bluuebunny/crossref_metadata_2025 huggingface dataset:
Preventing Transformation
Authors: Gough Nancy R.
Published: September 2007

The oncogene Myc, which is a transcription factor, is well known for its ability to transform cells. However, not all cells are equally sensitive to Myc-induced transformation. Partanen
et al
. compared the response of organized epithelial acini and disorganized or immature acini formed from mammary epithelial cells (untransformed MCF10A and immortalized cells) with the transforming ability of a conditionally activated form of Myc (MycER
tm
) that is activated by exposing the cells to tamoxifen. When the cells were plated in Matrigel (a three-dimensional matrix) and MycER
tm
was continuously activated, the cells formed misshapen acini with cells in the luminal space. Cells grown in the absence of activated Myc formed symmetrical acini that had hollow lumens lacking cells, and the acini were smaller because cell proliferation stopped sooner than it did in the cells with activated MycER
tm
. However, if tamoxifen was added after the cells grown on Matrigel had formed established organized acinar structures, then Myc lost its oncogenic activity: The morphology and size of the acini were unchanged, and cell proliferation was not induced. Cells in which the kinase LKB1, which is implicated in establishment of cellular polarity, was silenced formed disorganized acini with disrupted cell polarity when plated in Matrigel. However, these LKB1-deficient cells did become quiescent. Activation of Myc in these quiescent LKB1-deficient cells of the disorganized acini did stimulate reentry into the cell cycle, thus confirming the importance of epithelial organization as a brake for oncogenic transformation. The authors also addressed the apoptotic activity of Myc. Myc sensitized cells of fully organized acini to TRAIL (a death-inducing agent that activates apoptosis), which means that both TRAIL and Myc were required to promote apoptosis. However, in LKB1-deficient disorganized acini or immature acini, activation of MycER
tm
or TRAIL caused apoptosis and these two agents had an additive effect on cell death. Thus, disorganized epithelia are more sensitive to both the cell proliferative and apoptotic effects of Myc.

J. I. Partanen, A. I. Nieminen, T. P. Mäkelä, J. Klefstrom, Suppression of oncogenic properties of c-Myc by LKB1-controlled epithelial organization.
Proc. Natl. Acad. Sci. U.S.A.
104
, 14694-14699 (2007).
[Abstract]
[Full Text]
A synopsis of mineral deposits in the Archean and Proterozoic rocks of the Lake Nipigon Region, Thunder Bay District, Ontario
Authors: Smyk Mark C , Franklin James M
Published: September 2007

A variety of metallic and non-metallic mineral deposit types occur within Archean and Proterozoic rocks in the area encompassing the Lake Nipigon Region Geoscience Initiative. Archean deposit types include Algoma-type banded iron formation-hosted iron (e.g., Lake Nipigon iron range); volcanogenic massive sulphide copper–zinc (e.g., Onaman–Tashota belt); ultramafic intrusion-hosted chromium (e.g., Puddy–Chrome lakes); mafic to ultramafic intrusion-hosted copper–nickel – platinum group element (PGE) (e.g., Lac des Iles); and pegmatite-hosted deposits of rare metals (Li, Ta, Be), uranium, and molybdenum (e.g., Georgia Lake field, Black Sturgeon Lake, and Anderson Lake, respectively). Mesothermal lode gold deposits are prominent in the Beardmore–Geraldton camp. Superior-type iron formation occurs in Paleoproterozoic Gunflint Formation. "Red-bed" copper occurs in Mesoproterozoic Midcontinent Rift-related Osler Group volcanic and interflow sedimentary rocks. Native copper and copper sulphides occur in Mesoproterozoic Sibley Group sedimentary rocks, adjacent to ultramafic intrusions. These mafic to ultramafic intrusions, associated with Midcontinent Rift magmatism, host copper–nickel–PGE deposits (e.g., Seagull, Great Lakes Nickel). Silver-bearing veins occur in Paleoproterozoic Animikie Group sedimentary rocks in proximity to Midcontinent Rift-related mafic intrusions (e.g., Silver Islet, Silver Mountain). Lead–zinc–barite veins, uranium-bearing veins, and amethyst vein and replacement-type deposits may be cogenetic and formed at or near the unconformity between Sibley Group basal sandstone and underlying Archean granitic basement (e.g., Dorion, Black Sturgeon Lake, McTavish Township). The hydrothermal systems that produced all of these veins were probably driven by heat associated with Midcontinent rifting. Many occur in structures related to rift-bounding faults. Iron oxide – copper–gold deposits may occur near the English Bay intrusion.
Introduction to Special Issue of Canadian Journal of Earth Sciences: the Lake Nipigon Region Geoscience Initiative
Authors: Hollings Pete , Rayner Wally , Easton Mike
Published: September 2007

The Lake Nipigon Region Geoscience Initiative (LNRGI) was a 3-year collaborative geoscience data acquisition and compilation project that focussed on Lake Nipigon in Ontario and involved partnerships between mineral industry, university, and provincial and federal government geoscientists. A major objective of the initiative was to collect new geoscience information to better understand the geological history of the Nipigon region to inform land-use planning, identify areas of high mineral potential, and attract mineral exploration. The Special Issue on the LNRGI highlights the scientific successes of the Initiative in the fields of geology, petrology, geochemistry, geochronology, stratigraphy and basin analysis, mineral deposits, and surficial geology and geochemistry.
Proterozoic and Archean geology of the Nipigon Embayment: implications for emplacement of the Mesoproterozoic Nipigon diabase sills and mafic to ultramafic intrusions
Authors: Hart Thomas Robert , MacDonald Carole Anne
Published: September 2007

The Nipigon Embayment is underlain by Archean rocks of the English River, Wabigoon, and Quetico subprovinces, and intruded along the west side by late- to post-tectonic mafic to ultramafic intrusions. The early Mesoproterozoic ultramafic to felsic Badwater intrusion and felsic English Bay Complex are located in the northwest corner of the Nipigon Embayment. Three mafic to ultramafic intrusions, the Disraeli, Seagull, and Hele intrusions, are located south of Lake Nipigon, and the Kitto intrusion is located east of the lake. A number of mafic to ultramafic bodies (Jackfish (Island), Shillabeer, Kama Hill, Nipigon Bay) have only limited outcrops. The gabbroic Nipigon diabase sills intrude all other rocks in the Nipigon Embayment and generally have a consistent mineralogy and geochemistry, except for the Inspiration sill(s) and the McIntyre Sill. Geological and geophysical data suggest emplacement of the ultramafic intrusions by mechanisms similar to those controlling emplacement of the saucer-shaped diabase sills. These mechanisms are partially dependent on a series of pre-existing north-, northwest-, and northeast-trending faults formed prior to Keweenawan magmatism. The presence of sills, rather than dykes, indicates that the Nipigon Embayment was not extensional during the Keweenawan Midcontinent Rift, suggesting that the Nipigon Embayment is not a classic failed arm.
Sulfide saturation mechanisms in gabbroic intrusions in the Nipigon Embayment
Authors: Kissin Stephen A , Heggie Geoffrey J , Franklin James M , Somarin Alireza Karimzadeh
Published: September 2007

The Seagull and Kitto intrusions in the Nipigon Embayment of northwestern Ontario were studied to gain an understanding of the processes involved in sulfur saturation of the mafic to ultramafic magmas leading to the formation of platinum group element (PGE) concentrations. Profiles of sulfur, copper, nickel, gold, palladium, and platinum concentrations as a function of depth revealed that sulfur saturation occurred at the base of the Seagull intrusion. A higher grade horizon occurs well above the base of the intrusion, suggesting that a reef-type of process was significant here and possibly in the Kitto intrusion, as well. Olivine compositions indicate that, in both cases, the parental magmas were undersaturated with respect to sulfur. Sulfur, neodymium–samarium, and rubidium–strontium isotopic data suggest that assimilation of country rock and sulfide played a role, especially in the formation of basal concentrations of PGEs.
Multimedia exploration strategies for PGEs: insights from the Surficial Geochemistry Case Studies Project, Lake Nipigon Region Geoscience Initiative, northwestern Ontario
Authors: Dyer Richard D , Barnett Peter J
Published: September 2007

The Surficial Geochemistry Case Studies Project in the Lake Nipigon region involved detailed Quaternary mapping and multimedia geochemical sampling within five case study areas. Two of these areas, Lac des Iles and Tib Lake, contain known platinum group element (PGE) mineralization. The other three case study areas feature drainage catchments with lakes that contain anomalous levels of PGEs in bottom sediment. Surficial media sampled included till, soils, stream sediment, lake sediment, peat, surface water, and groundwater. Over Archean terrain, such as at Lac des Iles and Tib Lake, there is excellent geochemical contrast between the PGE prospective rock type (mafic to ultramafic intrusive) and the surrounding rock type (e.g., granitoid rocks). This geochemical contrast is mirrored in the geochemistry of most surficial media sampled during this project. Over the Nipigon Embayment, the geochemical contrast between mafic and ultramafic rocks (e.g., Seagull-type intrusions) and the surrounding diabase sill rocks is inherently weaker due to the relatively high background levels for copper, palladium, and gold in the Nipigon diabase sills. However, the results of stream-water geochemistry over the Seagull and Disraeli ultramafic intrusions highlight their unique geochemical footprint on the surficial landscape, in particular with respect to Cr, Mg, and Ni, compared with the surrounding Nipigon diabase. In addition, lake sediments underlain by the Seagull, Disraeli, and Hele intrusions have distinctly elevated Cr concentrations and Gd/Yb ratios compared with the surrounding areas underlain by Nipigon diabase sills or Sibley Group rocks. Therefore, exploration value can be maximized over the Nipigon Embayment by exploiting these geochemical contrasts in surficial media to discriminate between ultramafic rocks and the surrounding Nipigon diabase sills. The results of this study highlight the importance of chromium concentrations in surficial media as a diagnostic feature for the presence of ultramafic rocks, regardless of their age or location. In general, a cost-effective exploration strategy for PGE mineralization includes targeting the associated metals (Cr, Ni) within drift deposits (C-horizon till) and drainage media (stream sediment, lake sediment) to vector to prospective mafic–ultramafic intrusive rocks, prior to detailed (property scale) follow-up, involving the determination of base metals and PGEs within soil, till, stream sediment, and peat samples. Relative to the metals copper, nickel, and chromium (ppm levels), the PGEs have significantly lower initial concentrations (ppb levels), are less mobile in the surficial environment, have significantly shorter glacial dispersion trains, and are less reliably determined at the laboratory.
Mitochondrial DNA variation in cultivated and wild potato species (Solanumspp.)Contribution No. 87 from the Institute of Plant Genetics, Research Division of Portici.
Authors: Scotti N. , Cozzolino S. , Cardi T.
Published: September 2007

The European cultivated potato, Solanum tuberosum subsp. tuberosum , has 6 related cultivated species and more than 200 wild relatives. In Solanum spp., studies of cytoplasmic organelles have been mainly confined to the plastid DNA composition of cultivated and wild species. In this study, 53 genotypes of 30 potato species belonging to the subsections Estolonifera and Potatoe , 2 tomato species, and a black nightshade genotype were examined using PCR markers to evaluate mitochondrial DNA diversity and assess whether mtDNA variability was correlated with series classification, geographical origin, ploidy, and endosperm balance number (EBN). The markers used revealed interspecific mtDNA variability in Solanum spp. and identified 13 different haplotypes. Intraspecific variability was also observed in a few species and genomic regions. Cluster analysis allowed arrangement of the 13 haplotypes into 7 subgroups, and statistical association tests showed significant relationships between mitochondrial patterns detected by molecular analysis and ploidy, EBN, and geographical origin. On the whole, the evolutionary patterns for the genomic regions analyzed reflected the species relationships established on the basis of morphological and molecular (nuclear and plastidial DNA) data. The mtDNA variability shown is also important for better characterization of genetic resources for potato breeding.
dAP-2anddefective proventriculusregulateSerrateandDeltaexpression in the tarsus ofDrosophila melanogaster
Authors: Ciechanska Ewa , Dansereau David A. , Svendsen Pia C. , Heslip Tim R. , Brook William J.
Published: September 2007

The segmentation of the proximal–distal axis of the Drosophila melanogaster leg depends on the localized activation of the Notch receptor. The expression of the Notch ligand genes Serrate and Delta in concentric, segmental rings results in the localized activation of Notch, which induces joint formation and is required for the growth of leg segments. We report here that the expression of Serrate and Delta in the leg is regulated by the transcription factor genes dAP-2 and defective proventriculus. Previous studies have shown that Notch activation induces dAP-2 in cells distal and adjacent to the Serrate/Delta domain of expression. We find that Serrate and Delta are ectopically expressed in dAP-2 mutant legs and that Serrate and Delta are repressed by ectopic expression of dAP-2. Furthermore, Serrate is induced cell-autonomously in dAP-2 mutant clones in many regions of the leg. We also find that the expression of a defective proventriculus reporter overlaps with dAP-2 expression and is complementary to Serrate expression in the tarsal segments. Ectopic expression of defective proventriculus is sufficient to block joint formation and Serrate and Delta expression. Loss of defective proventriculus results in localized, ectopic Serrate expression and the formation of ectopic joints with reversed polarity. Thus, in tarsal segments, dAP-2 and defective proventriculus are necessary for the correct proximal and distal boundaries of Serrate expression and repression of Serrate by defective proventriculus contributes to tarsal segment asymmetry. The repression of the Notch ligand genes Serrate and Delta by the Notch target gene dAP-2 may be a pattern-refining mechanism similar to those acting in embryonic segmentation and compartment boundary formation.
Generation and mapping of SCAR and CAPS markers linked to the seed coat color gene in Brassica napus using a genome-walking technique
Authors: Xiao Shushu , Xu Jinsong , Li Yuan , Zhang Lei , Shi Shijun , Shi Shuwen , Wu Jiangsheng , Liu Kede
Published: September 2007

The yellow seed coat trait in No. 2127-17, a resynthesized purely yellow Brassica napus line, is controlled by a single partially dominant gene, Y. A double-haploid population derived from the F1 of No. 2127-17 × ‘ZY821’ was used to map the seed coat color phenotype. A combination of AFLP analysis and bulked segregant analysis identified 18 AFLP markers linked to the seed coat color trait. The 18 AFLP markers were mapped to a chromosomal region of 37.0 cM with an average of 2.0 cM between adjacent markers. Two markers, AFLP-K and AFLP-H, bracketed the Y locus in an interval of 1.0 cM, such that each was 0.5 cM away from the Y locus. Two other markers, AFLP-A and AFLP-B, co-segregated with the seed color gene. For ease of use in breeding programs, these 4 most tightly linked AFLP markers were converted into reliable PCR-based markers. SCAR-K, which was derived from AFLP-K, was assigned to linkage group 9 (N9) of a B. napus reference map consisting of 150 commonly used SSR (simple sequence repeat) markers. Furthermore, 2 SSR markers (Na14-E08 and Na10-B07) linked to SCAR-K on the reference map were reversely mapped to the linkage map constructed in this study, and also showed linkage to the Y locus. These linked markers would be useful for the transfer of the dominant allele Y from No. 2127-17 to elite cultivars using a marker-assisted selection strategy and would accelerate the cloning of the seed coat color gene.
Development, characterization, and transferability to other Solanaceae of microsatellite markers in pepper (Capsicum annuumL.)
Authors: Nagy István , Stágel Anikó , Sasvári Zsuzsanna , Röder Marion , Ganal Martin
Published: September 2007

A novel set of informative microsatellite markers for pepper ( Capsicum annuum L.) is provided. Screening of approximately 168 000 genomic clones and 23 174 public database entries resulted in a total of 411 microsatellite-containing sequences that could be used for primer design and functional testing. A set of 154 microsatellite markers originated from short-insert genomic libraries and 257 markers originated from database sequences. Of those markers, 147 (61 from genomic libraries and 86 from database sequences) showed specific and scoreable amplification products and detected polymorphisms between at least 2 of the 33 lines of a test panel consisting of cultivated and wild Capsicum genotypes. These informative markers were subsequently surveyed for allelic variation and information content. The usefulness of the new markers for diversity and taxonomic studies was demonstrated by the construction of consistent phylogenetic trees based on the microsatellite polymorphisms. Conservation of a subset of microsatellite loci in pepper, tomato, and potato was proven by cross-species amplification and sequence comparisons. For several informative pepper microsatellite markers, homologous expressed sequence tag (EST) counterparts could be identified in these related species that also carry microsatellite motifs. Such orthologs can potentially be used as reference markers and common anchoring points on the genetic maps of different solanaceous species.
Mutation analysis ofDrosophiladikar/CG32394, homologue of the chromatin-remodelling geneCECR2
Authors: Keuling Angela , Yang Fang , Hanna Scott , Wang Huaien , Tully Tim , Burnham Amanda , Locke John , McDermid Heather E.
Published: September 2007

The mammalian CECR2 protein contains a highly conserved bromodomain and forms a chromatin-remodelling complex with the ISWI homologue SNF2L. Mutation of the mouse CECR2 homologue results in a neural tube defect. Here we describe the characterization of the Drosophila melanogaster homologue of CECR2. Originally annotated as 2 genes, dikar and CG32394 now appear to encode both a long dikar/CG32394 transcript homologous to CECR2 and a truncated transcript missing the bromodomain. This truncated transcript may be specific to Diptera, as it is predicted from the genomic sequences of several other dipteran species but it is not predicted in the honey bee, Apis mellifera , and it is not found in mammals. Five different P element–mediated 5′ deletions of the Drosophila dikar gene were generated. All mutants were homozygous-viable and the 3 mutants examined further displayed continued, albeit aberrant, transcription of dikar/CG32394. In a previous study, a dikar insertion mutation was associated with long-term memory deficits. However, the 2 deletion mutants tested here showed normal long-term memory, suggesting that the memory deficit associated with the dikar P element insertion is not due to disruption of dikar. No genetic interaction was seen between Iswi and dikar mutations. This study therefore suggests that the lack of a visible phenotype in dikar mutants is due to compensation by a second gene, possibly acf1.
Different patterns of genealogical relationships found in the two major QTLs causing reduction of seed shattering during rice domestication
Authors: Onishi Kazumitsu , Takagi Kyoko , Kontani Manabu , Tanaka Takumi , Sano Yoshio
Published: September 2007

The three quantitative trait loci (qSH1, qSH3, and qSH4) causing reduction of seed shattering were investigated to examine their relative importance during rice domestication. The qSH1 and qSH4 loci showed a distinct effect on the reduction of shattering, compared with the qSH3 locus. Fine mapping and sequence analysis strongly suggested that the qSH1 and qSH4 loci are the same as the recently reported genes. A non-shattering allele at qSH1 drastically changed the shattering phenotype to a non-shattering phenotype even in the presence of shattering alleles at the qSH3 and qSH4 loci, showing that qSH1 is genetically epistatic to the other loci. The level of the reduction in sequence diversity was compared between the qSH1 and qSH4 regions. The sequence diversity was severely reduced in the qSH1 region of Oryza sativa subsp. japonica compared with that of O. sativa subsp. indica, despite that the level of diversity was similarly reduced at the qSH4 region in the 2 subspecies. Phylogenetic reconstruction based on the combined sequences of the flanking sites showed different patterns in the 2 subspecies. The 2 subspecies formed a single clade with respect to qSH4, whereas they were separated into different lineages with respect to qSH1, suggesting that these loci had different histories during rice domestication.
Genetic mapping of genes for susceptibility to black spot disease in Japanese pears
Authors: Terakami S. , Adachi Y. , Iketani H. , Sato Y. , Sawamura Y. , Takada N. , Nishitani C. , Yamamoto T.
Published: September 2007

Black spot disease, which is caused by the Japanese pear pathotype of Alternaria alternata (Fr.) Keissler, is one of the most harmful diseases in Japanese pear cultivation. We identified the exact positions and linkage groups (LGs) of the genes for susceptibility to black spot in the Japanese pear ( Pyrus pyrifolia Nakai) cultivars ‘Osa Nijisseiki’ (gene Ani) and ‘Nansui’ (gene Ana). Segregation of susceptibility and resistance fitted the expected ratio of 1:1 in progeny of ‘Nansui’ but showed a slight distortion in progeny of ‘Osa Nijisseiki’. We mapped the genes for susceptibility to black spot in both populations using a genome scanning approach. The simple sequence repeat (SSR) markers CH04h02 and CH03d02 showed tight linkage to Ani and Ana. Although Ani and Ana are derived from different sources, both genes are located at the top region of LG 11. Information about the positions of the susceptibility genes and the molecular markers linked to them will be useful for marker-assisted selection in pear breeding programs.
Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross
Authors: Gyenis L. , Yun S.J. , Smith K.P. , Steffenson B.J. , Bossolini E. , Sanguineti M.C. , Muehlbauer G.J.
Published: September 2007

Hordeum vulgare subsp. spontaneum is the progenitor of cultivated barley (Hordeum vulgare L.). Domestication combined with plant breeding has led to the morphological and agronomic characteristics of modern barley cultivars. The objective of this study was to map the genetic factors that morphologically and agronomically differentiate wild barley from modern barley cultivars. To address this objective, we identified quantitative trait loci (QTLs) associated with plant height, flag leaf width, spike length, spike width, glume length in relation to seed length, awn length, fragility of ear rachis, endosperm width and groove depth, heading date, flag leaf length, number of tillers per plant, and kernel color in a Harrington/OUH602 advanced backcross (BC2F8) population. This population was genotyped with 113 simple sequence repeat markers. Thirty QTLs were identified, of which 16 were newly identified in this study. One to 4 QTLs were identified for each of the traits except glume length, for which no QTL was detected. The portion of phenotypic variation accounted for by individual QTLs ranged from about 9% to 54%. For traits with more than one QTL, the phenotypic variation explained ranged from 25% to 71%. Taken together, our results reveal the genetic architecture of morphological and agronomic traits that differentiate wild from cultivated barley.
Immunological detection of changes in genomic DNA methylation during early zebrafish development
Authors: MacKay Amy B. , Mhanni Aizeddin A. , McGowan Ross A. , Krone Patrick H.
Published: September 2007

DNA methylation reprogramming, the erasure of DNA methylation patterns shortly after fertilization and their reestablishment during subsequent early development, is essential for proper mammalian embryogenesis. In contrast, the importance of this process in the development of non-mammalian vertebrates such as fish is less clear. Indeed, whether or not any widespread changes in DNA methylation occur at all during cleavage and blastula stages of fish in a fashion similar to that shown in mammals has remained controversial. Here we have addressed this issue by applying the techniques of Southwestern immunoblotting and immunohistochemistry with an anti–5-methylcytosine antibody to the examination of DNA methylation in early zebrafish embryos. These techniques have recently been utilized to demonstrate that development-specific changes in genomic DNA methylation also occur in Drosophila melanogaster and Dictyostelium discoideum , both organisms for which DNA methylation was previously not thought to occur. Our data demonstrate that genome-wide changes in DNA methylation occur during early zebrafish development. Although zebrafish sperm DNA is strongly methylated, the zebrafish genome is not detectably methylated through cleavage and early blastula stages but is heavily remethylated in blastula and early gastrula stages.
Construction of a genetic linkage map forSaccharum officinarumincorporating both simplex and duplex markers to increase genome coverage
Authors: Aitken K.S. , Jackson P.A. , McIntyre C.L.
Published: September 2007

Saccharum officinarum L. is an octoploid with 80 chromosomes and a basic chromosome number of x = 10. It has high stem sucrose and contributes 80% of the chromosomes to the interspecific sugarcane cultivars that are grown commercially for sucrose. A genetic linkage map was developed for S. officinarum (clone IJ76-514) using a segregating population generated from a cross between Q165 (a commercial sugarcane cultivar) and IJ76-514. In total, 40 AFLP and 72 SSR primer pairs were screened across the population, revealing 595 polymorphic bands inherited from IJ76-514. These 595 markers displayed a frequency distribution different from all other sugarcane genetic maps produced, with only 40% being simplex markers (segregated 1:1). Of these 240 simplex markers, 178 were distributed on 47 linkage groups (LGs) and 62 remained unlinked. With the addition of 234 duplex markers and 80 biparental simplex markers (segregating 3:1), 534 markers formed 123 LGs. Using the multi-allelic SSR markers, repulsion phase linkage, and alignment with the Q165 linkage map, 105 of the 123 LGs could be grouped into 10 homology groups (HGs). These 10 HGs were further assigned to the 8 HGs observed in cultivated sugarcane and S. spontaneum . Analysis of repulsion phase linkage indicated that IJ76-514 is neither a complete autopolyploid nor an allopolyploid. Detection of 28 repulsion linkages that occurred between 6 pairs of LGs located in 4 HGs suggested the occurrence of limited preferential chromosome pairing in this species.
The mitochondrial genome of Ruspolia dubia (Orthoptera: Conocephalidae) contains a short A+T-rich region of 70 bp in length
Authors: Zhou Zhijun , Huang Yuan , Shi Fuming
Published: September 2007

The complete sequence (14 971 bp) of the Ruspolia dubia mitochondrial genome was determined and annotated. The genome contains the gene content, base composition, and codon usage typical of metazoan mitochondrial genomes. All 37 genes are conserved in the positions observed most frequently in insect mitochondrial genome structures. The secondary structures of both small subunit and large subunit rRNA were predicted. The most unusual features found were the initiation codon (TTA) of COI and a short A+T-rich region of 70 bp in length. In addition, a short, highly conserved polythymidine stretch that was previously described in Orthoptera and Diptera was also present in the A+T-rich region.
5S ribosomal RNA genes in six species of Mediterranean grey mullets: genomic organization and phylogenetic inference
Authors: Gornung Ekaterina , Colangelo Paolo , Annesi Flavia
Published: September 2007

This paper describes a study of the 5S ribosomal RNA genes (5S rDNA) in a group of 6 species belonging to 4 genera of Mugilidae. In these 6 species, the relatively short 5S rDNA repeat units, generated by PCR and ranging in size from 219 to 257 bp, show a high level of intragenomic homogeneity of both coding and spacer regions (NTS-I). Phylogenetic reconstructions based on this data set highlight the greater phylogenetic and genetic diversity of Mugil cephalus and Oedalechilus labeo compared with the genera Liza and Chelon. Comparative sequence analysis revealed significant conservation of the short 5S rDNA repeat units across Chelon and Liza. Moreover, a second size class of 5S rDNA repeat units, ranging from roughly 800 to 1100 bp, was produced in the Liza and Chelon samples. Only short 5S rDNA repeat units were found in M. cephalus and O. labeo. The sequences of the long 5S rDNA repeat units, obtained in Chelon labrosus and Liza ramada , differ owing to the presence of 2 large insertion/deletions (indels) in the spacers (NTS-II) and show considerable sequence identity with NTS-I spacers. Interspecific sequence variation of NTS-II spacers, excluding the indels, is low. Southern-blot hybridization patterns suggest an intermixed arrangement of short and long repeat units within a single chromosome locus.
Molecular markers linked to theRf2fertility restorer gene in cotton
Authors: Wang Fei , Stewart James McD. , Zhang Jinfa
Published: September 2007

Cytoplasmic male sterility (CMS) is a maternally inherited trait in which plants do not produce viable pollen. Fertility in plants with CMS can be recovered by nuclear restorer genes. Most restorer genes cloned so far are members of the pentatricopeptide repeat (PPR) protein family. The objective of our study was to use the CMS-D8 and restoration (Rf2) system of cotton ( Gossypium hirsutum L.) to develop more DNA markers for the Rf2gene. In a backcross population with 112 plants, segregation of male fertility was 1 fertile : 1 sterile. Three new RAPD markers were identified for Rf2, one of which was converted to a CAPS marker. In addition, 2 AFLP markers and 1 SSR marker were identified to be linked to the fertility restorer gene (Rf2). PPR motif primers were designed based on the conserved PPR motifs and used in combination with AFLP primers to test the mapping population, and 1 PPR-AFLP marker was identified. A linkage map with 9 flanking markers including 1 from a previous study was constructed.
Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes
Authors: Coyne C.J. , McClendon M.T. , Walling J.G. , Timmerman-Vaughan G.M. , Murray S. , Meksem K. , Lightfoot D.A. , Shultz J.L. , Keller K.E. , Martin R.R. , Inglis D.A. , Rajesh P.N. , McPhee K.E. , Weeden N.F. , Grusak M.A. , Li C.-M. , Storlie E.W.
Published: September 2007

Pea ( Pisum sativum L.) has a genome of about 4 Gb that appears to share conserved synteny with model legumes having genomes of 0.2–0.4 Gb despite extensive intergenic expansion. Pea plant inventory (PI) accession 269818 has been used to introgress genetic diversity into the cultivated germplasm pool. The aim here was to develop pea bacterial artificial chromosome (BAC) libraries that would enable the isolation of genes involved in plant disease resistance or control of economically important traits. The BAC libraries encompassed about 3.2 haploid genome equivalents consisting of partially HindIII-digested DNA fragments with a mean size of 105 kb that were inserted in 1 of 2 vectors. The low-copy oriT-based T-DNA vector (pCLD04541) library contained 55 680 clones. The single-copy oriS-based vector (pIndigoBAC-5) library contained 65 280 clones. Colony hybridization of a universal chloroplast probe indicated that about 1% of clones in the libraries were of chloroplast origin. The presence of about 0.1% empty vectors was inferred by white/blue colony plate counts. The usefulness of the libraries was tested by 2 replicated methods. First, high-density filters were probed with low copy number sequences. Second, BAC plate-pool DNA was used successfully to PCR amplify 7 of 9 published pea resistance gene analogs (RGAs) and several other low copy number pea sequences. Individual BAC clones encoding specific sequences were identified. Therefore, the HindIII BAC libraries of pea, based on germplasm accession PI 269818, will be useful for the isolation of genes underlying disease resistance and other economically important traits.
Genetic analysis and fine mapping of a dynamic rolled leaf gene,RL10(t), in rice (Oryza sativaL.)
Authors: Luo Zengke , Yang Zhenglin , Zhong Bingqiang , Li Yunfeng , Xie Rong , Zhao Fangming , Ling Yinghua , He Guanghua
Published: September 2007

A dynamically rolled leaf mutant (rl10) was identified from a spontaneous mutation in an Oryza sativa L. subsp. indica line, II-32B. The leaf chlorophyll content of rl10 is higher than that of the wild type. Genetic analysis using 3 F2segregating populations derived from crosses between rl10 and the rice lines Mian5B, II-32B, and D62B, respectively, confirmed that the rolled leaf trait of rl10 is controlled by a single recessive gene. Of 719 SSR primer pairs that showed polymorphism between D62B and rl10, 151 were adopted to map the RL10(t) gene using an F2segregating population of the cross rl10 × D62B, which contained 352 recessive plants. RL10(t) was primarily mapped on the long arm of chromosome 9, 5.09 cM from marker RM105 and 5.13 cM from marker RM3912. Using a novel set of 22 primer pairs between RM105 and RM3912, RL10(t) was further mapped between markers rlc3 (0.72 cM in distance) and rlc12 (0.1 cM in distance) using an F2/F3population containing 1172 recessive individuals. Mapped position analysis and homology analysis of the 20 genes within the 194-kb region between these 2 markers both indicated that a gene encoding a Myb-like domain transcription factor with homology to Arabidopsis KANADI (annotated in PAC clone AP005904) is the most probable candidate for RL10(t). This study enables further investigation of whether KANADI-like Myb genes are involved in leaf polarity modeling in monocots, as they are in dicots.
Ty1-copiaretrotransposon-based SSAP marker development and its potential in the genetic study of cucurbits
Authors: Lou Qunfeng , Chen Jinfeng
Published: September 2007

Three long terminal repeat (LTR) sequences of Ty1-copia retrotransposons were identified in cucumber ( Cucumis sativus L.) and named Tcs 1, Tcs 2, and Tcs 3. A sequence-specific amplification polymorphism (SSAP) marker system based on these LTR sequences displayed a higher level of polymorphism than AFLPs in cucumber. This marker system could also detect loci in other Cucumis species for genetic diversity analysis. The three Tcs LTRs existed within the exons of genes because of the effective amplification band patterns from the cDNA templates. The potential usefulness of the SSAP marker system in studies of the evolution of genes or genomes was verified after exploring loci changes in first and second generations of a synthetic allotetraploid in Cucumis. This study is the first report of the development of a retrotransposon-based marker system and the SSAP technique in cucurbits.
Localization of QTLs for seed color using recombinant inbred lines of Brassica napus in different environments
Authors: Fu Fu-You , Liu Lie-Zhao , Chai You-Rong , Chen Li , Yang Tao , Jin Meng-Yang , Ma Ai-Fen , Yan Xing-Ying , Zhang Zheng-Sheng , Li Jia-Na
Published: September 2007

Yellow seed is one of the most important traits of Brassica napus L. Efficient selection of the yellow-seed trait is one of the most important objectives in oilseed rape breeding. Two recombinant inbred line (RIL) populations (RIL-1 and RIL-2) were analyzed for 2 years at 2 locations. Four hundred and twenty SSR, RAPD, and SRAP marker loci covering 1744 cM were mapped in 26 linkage groups of RIL-1, while 265 loci covering 1135 cM were mapped in 20 linkage groups of RIL-2. A total of 19 QTLs were detected in the 2 populations. A major QTL was detected adjacent to the same marker (EM11ME20/200) in both maps in both years. This major QTL could explain 53.71%, 39.34%, 42.42%, 30.18%, 24.86%, and 15.08% of phenotypic variation in 6 combinations (location × year × population). BLASTn analysis of the sequences of the markers flanking the major QTL revealed that the homologous region corresponding to this major QTL was anchored between genes At5g44440 and At5g49640 of Arabidopsis thaliana chromosome 5 (At C5). Based on comparative genomic analysis, the bifunctional gene TT10 is nearest to the homologue of EM11ME20/200 on At C5 and can be considered an important candidate gene for the major QTL identified here. Besides providing an effective strategy for marker-assisted selection of the yellow-seed trait in B. napus, our results also provide important clues for cloning of the candidate gene corresponding to this major QTL.
GISH analysis of meiotic chromosome pairing inSolanum lycopersicoidesintrogression lines of cultivated tomato
Authors: Ji Yuanfu , Chetelat Roger T.
Published: September 2007

Meiotic chromosome pairing was studied in introgression lines of cultivated tomato, Lycopersicon esculentum (= Solanum lycopersicum ), containing 1 or 2 chromosome segments from the wild species Solanum lycopersicoides . Genomic in situ hybridization (GISH) was used to compare the relative lengths at diakinesis of the different introgressed segments and to measure the chiasmate arm frequency for the chromosome pair involved in the introgression(s). Longer segments generally produced stronger GISH signals than shorter segments. GISH signal intensity also depended on whether or not an introgressed segment encompassed the centromeric region. For example, a 29 cM segment that included the centromeric region produced a stronger GISH signal than a 42 cM segment that did not. In each line the chromosome arm containing the homeologous segment showed a reduction in chiasmate arm frequency that was most pronounced in lines with long segments. This reduction was accompanied by an increased chiasmate arm frequency on the other arm. Double introgression lines, heterozygous in repulsion phase for 2 introgressions on opposite chromosome arms, showed a lower frequency of chiasmata than single introgression lines. Pairing failure, indicated by the presence of univalents, was highest in the double introgression and whole chromosome substitution lines. These results are discussed with respect to observations of suppressed recombination in these stocks and potential practical implications for reducing linkage drag in breeding programs.
Local and regional factors affecting atmospheric mercury speciation at a remote location
Authors: Manolopoulos Helen , Schauer James J. , Purcell Mark D. , Rudolph Todd M. , Olson Mark L. , Rodger Bruce , Krabbenhoft Dave P.
Published: September 2007

Atmospheric concentrations of elemental (Hg0), reactive gaseous (RGM), and particulate (PHg) mercury were measured at two remote sites in the midwestern United States. Concurrent measurements of Hg0, PHg, and RGM obtained at Devil’s Lake and Mt. Horeb, located approximately 65 km apart, showed that Hg0 and PHg concentrations were affected by regional, as well as local sources, while RGM was mainly impacted by local sources. Plumes reaching the Devil’s Lake site from a nearby coal-fired power plant significantly impacted SO2 and RGM concentrations at Devil’s Lake, but had little impact on Hg0. Our findings suggest that traditional modeling approaches to assess sources of mercury deposited that utilize source emissions and large-scale grids may not be sufficient to predict mercury deposition at sensitive locations due to the importance of small-scale sources and processes. We suggest the use of a receptor-based monitoring to better understand mercury source–receptor relationships.
Phosphorus recovery from anaerobic digester supernatants using a pilot-scale struvite crystallization process
Authors: Mavinic D.S. , Koch F.A. , Huang H. , Lo K.V.
Published: September 2007

The performance of a pilot-scale, struvite crystallization process, for recovering phosphorus from various supernatants, was investigated. Using synthetic supernatant, as well as anaerobic digester supernatants from two full-scale wastewater treatment plants located in Vancouver, B.C., Canada, it was found that over 90% phosphate removal efficiency was achieved through controlling the supersaturation ratio, operational pH and magnesium dosage in the supernatant. With a high supersaturation ratio, or high operational pH, or high magnesium dosage, excellent phosphate removal was achieved. However, an operational pH greater than 8 was not necessary;; it was possible to control the process using a high magnesium dosage in place of a higher operating pH, but without a compromise in phosphate removal. Chemical analysis of the harvested crystals indicated very pure struvite (in excess of 91%), with only small amounts of residual calcium, carbonate, and trace metals. Most crystals exceeded 2 mm in mean diameter.
Biological denitrification of reverse osmosis brine concentrates: II. Fluidized bed adsorber reactor studies
Authors: Ersever Ilknur , Ravindran Varadarajan , Pirbazari Massoud
Published: September 2007

This phase of the study (Part II) investigates the application of a high-rate fluidized bed adsorber reactor (FBAR) process for biological denitrification of reverse osmosis (RO) brine concentrate. The companion paper (Part I) reported the first phase of the project, describing the batch and chemostat biokinetic studies employed for evaluating the process feasibility, and for optimizing the reaction conditions including the carbon and energy source, pH, temperature, and the carbon-to-nitrogen ratio. This paper describes the next stage of the study involving FBAR experiments using granular activated carbon (GAC) for denitrification and sulfate reduction conducted at different hydraulic retention times, and nitrate concentrations. These experiments showed that nitrate removal efficiencies in excess of 99% were achieved. Similar FBAR experiments conducted with sand showed that initially less nitrate removal was experienced, but under steady-state conditions over 99% removal was achieved. Additionally, this study examined the simultaneous denitrification and sulfate removal in a similar FBAR process. A second FBAR, employed to remove the remaining sulfate from the first FBAR, achieved over 99% removal. A biofiltration process was designed and operated to effectively eliminate hydrogen sulfide in the sulfate-reducing FBAR process. The sulfate reduction FBAR was also responsible for the removal of toxic metals and metalloids present in the brine concentrate by a combination of sulfide precipitation and sorption onto iron sulfides.
Variation in North American regulatory guidance for heavy metal surface soil contamination at commercial and industrial sites
Authors: Jennings Aaron A. , Ma Jun
Published: September 2007

The health implications and remediation obligations of contaminated soils are significant issues in many urban areas of North America. For commercial and industrial sites, health concerns impact brownfield redevelopment and the conversion of fallow private land into public resources. To help manage health risks, regulatory agencies provide guidance values to identify maximum acceptable levels of contamination. Currently, these guidance values differ by as much as 5 orders of magnitude for some metals. The variability in North American guidance for Cd, Cr, Cu, Ni, Pb, and Zn surface soil contamination at commercial and industrial sites is examined. Ordered column diagrams illustrate the magnitude and dispersion of guidance values. Statistical analysis is used to investigate the significance of variations. Results indicate that commercial and industrial site guidance is more variable than residential site guidance and that even when the values are treated as lognormal random variables, some appear to be “uncharacteristic” outliers. The most significant regional trends are differences between US and Canadian guidance, but individual jurisdiction differences dominate over regional trends. When current guidance values sets were used in Hazard Index analysis applied to 20 sample urban brownfield sites, the results varied by 2 orders of magnitude.
Full-scale demonstration of an ultrasonic disintegration technology in enhancing anaerobic digestion of mixed primary and thickened secondary sewage sludge
Authors: Xie Rongjing , Xing Yongjie , Ghani Yahya Abdul , Ooi Kian-eng , Ng Siew-wah
Published: September 2007

For a country like Singapore with limited natural resources, innovative technologies are required to reduce sludge disposal volume and increase biogas production to recover energy in the wastewater treatment process. Ultrasound disintegration technology is potentially useful since it disintegrates sludge solids and enhances anaerobic digestion. The technology was tested in the field under tropical conditions with a full-scale ultrasonic facility and two 5000 m3 egg-shaped digesters. Each digester was fed with mixed primary (one-third) and thickened activated (two-thirds) sludge of identical quality and volumes of up to 200 m3·d–1. For the two digesters, all operating conditions were the same except for the inclusion (test) and omission (control) of the ultrasonic device to pre-treat the sludge feed. In comparison with the control, the five-month field study showed that ultrasound pre-treatment of the sludge increased the daily biogas production up to 45%. There were no significant differences in biogas composition from the two digesters. When translating the increases in biogas production into its source (volatile suspended solids), an increase in sludge solids removal of up to 30% is expected under optimal operation conditions.
Coarse woody debris and soil respiration in a clearcut on the Olympic Peninsula, Washington, U.S.A.
Authors: Marra James L. , Edmonds Robert L.
Published: September 2007

Coarse woody debris (CWD) and soil respiration rates were measured using soda lime traps on a clearcut site in the Hoh River Valley on the west side of the Olympic Peninsula, Washington. The influence of species of CWD (western hemlock (Tsugaheterophylla (Raf.) Sarg.) and Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco)), decay class, and log diameter on respiration rates was determined. CWD and soil respiration were measured every 4 weeks from October 1991 to November 1992 along with CWD and soil temperature and moisture contents. Western hemlock logs respired at a significantly higher rate (4.05 g CO2•m−2•day−1) than Douglas-fir logs (2.94 g CO2•m−2•day−1). There were no significant differences between respiration rates for decay classes 1–2, 3, and 5 logs (4.47, 3.69, and 4.28 g CO2•m−2•day−1, respectively), and there was no strong relationship between CWD respiration rate and log diameter. The highest average respiration rate was from the soil in the clearcut (5.22 g CO2•m−2•day−1). Averaged for the year, log and soil respiration rates in the clearcut site were similar to those in an adjacent old-growth forested site. However, seasonal fluctuations were greater on the clearcut site. Higher summer respiration rates and lower winter rates observed on the clearcut relative to the old-growth site appeared to be driven more by temperature than by moisture. Clear-cutting also resulted in higher summer CWD and soil temperatures and lower winter temperatures compared with the old-growth site.