggests that it may play an important role in the regulation of mitochondrial activities to coordinate the physiological adaptation to anoxia.Key words: mitochondria, RNA processing, anoxia, freezing, Trachemys scripta.
Barley elongation factor 1α: genomic organization, DNA sequence, and phylogenetic implications
Authors: Nielsen Peter S. , Kleinhofs Andris , Olsen Odd-Arne
Published: May 2008

A full length cDNA clone encoding the 447 amino acid long barley (Hordeum vulgare cv. Bomi) endosperm elongation factor 1α (eF-1α) was isolated by a differential screening procedure. RFLP mapping of eF-1α showed that the barley genome contains a small eF-1α gene family of 4 copies, with 1 copy of the gene being located on each of chromosomes 2, 4, 6, and 7. Analysis of barley endosperm total proteins by Western blot with antibodies directed towards wheat eF-1α and the sea urchin 51 kDa proteins gave a single band of the expected molecular weight. Amino acid sequence comparison with other plant eF-1α sequences showed that the isolated barley endosperm eF-1α is more similar to the published wheat eF-1α sequence than to eF-1α sequences previously published for the barley cultivars Igri and Dicktoo. The phylogenetic analysis suggests that the barley eF-1α gene family can be divided into two subfamilies and that two ancestral genes existed before the divergence of monocotyledonous and dicotyledonous plants.Key words: endosperm, gene family, RFLP.
Identification of the entire chromosome complement of bread wheat by two-colour FISH
Authors: Pedersen C. , Langridge P.
Published: May 2008

Using the Aegilops tauschii clone pAs1 together with the barley clone pHvG38 for two-colour fluorescence in situ hybridization (FISH) the entire chromosome complement of hexaploid wheat was identified. The combination of the two probes allowed easy discrimination of the three genomes of wheat. The banding pattern obtained with the pHvG38 probe containing the GAA-satellite sequence was identical to the N-banding pattern of wheat. A detailed idiogram was constructed, including 73 GAA bands and 48 pAs1 bands. Identification of the wheat chromosomes by FISH will be particularly useful in connection with the physical mapping of other DNA sequences to chromosomes, or for chromosome identification in general, as an alternative to C-banding.Key words: Triticum aestivum, chromosome identification, fluorescence in situ hybridization, repetitive DNA sequences.
Comparing the distribution of RAPD and RFLP markers in a high density linkage map of sugar beet
Authors: Nilsson N.-O. , Halldén C. , Hansen M. , Hjerdin A. , Säll T.
Published: May 2008

The distribution of RAPD markers was compared with that of RFLP markers in a high density linkage map of sugar beet. The same mapping population of 161 F2individuals was used to generate all the marker data. The total map comprises 160 RAPD and 248 RFLP markers covering 508 cM. Both the RAPD and the RFLP markers show a high degree of clustering over the nine linkage groups. The pattern is compatible with a strong distal localization of recombination in the sugar beet. It leads generally to one major cluster of markers in the centre of each linkage group. In regions of high marker density, dominant RAPD markers present in either linkage phase and codominant RFLP markers are subclustered relative to each other. This phenomenon is shown to be attributable to: (i) effects of the mapping procedure when dominant and codominant data are combined, (ii) effects of the mapping procedure when dominant data in both linkage phases are combined, and (iii) genuine differences in the way RAPD and RFLP markers are recruited.Key words: sugar beet, linkage map, RAPD, RFLP, clustering.
Laser isolation of plant sex chromosomes: studies on the DNA composition of the X and Y sex chromosomes of Silene latifolia
Authors: Scutt Charles P. , Kamisugi Yasuko , Gilmartin Philip M. , Sakai Fukumi
Published: May 2008

X and Y sex chromosomes from the dioecious plant Silene latifolia (white campion) were isolated from mitotic metaphase chromosome preparations on polyester membranes. Autosomes were ablated using an argon ion laser microbeam and isolated sex chromosomes were then recovered on excised fragments of polyester membrane. Sex chromosome associated DNA sequences were amplified using the degenerate oligonucleotide primed polymerase chain reaction (DOP–PCR) and pools of DOP–PCR products were used to investigate the genomic organization of the S. latifolia sex chromosomes. The chromosomal locations of cloned sex chromosome repeat sequences were analysed by fluorescence in situ hybridization and data complementary to laser ablation studies were obtained by genomic in situ hybridization. In combination, these studies demonstrate that the X and Y sex chromosomes of S. latifolia are of very similar DNA composition and also that they share a significant repetitive DNA content with the autosomes. The evolution of sex chromosomes in Silene is discussed and compared with that in another dioecious species, Rumex acetosa.Key words: FISH, GISH, laser-microdissection, sex chromosome, Silene latifolia.
Structural organization of an alienThinopyrum intermediumgroup 7 chromosome in U.S. soft red winter wheat (Triticum aestivumL.)
Authors: Francki M. G. , Crasta O. R. , Sharma H. C. , Ohm H. W. , Anderson J. M.
Published: May 2008

Barley yellow dwarf virus (BYDV) resistance in soft red winter wheat (SRWW) cultivars has been achieved by substituting a group 7 chromosome from Thinopyrum intermedium for chromosome 7D. To localize BYDV resistance, a detailed molecular genetic analysis was done on the alien group 7 Th. intermedium chromosome to determine its structural organization. Triticeae group 7 RFLP markers and rye specific repetitive sequences used in the analysis showed that the alien chromosome in the P29 substitution line has distinguishing features. The 350–480 bp rye telomeric sequence family was present on the long arm as determined by Southern and fluorescence in situ hybridization. However, further analysis using a rye dispersed repetitive sequence indicated that this alien chromosome does not contain introgressed segments from the rye genome. The alien chromosome is homoeologous to wheat chromosomes 7A and 7D as determined by RFLP analysis. Presence of the waxy gene on chromosomes 7A, 7B, and 7D but its absence on the alien chromosome in P29 suggests some internal structural differences on the short arm between Th. intermedium and wheat group 7 chromosomes. The identification of rye telomeric sequences on the alien Thinopyrum chromosome and the homoeology to wheat chromosomes 7A and 7D provide the necessary information and tools to analyze smaller segments of the Thinopyrum chromosome and to localize BYDV resistance in SRWW cultivars.Key words: barley yellow dwarf virus, Thinopyrum intermedium, rye repetitive sequences, RFLP, homoeologous group 7.
On the origins of the tetraploidBromusspecies (sectionBromus, Poaceae): insights from internal transcribed spacer sequences of nuclear ribosomal DNA
Authors: Ainouche Malika L. , Bayer Randall J.
Published: May 2008

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA from 22 diploid and tetraploid annual Bromus species of section Bromus (Poaceae) and three species belonging to other Bromus sections, Bromus catharticus (section Ceratochloa), Bromus anomalus (section Pnigma), and Bromus sterilis (section Genea), were investigated by PCR amplification and direct sequencing. The length of the ITS-1 region varied from 215 to 218 bp, and that of the ITS-2 region from 215 to 216 bp, in the species analyzed. ITS-1 was more variable and provided more informative sites (49) than ITS-2 (32). No variation was encountered within species. In pairwise comparison among species of section Bromus, sequence divergence ranged from 0.0 to 8.0% for the combined ITS-1 and ITS-2 regions. Parsimony analysis using Avena longiglumis and Hordeum vulgare as outgroups resulted in well-resolved phylogenetic trees and showed that section Bromus is monophyletic according to the species analyzed outside of the section. The analysis clarified the phylogenetic relationships among monogenomic (diploid) species. Introduction of the allotetraploid species did not change the general topology of the trees obtained using only the diploid species. Although some tetraploid–diploid species relationships will have to be clarified with faster evolving markers, the ITS sequences are shown to be useful for assessing evolutionary relationships among closely related Bromus species, as well as for clarifying taxonomic problems in previously controversial cases (e.g., Bromus alopecuros and Bromus caroli–henrici). New hypotheses are proposed concerning the origin of several allotetraploid species. For example, it is shown that the tetraploid Bromus hordeaceus diverged earlier than all other species of section Bromus, excluding the diploid B. caroli–henrici, which is found to be basal in this group. The tetraploid Bromus arenarius, which was considered a hybrid between sections Bromus and Genea, and the tetraploid Bromus adoensis are sister taxa within section Bromus; they belong in a weakly differentiated clade with the diploids Bromus brachystachys, Bromus japonicus, Bromus squarrosus, Bromus arvensis, and Bromus intermedius.Key words: Bromus, allopolyploidy, ITS, ribosomal DNA, phylogeny.
The relationship between genetic and cytogenetic maps of pea. II. Physical maps of linkage mapping populations
Authors: Hall K. J. , Parker J. S. , Ellis T. H. N. , Turner L. , Knox M. R. , Hofer J. M. I. , Lu J. , Ferrandiz C. , Hunter P. J. , Taylor J. D. , Baird K.
Published: May 2008

A cytogenetic analysis of inbred lines that have been used to generate genetic maps of pea is presented. Mitotic karyotyping of the inbred lines and meiotic studies of their F1hybrids have been used to test the prediction that structural differences exist between the parental lines. The results are not compatible with the previously published molecular data. A reordered and updated linkage map of pea is presented that is consistent with the cytogenetic data.Key words: Pisum, linkage map, recombination, synaptonemal complex, chiasmata.
Identical megabase transgenes on mouse chromosomes 3 and 4 do not promote ectopic pairing or synapsis at meiosis
Authors: Moens P. B. , Heddle J. A. M. , Spyropoulos B. , Heng H. H. Q.
Published: May 2008

To investigate ectopic interactions at the chromatin level, we examined the meiotic organization of 1–2 mb phage λ transgenes on mouse chromosomes 3 and 4 by fluorescence in situ hybridization in combination with immunocytology of meiotic chromosomes. At early meiotic prophase, the transgenes are sufficiently dispersed in the nuclear volume to permit potential DNA–DNA interactions, but no synaptonemal complexes form between the sites of transgenes residing on different chromosomes. At later stages, when the chromatin is more condensed, the transgenes on different chromosomes are not preferentially associated as they are when they are on the same chromosome. At diplotene and metaphase I, no formations were observed that could be interpreted as reciprocal crossovers or chiasmata between the transgenes located on chromosomes 3 and 4. It appears that in normal fertile mice, a 1- to 2-mb homology is insufficient to initiate synapsis between nonhomologs, and it is concluded that homology is assessed within the broader context of the chromosome to initiate synapsis at meiotic prophase.Key words: transgenes, ectopic pairing, meiosis, synaptonemal complex, immunocytology, FISH.
Structure of the rye midget chromosome analyzed by FISH and C-banding
Authors: Jackson S. A. , Jiang J. , Friebe B. , Gill B. S.
Published: May 2008

The diminutive "midget" chromosome derived from rye (Secale cereale) was analyzed by C-banding and fluorescence in situ hybridization (FISH) using DNA probe pSau3A9 that is located in the centromeres of cereal chromosomes. FISH signals were detected at one end and overlapped one of the two telomeres of the midget, indicating that the midget is a telocentric chromosome. The FISH and C-banding results show that the centromere of the midget chromosome is smaller than those of normal wheat and rye chromosomes. These results indicate that one of the breakpoints occurred in the middle of the centromere of rye chromosome 1R during generation of the midget.Key words: Secale cereale, midget chromosome, centromere, telomere
Maternal effects influencing DNA endoreduplication in developing endosperm of Zea mays
Authors: Kowles R. V. , Yerk G. L. , Haas K. M. , Phillips R. L.
Published: May 2008

A large proportion of the nuclei in developing endosperm of Zea mays L. undergoes endoreduplication. Nuclear preparations of the entire endosperm from maize kernels of inbred lines, their reciprocal hybrids, and in some cases, F2 and F3 endosperm tissue were evaluated using flow cytometry. Data relative to DNA endoreduplication patterns, percentage of nuclei undergoing endoreduplication, and mean DNA content per nucleus were obtained. The patterns of endoreduplication and extent of DNA amplification differ among some inbreds. In all experiments, the endoreduplication patterns show that the F1 endosperm is more similar to the maternal parent than to the paternal parent. F2 endosperms reveal little difference in endoreduplication patterns among individuals within an F2 family and no more variation than the F1 endosperms. In contrast, F3 endosperms showed greater variation among their endoreduplication patterns. These results indicate a maternal effect on endoreduplication; that is, the genotype of the maternal parent's nuclear genome exerts control over the endoreduplication activities of endosperm tissue.Key words: endosperm, endoreduplication, maternal effect, flow cytometry, Zea mays L.
Analysis of tetraploidElymusspecies using wheat microsatellite markers and RAPD markers
Authors: Sun Gen-Lou , Salomon Björn , Bothmer Roland von
Published: May 2008

An analysis of Amplification fragment polymorphism of DNA from 27 accessions of 19 tetraploid Elymus species was carried out using 18 wheat microsatellite (WMS) primer pairs and 10 decamer primers. Ten WMS primer pairs produced multiple polymorphism on all accessions tested. Two independent phenograms, one based on WMS-PCR and one on RAPDs, separated the 19 tetraploid species into two main groups, viz., the SH genome species group and the SY genome species group. The results coincide with the genomic classification of these species and hence support previous studies showing that Elymus is not a monophyletic genus. The assays indicated that accessions within a species cluster together, which concurs with the morphological classification. Interspecific and intraspecific polymorphisms were detected by the WMS-PCR and RAPD analyses. Variation was observed among accessions of Elymus caninus. The WMS-PCR detected a much higher level of polymorphism than the RAPD analysis. WMSs seem to be more efficient markers than RAPD markers for studying the population diversity of Elymus species. The potential of cross-species amplification of microsatellite markers as an additional source for genetic analysis and applications in Elymus is discussed in the context of these results.Key words: Elymus, wheat, RAPD, phenetics, microsatellites.
Characterisation and inheritance of polymorphic plastid microsatellites inAbies
Authors: Vendramin G. G. , Ziegenhagen B.
Published: May 2008

Two polymorphic microsatellite loci were identified and sequenced in the genus Abies, using primer pairs derived from chloroplast simple sequence repeats (SSRs) of Pinus thunbergii. PCR products exhibited considerable length variation among six different Abies species and within Abies alba. F1progeny of both an interspecific and an intraspecific reciprocal cross confirmed that the two SSRs were predominantly paternally inherited. The maternal size variant predominantly occurred in the megagametophytes analysed. First analysis of the two chloroplast microsatellites in seven natural populations of A. alba revealed 36 different haplotypes. The use of these highly polymorphic SSRs as potential markers in population genetics is discussed.Key words: Abies, chloroplast simple sequence repeats, sequences, inheritance, intraspecific variation, population genetics.
Rate-dependent soil behavior in seismic site response analysis
Authors: Park Duhee , Hashash Youssef M.A.
Published: May 2008

One-dimensional site response analysis is widely used in estimating local seismic site effects. The soil behavior in the analysis is often assumed to be independent of the rate of seismic loading. Laboratory test results, on the other hand, indicate that cyclic cohesive soil behavior is influenced by the rate of loading. Three models of rate-dependent dynamic soil behavior were derived based on available laboratory data. The models were implemented and evaluated in a modified one-dimensional equivalent linear site response analysis approach. Results show that rate-dependent shear modulus and damping can have a pronounced influence on propagated weak ground motion but a secondary influence on propagated strong motion. Rate dependence of the damping ratio has a greater impact on the computed response than rate dependence of the shear modulus. This paper highlights the relevance of the compatibility between frequencies at which dynamic soil properties are measured and their use in site response analysis.
Generalized dynamic Winkler model for nonlinear soil–structure interaction analysis
Authors: Allotey Nii , El Naggar M. Hesham
Published: May 2008

The beam on nonlinear Winkler foundation (BNWF) model is widely used in soil–structure interaction (SSI) analysis owing to its relative simplicity. This paper focuses on the development of a versatile dynamic BNWF model for the analysis of shallow and deep foundations. The model is developed as a stand-alone module to be incorporated in commercial nonlinear structural analysis software. The features of the model discussed are the loading and unloading rules, slack zone development, the modeling of cyclic degradation and radiation damping. The model is shown to be capable of representing various response features observed in SSI experiments. In addition, the predictions of the model for centrifuge tests of piles in weakening and partially weakening soil are shown to be in good agreement with the experimental results. This agreement demonstrates the potential of the model as a useful tool for design engineers involved in seismic design, especially performance-based design.
Finite element analyses of steep man-made cuts in Dublin boulder clay
Authors: Kovacevic N. , Miligan G. W.E. , Menkiti C. O. , Long M. , Potts D. M.
Published: May 2008

This paper describes finite element analyses undertaken to gain an insight into the short-term behaviour of temporary steep slopes in Dublin boulder clay for cut and cover sections of the recently completed Dublin Port Tunnel. The analyses of two steep slopes are reported: (i) an unsupported slope for a full-scale trial excavation and (ii) a partly nailed slope for a prototype cut and cover structure. It has been found that a major contribution to the stability of these cuts is an increase in the effective stress (and thus strength) due to both (i) depressed pore-water pressures (suctions) and (ii) a tendency of the Dublin boulder clay to dilate during undrained excavation in this low permeability and very dense material. However, the presence of even thin, discontinuous but recharged granular lenses of a higher permeability significantly reduces the time to failure.
Twenty-ninth Canadian Geotechnical Colloquium: The role of advanced numerical methods and geotechnical field measurements in understanding complex deep-seated rock slope failure mechanisms
Authors: Eberhardt Erik
Published: May 2008

The underlying complexity associated with deep-seated rock slope stability problems usually restricts their treatment to phenomenological studies that are largely descriptive and qualitative. Quantitative assessments, when employed, typically focus on assessing the stability state but ignore factors related to the slope’s temporal evolution including rock mass strength degradation, internal shearing, and progressive failure, all of which are key processes contributing to the final collapse of the slope. Reliance on displacement monitoring for early warning and the difficulty in interpreting the data without a clear understanding of the underlying mechanisms has led to a situation where predictions are highly variable and generally unreliable. This paper reviews current knowledge regarding prefailure mechanisms of massive rock slopes and current practices used to assess the hazard posed. Advanced numerical modelling results are presented that focus on the importance of stress- and strain-controlled rock mass strength degradation leading to failure initiation. Efforts to address issues related to parameter and model uncertainty are discussed in the context of a high alpine research facility, the “Randa In Situ Rockslide Laboratory”, where state-of-the-art instrumentation systems and numerical modelling are being used to better understand the mechanisms controlling prefailure deformations over time and their evolution leading to catastrophic failure.
Flowsliding in Sensitive Soils
Authors: Mitchell R. J. , Markell A. R.
Published: May 2008

The susceptibility of sensitive soils to large flowslides is a serious geotechnical problem. Scientific study of this natural phenomenon is necessary if future losses of life and property are to be avoided. Rational methods of flowslide terrain evaluation are required for project planning and development.Published information on 41 documented landslides was supplemented by air photo studies, field studies, and data from a variety of soils reports in order to compare the characteristics of flowslide terrain with more stable terrain that was equally well dissected by river valleys. The phenomenon of flowsliding was also considered from an analytical approach. These studies indicate that landslides in sensitive soils can be generally classified as simple rotational slips, retrogressive rotational flowsliding, or earthflows. An earthflow involves undrained extrusion of sensitive soils and is a continuous flow process that occurs only when the stability number, Ns = γH/Cu, for the material in the slope exceeds the number 6 within the depth of potential flow.A general relationship was found to exist between the stability number, Ns, and the distance of retrogression although secondary factors such as sensitivity, stratigraphy, topography, and the presence of materials susceptible to liquefaction appear to vary the limits of flowsliding.
Stability of Road Embankments in Soft Clay
Authors: Flaate Kaare , Preber Terje
Published: May 2008

Slides in soft marine clays frequently occur during construction of road embankments in Norway. This paper outlines the routine procedure used for a stability analysis of such embankments, based on a total stress concept. Using these procedures, eight slides were investigated, and it was found that the minimum factor of safety obtained could give a too conservative picture of the actual conditions. The minimum factor of safety, which is the one normally used, varied between 0.73 and 1.10. Taking all uncertainties into consideration, an analysis based on a total stress concept as outlined herein must be considered acceptable. The study gives no basis for evaluating the accuracy of the measured shear strength values.
Observations on static and cyclic sand-liquefaction methodologies
Authors: McRoberts E. C. , Sladen J. A.
Published: May 2008

The paper focuses on a review of elements of the liquefaction of sand. Consideration is given to both the static and cyclic approach, and the bases for many of the divergent opinions that currently exist are given. The objective of the paper is to state the arguments and to explore common ground. By considering the inconsistencies that currently exist it is hoped that future work will address issues raised. The real difficulties associated with measurement of the parameters necessary for existing design approaches are highlighted. Because of these difficulties, it is prudent to consider several methods when evaluating liquefaction potential, and practising engineers must often rely on traditional approaches. The state of practice would be improved more by research to address these difficulties than by the development of more elaborate methods of analysis, which are often not justified by the level of precision associated with input parameter measurements. Key words : liquefaction, steady-state, cyclic mobility, critical state.
Use of a groundwater flow model to explain strong upward gradients in rock formation underneath the Mercier site
Authors: Isabel Denis , Gélinas Pierre , Locat Jacques
Published: May 2008

The groundwater pollution case at Mercier is a very complex one. Groundwater flow modeling has been a valuable tool in the assessment of this large environmental problem. However, due to the complexity of the hydrogeological setting, the modeling has been performed with various simple case models in lieu of a large complex model. Here we report the results of one of these piecewise modeling tasks that proved very useful in the explanation of the strong upward gradients observed in the bedrock aquifer. These results and their interpretation prove the usefulness of the piecewise modeling strategy in this case. Key words : ground water modeling, finite elements.
A geological approach toward developing a mudrock-durability classification system
Authors: Dick Jeffrey C. , Shakoor Abdul , Wells Neil
Published: May 2008

Relationships between durability and lithologic characteristics of 61 mudrock samples from North America were investigated with the objective of developing a mudrock-durability classification based on lithologic characteristics. Second-cycle slake-durability index (Id2) was used as a measure of durability, whereas clay content, clay-mineral composition, texture, microfracture frequency, absorption, adsorption, dry density, void ratio, and Atterberg limits were used to characterize mudrock lithology. Based upon the amount of clay-size material, the presence or absence of laminations, and the degree of induration, the mudrocks were subdivided into claystones, mudstones, siltstones, shales, and argillites. The relationships between durability and lithologic characteristics were investigated separately for each class of mudrocks. The results show that different lithologic characteristics best correlate with the durability of each class of mudrocks. The durability of claystones correlates best with the amount of expandable clay minerals and that of mudstones with the frequency of microfractures. The degree of consolidation, as expressed by absorption, influences the durability of both siltstones and shales. The durability of argillites is related to their crystalline texture. Lithologic characteristics can be quantitatively related to a durability classification proposed herein that recognizes three classes of durability: low (Id2 < 50%), medium (Id2 = 50%–85%), and high (Id2 > 85%). Key words : mudrock, durability, lithologic characteristics, classification.
Displacement pile behaviour in glacial clay
Authors: Lehane B.M. , Jardine R.J.
Published: May 2008

The paper describes a programme of field experiments with heavily instrumented displacement piles installed in a stiff, lodgement till. Measurements of the effective stresses recorded at various levels along the pile shaft during installation, equalization, and load testing are presented. Shaft capacity is shown to be governed by an effective stress failure criterion, with the mobilized stresses depending on the clay consistency, distance from the pile tip, shaft surface texture, type of loading, installation rate, and degree of equalization. Key words : displacement pile, instrumentation, glacial till.
Hyperbolic method for settlements in clays with vertical drains
Authors: Tan Siew-Ann
Published: May 2008

Estimation of the total primary settlement is critical in determining when the required compression has been achieved and a surcharge loading can be removed. Conventionally, the total primary settlement is predicted using laboratory-determined compressibility data. However, the rectangular hyperbolic-fitting method allows estimation of the total primary settlement during the process of consolidation. In this paper, the hyperbolic-fitting method is extended to the case of consolidation with combined vertical and radial flow, which occurs when vertical drains are used to speed consolidation. Solutions are presented for the slope of the first linear segments between the 50 and 90% settlement points of the theoretical hyperbolic plots (time/settlement versus time). The proposed hyperbolic-fitting method was tested using data from the case history of the Changi Airport field test in Singapore, where Geodrains and sand drains were used for soil improvement following land reclamation and prior to airfield pavement construction. The predictions of the proposed method agree well with the measured and estimated soil settlements from compressibility calculations. The method can complement existing methods to provide a practical means of monitoring the progress of consolidation in field applications using drains and surcharge, and to determine the appropriate time for surcharge removal, if required. Key words : consolidation, vertical drains, settlements, hyperbolic method.
Uniqueness of steady state and liquefaction potential
Authors: Negussey D. , Islam M.S.
Published: May 2008

A given sand is presumed to have a unique steady-state line. The proximity of an initial state to the steady-state line is considered to be a measure of liquefaction potential. This line of reasoning and application in practice is based on data obtained predominantly from triaxial tests in compression-mode loading. In such tests, relative orientations of bedding plane and principal stress directions remain fixed while stress states along actual failure surfaces may range from active to passive. This study examines the uniqueness of the steady state relative to the mode of loading, form of consolidation, and initial anisotropy as induced by bedding orientation. A sample-preparation method was developed to form triaxial samples with different bedding orientations. Steady states of a uniform sand reached under compressional and extensional modes of triaxial undrained loading of samples with different bedding orientation are compared. Effects of isotropic and anisotropic consolidation are examined. The results indicate the steady-state line obtained for compression-mode loading is different from and does not apply for extension-mode loading. Use of a compression side steady-state line for extension-mode failure states would result in overestimation of steady-state strengths and unconservative stability evaluations. Key words : anisotropy, compression, extension, liquefaction, sand, steady state, triaxial.
Analyse dendroécologique d'une sapinière issue d'un chablis dans la zone boréale, Québec
Authors: Morin Hubert
Published: May 2008

This paper presents a model of the recent dynamics of a boreal fir population (Abiesbalsamea (L.) Mill.) exposed to a major disturbance, taking a blowdown as an example. The blowdown was precisely dated with the use of reaction wood. Age structures and growth curves were used to reveal the population history and to follow the evolution of the regeneration. The blowdown occurred in 1947. The majority of the firs of the actual population were established before the event. Their age structure conforms to the normal distribution. The original population, which was blown down, was replaced by a similar population in terms of the species' relative proportion. The blowdown is associated with a spruce budworm (Choristoneurafumiferana (Clem.)) outbreak which began around 1944. The population growth curve shows a distinct growth release following these two disturbances. The regeneration mechanisms of this site could serve as a model applicable to more complex but just as devastating disturbances, such as spruce budworm outbreaks.
Recapture of marked spruce bark beetles (Ipstypographus) in pheromone traps using area-wide mass trapping
Authors: Weslien Jan , Lindelöw Åke
Published: May 2008

Mark–release–recapture experiments were performed with Ipstypographus (L.) populations to estimate recapture rates (number recaptured/number released) in pheromone traps. The recapture rate of bark beetles marked during spring emergence during 2 consecutive years was about 8% in trap groups set 100 m from release sites and decreased to about 2% in trap groups set 1200–1600 m away. The rate at which recapture declined with distance was slower than predicted by a model in which the decrease in recapture depends only on the dilution of released beetles. Sixty percent of the variation in recapture rates was explained by the distance between release and recapture points. The relationship between distance and rate of recapture was used to estimate the rate at which regional beetle populations may be captured using area-wide mass trapping.
Conduction pathways in the nervous system ofSaccoglossussp. (Enteropneusta)
Authors: Cameron C. B. , Mackie G. O.
Published: May 2008

A species of Saccoglossus from Barkley Sound, British Columbia, was observed in the field and found to exhibit a startle withdrawal response. Optical and electron microscopy of the nerve cords failed to reveal giant axons. The dorsal collar cord and ventral trunk cord consist of small axons with a mean diameter of 0.4 μm. The majority of the axons run longitudinally and there is no indication of a specialized integrative centre. Electrical recordings from the nerve cords show events interpreted as compound action potentials. The potentials are through-conducted from proboscis to trunk. Such propagated events probably mediate startle withdrawal. Conduction velocities did not exceed 40 cm∙s−1in any part of the nervous system.