bluuebunny/crossref_metadata_2025 huggingface dataset:
A genetic linkage map forStevia rebaudiana
Authors: Yao Y , Ban M , Brandle J
Published: April 2011

To lay a foundation for molecular breeding efforts, the first genetic linkage map for Stevia rebaudiana has been constructed using segregation data from a pseudo test-cross F1population. A total of 183 randomly amplified polymorphic DNA (RAPD) markers were analysed and assembled into 21 linkage groups covering a total distance of 1389 cM, with an average distance between markers of of 7.6 cM. The 11 largest linkage groups consisted of 4-19 loci, ranged in length from 56 to 174 cM, and accounted for 75% of the total map distance. Fifteen RAPD loci were found to be unlinked. From the 521 primers showing amplification products, 185 (35.5%) produced a total of 293 polymorphic fragments, indicating a high level of genetic diversity in stevia. Most of the RAPD markers in stevia segregated in normal Mendelian fashion.Key words: stevia, open-pollinated, genome map, RAPD.
Comparison of salt tolerance during seed germination and vegetative growth in tomato by QTL mapping
Authors: Foolad M R
Published: April 2011

The purpose of this study was to determine the genetic relationship between salt tolerance during seed germination and vegetative growth in tomato by comparing quantitative trait loci (QTLs) which confer salt tolerance at these two developmental stages. A salt-sensitive Lycopersicon esculentum line (NC84173; maternal and recurrent parent) was hybridized with a salt-tolerant accession (LA722) of Lycopersicon pimpinellifolium, and BC1and BC1S1populations were developed. The BC1population was used for RFLP mapping and the BC1S1population for evaluation of salt tolerance during germination and vegetative growth. The results indicated the presence of a small but significant correlation (r = -0.22, p < 0.05) between rate of seed germination and the percentage of plant survival under salt stress. Seven and five QTLs were identified for salt tolerance during seed germination and vegetative growth, respectively. While in most cases the location of QTLs for germination was different from that for vegetative growth, there were some coincidences in QTL locations; this was consistent with the small phenotypic correlation observed between the two traits. The overall results indicated that, in these tomato genetic materials, salt tolerance during seed germination was independent of that during vegetative growth. However, simultaneous improvement of tolerance at the two developmental stages should be possible through marker-assisted selection and breeding.Key words: Lycopersicon esculentum, L. pimpinellifolium, salt tolerance, seed germination vegetative growth, restriction fragment length polymorphism (RFLP), quantitative trait loci (QTLs).
Inheritance of a chromosomal polymorphism in odd-year pink salmon from southeastern Alaska
Authors: Phillips R B , Matsuoka M P , Smoker W W , Gharrett A J
Published: April 2011

In previous work we found a high frequency of heterozygotes for a fission translocation involving the seventh chromosome pair in odd-year populations of pink salmon (Oncorhynchus gorbuscha) sampled from Washington State to south central Alaska. The populations from southeastern Alaska and northern British Columbia had high frequencies of heterozygotes for a second rearrangement of this same chromosome pair. In these fish one fission product, the larger acrocentric chromosome bearing the nucleolar organizer region (NOR), has undergone an inversion to produce a submetacentric chromosome. In this paper, we present inheritance data on pink salmon from the Gastineau hatchery stock in Juneau, Alaska, where individuals with the two rearrangements are found. Although most of the fish were either homozygous for the normal cytotype or heterozygous for the inversion cytotype, a few individuals heterozygous for the fission cytotype were found. Ten males and ten females were karyotyped, and crosses were set up in all combinations. Individuals with both rearrangements were found in crosses between the two types of heterozygotes, and the ratios of cytotypes in the progeny did not deviate significantly from the expected values. No significant difference in viability of offspring from crosses between individuals with different cytotypes was found up to the age of hatching.Key words: salmon, chromosomal polymorphism, translocation, inversion, cytotype.
Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus
Authors: Rajagopal J , Das S , Khurana D K , Srivastava P S , Lakshmikumaran M
Published: April 2011

This report aims to describe the identification and molecular characterization of a 145-bp tandem repeat family that accounts for nearly 1.5% of the Populus genome. Three members of this repeat family were cloned and sequenced from Populus deltoides and P. ciliata. The dimers of the repeat were sequenced in order to confirm the head-to-tail organization of the repeat. Hybridization-based analysis using the 145-bp tandem repeat as a probe on genomic DNA gave rise to ladder patterns which were identified to be a result of methylation and (or) sequence heterogeneity. Analysis of the methylation pattern of the repeat family using methylation-sensitive isoschizomers revealed variable methylation of the C residues and lack of methylation of the A residues. Sequence comparisons between the monomers revealed a high degree of sequence divergence that ranged between 6% and 11% in P. deltoides and between 4.2% and 8.3% in P. ciliata. This indicated the presence of sub-families within the 145-bp tandem family of repeats. Divergence was mainly due to the accumulation of point mutations and was concentrated in the central region of the repeat. The 145-bp tandem repeat family did not show significant homology to known tandem repeats from plants. A short stretch of 36 bp was found to show homology of 66.7% to a centromeric repeat from Chironomus plumosus. Dot-blot analysis and Southern hybridization data revealed the presence of the repeat family in 13 of the 14 Populus species examined. The absence of the 145-bp repeat from P. euphratica suggested that this species is relatively distant from other members of the genus, which correlates with taxonomic classifications. The widespread occurrence of the tandem family in the genus indicated that this family may be of ancient origin.Key words: Satellite DNA, centromeric DNA, genome organization, phylogeny.
Two highly divergent 5S rDNA unit size classes occur in composite tandem array in European larch (Larix deciduaMill.) and Japanese larch (Larix kaempferi(Lamb.) Carr.)
Authors: Trontin Jean-François , Grandemange Catherine , Favre Jean-Michel
Published: April 2011

The 5S ribosomal DNA unit structure and organization have been investigated in Larix decidua and Larix kaempferi using selective amplification of gene and spacer, sequence analysis and homologous probe hybridization. Two highly divergent unit size classes of approximately 650 and 870 bp were detected in both species. Sequence analysis in Larix decidua revealed that length variations occur in the middle spacer region and are the result of duplications (in the long spacers) and considerable sequence heterogeneity. Conversely, the transcribed region is of uniform length (120 bp), and the nucleotide sequence of one Larix decidua clone is similar to that reported for other gymnosperms. Sequence comparison of the larch spacers with two other Pinaceae species (Pinus radiata and Picea glauca) showed that the 5' and 3' regions flanking the gene (40 and 60 bp, respectively) are quite conserved, suggesting a regulatory role. Moreover, a small element of about 70 bp located in the middle spacer region was found to be common to the larch long units and the six Pinus radiata spacer clones previously sequenced (64% sequence identity). The short and long unit size classes are mainly organized in composite tandem array(s) with evidence of extensive zones of strict alternation in both species. Mechanisms underlying this unusual association of divergent units in larch 5S rDNA arrays are discussed.Key words: 5S rRNA genes, spacer variations, cluster organization, sequence comparison, Gymnosperms.
The genome of the olive fruit flyBactrocera oleae: localization of molecular markers by in situ hybridization to the salivary gland polytene chromosomes
Authors: Zambetaki Anna , Zacharopoulou Antigone , Scouras Zacharias G , Mavragani-Tsipidou Penelope
Published: April 2011

Nine specific DNA probes (genomic or cDNA) from Ceratitis capitata have been mapped by in situ hybridization to the salivary gland polytene chromosomes of the olive fruit fly Bactrocera oleae, a major agricultural pest, thus establishing molecular markers for the 5 autosomal chromosomes. Taking into account the present results, as well as previous data obtained mainly by in situ hybridizations, chromosomal homologies among B. oleae, C. capitata and B. tryoni are established. Data show extensive linkage group conservation among the 3 taxa of the economically important and globally distributed family, the Tephritidae.Key words: Bactrocera oleae, Tephritidae, salivary gland, polytene chromosomes, in situ hybridization, mapping.
Initiation and progression of homologous chromosome synapsis in Crepis capillaris: Variations on a theme
Authors: Banerjee R , Jones G H
Published: April 2011

The model cytogenetic plant species Crepis capillaris (2x = 6), in which all 3 chromosomes are readily distinguished, was used to analyse the initiation and progression of meiotic synapsis in a large sample of spread and silver-stained pollen mother cells. Particular emphasis was placed on detecting general patterns or trends of synaptic order, both among different bivalents and within (along) individual bivalents, and investigating the consistency or otherwise of these synaptic patterns. The order of synaptic progression and completion was partly related to chromosome length; as in other species, shorter bivalents tended to complete synapsis ahead of longer ones. Individual bivalents also showed distinct patterns of synapsis, with a tendency for subterminal regions to initiate synapsis early, followed by multiple synaptic initiations in internal bivalent regions. However, the analysis showed that these synaptic patterns are only general trends and significant variations in synaptic order and pattern, among and within bivalents, occur in individual cells.Key words: meiosis, synapsis, synaptonemal complex, Crepis.
Phylogeny in the genus Hordeum based on nucleotide sequences closely linked to the vrs1 locus (row number of spikelets)
Authors: Komatsuda Takao , Tanno Ken-ichi , Salomon Björn , Bryngelsson Tomas , Bothmer Roland von
Published: April 2011

The phylogenetic relationship between four basic genomes designated H, I, Xa, and Xu in the genus Hordeum was studied using a nuclear DNA sequence. The sequence, cMWG699, is single copy in the H. vulgare genome, and tightly linked to the vrs1 locus which controls two- and six-rowed spikes. DNA fragments homologous to cMWG699 were amplified from diploid Hordeum species and the nucleotide sequences were determined. A phylogeny based on both base substitutions and an insertion-deletion event showed that the H- and Xa-genome groups are positioned in one monophyletic group indicating that the Xa-genome taxa should be included in the H-genome group. The large H-genome group is highly homogeneous. The I and Xu genomes are distinctly separated from H and Xa, and form sister groups. Another phylogeny pattern based on data excluding the insertion-deletion gave a result that the Xa genome forms a sister group to the H-genome group. The difference between the H and Xa genomes was affected only by a single base insertion-deletion event, thus the H and Xa genomes are likely to be closely related. The I and Xu genomes were again distinctly separated from the H and Xa genomes.Key words: genome DNA, molecular markers, restriction maps, barley, Psathyrostachys.
Within- and between-individual length heterogeneity of the rDNA-IGS inMiscanthus sinensisvar.glaber(Poaceae): Phylogenetic analyses
Authors: Chou Chang-Hung , Chiang Yu-Chung , Chiang Tzen-Yuh
Published: April 2011

The variability in the intergenic spacer (IGS) region between 17S and 25S rRNA genes of ribosomal DNA (rDNA) gene family was surveyed in Miscanthus sinensis var. glaber. Length heterogeneity, with sizes from 1782 to 2212 base pairs, of the IGS resulted from the variation of copy numbers of the A and B subrepeats. These repeated elements were located upstream of the presumptive polymerase I promoter, which was the region corresponding to the nontranscribed spacer (NTS). Length heterogeneity was detected both within and between individuals of Miscanthus sinensis var. glaber. Neighbor-joining analyses of repetitive A elements indicated that both unequal crossing-over and preferential conversion may have affected the hot-spot regions of the IGS in concert. Within-individual polymorphism and the reconstructed phylogeny suggested that interspecific hybridization has also contributed to length heterogeneity.Key words: concerted evolution, hybridization, length heterogeneity, Miscanthus sinensis var. glaber, rDNA, IGS.
Loss of heterozygosity and accelerated genotype fixation in rice hybrids
Authors: Wang RR -C , Li X -M , Chatterton N J
Published: April 2011

Loss of heterozygosity is reported in rice hybrids of a particular heritage. Hybrids derived from a plant selected from the Chinese rice cultivar 'Zhongxin No. 1' exhibited somatic variations as evidenced by having both segregating and uniform panicle rows in F2progenies. F3plants from uniform F2rows were found to be homozygous for all 14 RAPD (random amplified polymorphic DNA) markers, of which two co-dominant markers were located on chromosome 2 and five other markers were on five different chromosomes. RAPD markers unique to either parent were present or absent in all F2plants within some panicle rows, yet segregated in a Mendelian manner in other panicle rows. The molecular data suggest that somatic cells in these hybrids do not always contain both parental homologues of some chromosomes. These findings support the hypothesis that somatic chromosome pairing and recombination lead to loss of heterozygosity and non-identical daughter cells following mitosis. Sequential mitotic assortment of chromosome homologues of a plant's genome can lead to homozygous or nearly homozygous somatic cells that eventually develop into reproductive cells. As a result of this unique mechanism in rice hybrids derived from Zhongxin No. 1, uniform or less-segregating progenies can be identified from F2or F3panicle rows at a much higher frequency than normally expected. This phenomenon can be utilized to shorten the breeding cycle of rice, or other crops when plants containing gene(s) for mitotic pairing are identified, or when the genes are isolated from rice and effectively transferred into other crops.Key words: LOH, in vivo somatic variation, homozygous F2, RAPD, apomixis.
Molecular analysis of a 21.1-kb fragment of wheat chloroplast DNA bearing RNA polymerase subunit (rpo) genes
Authors: Ohnishi Y , Tajiri H , Matsuoka Y , Tsunewaki K
Published: April 2011

The entire nucleotide sequence of a 21.1-kb fragment of wheat chloroplast (ct) DNA was determined. This fragment carries 18 intact genes and parts of two additional genes, including the three RNA polymerase genes rpoB, rpoC1, and rpoC2. The gene arrangement of this region is conserved in wheat, rice, and maize, but not in non-grass species. Comparison of these 20 genes in wheat, rice, and maize showed that tRNA genes evolved more slowly than protein-coding genes in the chloroplast genome. Intergenic regions evolved much faster than both types of genes. Although the 19 genes of wheat, except for orf42, showed high identity to those of other plants, there were three novel structural features in the wheat rpoC2 gene; a deletion of 81 bp in the middle region, a variable insertion (408 bp), and a nonsense mutation in the 3' terminal region, resulting in truncation of a sequence of ca. 10 amino acids. An intermolecular recombination between the stretches of CTTAT and CTTTT was suggested as the mechanism of the 81-bp deletion in the wheat rpoC2 gene. Evolutionary distance between the chloroplast genomes of wheat and maize was larger than those between wheat and rice and between rice and maize.Key words: common wheat, chloroplast genes, evolutionary divergence, phylogeny.
Isolation of microsatellite and RAPD markers flanking theYr15gene of wheat using NILs and bulked segregant analysis
Authors: Chagué V , Fahima T , Dahan A , Sun G L , Korol A B , Ronin Y I , Grama A , Röder M S , Nevo E
Published: April 2011

Microsatellite and random amplified polymorphic DNA (RAPD) primers were used to identify molecular markers linked to the Yr15 gene which confer resistance to stripe rust (Puccina striiformis Westend) in wheat. By using near isogenic lines (NILs) for the Yr15 gene and a F2mapping population derived from crosses of these lines and phenotyped for resistance, we identified one microsatellite marker (GWM33) and one RAPD marker (OPA19800) linked to Yr15. Then, bulked segregant analysis was used in addition to the NILs to identify RAPD markers linked to the target gene. Using this approach, two RAPD markers linked to Yr15 were identified, one in coupling (UBC199700) and one in repulsion phase (UBC2121200). After Mapmaker linkage analysis on the F2population, the two closest markers were shown to be linked to Yr15 within a distance of about 12 cM. The recombination rates were recalculated using the maximum likelihood technique to take into account putative escaped individuals from the stripe rust resistance test and obtain unbiased distance estimates. As a result of this study, the stripe rust resistance gene Yr15 is surrounded by two flanking PCR markers, UBC199700and GWM33, at about 5 cM from each side.Key words: wheat, Triticum dicoccoides, Yr15 stripe rust resistance gene, genetic mapping, microsatellite markers, RAPD markers.
Quantitative trait loci for root-penetration ability and root thickness in rice: Comparison of genetic backgrounds
Authors: Zheng Hong-gang , Babu, Md. R Chandra , Pathan M Safiullah , Ali Liakat , Huang Ning , Courtois Brigitte , Nguyen Henry T
Published: April 2011

Drought is the major abiotic stress limiting rice (Oryza sativa) production and yield stability in rainfed lowland and upland ecosystems. Root systems play an important role in drought resistance. Incorporation of root selection criteria in drought resistance improvement is difficult due to lack of reliable and efficient screening techniques. Using a wax-petrolatum layer system simulated to compacted soil layers, root traits were evaluated in a doubled haploid (DH) population derived from the cross between 'IR64' and 'Azucena'. Twelve putative QTLs (quantitative trait loci) were detected by interval mapping comprising four QTLs for root-penetration ability, four QTLs for root thickness, two QTLs for penetrated root number, and two QTLs for total root number. These QTLs individually explained 8.4% to 16.4% of the phenotypic variation. No QTL was detected for maximum penetrated root length by interval mapping. One QTL located between RG104 and RG348 was found to influence both root-penetration ability and root thickness. QTLs for root-penetration ability and root thickness were compared across two populations, 'IR64'-'Azucena' and 'CO39'-'Moroberekan', and different testing conditions. The identified consistent QTLs could be used for marker-assisted selection for deep and thick roots with high root-penetration ability in rice. Key words: quantitative trait loci, root-penetration ability, root thickness, rice, drought.
Genomic organization of the 260 kb surrounding thewaxylocus in a Japonica rice
Authors: Nagano Hironori , Wu Lihua , Kawasaki Shinji , Kishima Yuji , Sano Yoshio
Published: April 2011

The present study was carried out to characterize the molecular organization in the vicinity of the waxy locus in rice. To determine the structural organization of the region surrounding waxy, contiguous clones covering a total of 260 kb were constructed using a bacterial artificial chromosome (BAC) library from the Shimokita variety of Japonica rice. This map also contains 200 overlapping subclones, which allowed construction of a fine physical map with a total of 64 HindIII sites. During the course of constructing the map, we noticed the presence of some repeated regions which might be related to transposable elements. We divided the 260-kb region into 60 segments (average size of 5.7 kb) to use as probes to determine their genomic organization. Hybridization patterns obtained by probing with these segments were classified into four types: class 1, a single or a few bands without a smeared background; class 2, a single or a few bands with a smeared background; class 3, multiple discrete bands without a smeared background; and class 4, only a smeared background. These classes constituted 6.5%, 20.9%, 3.7%, and 68.9% of the 260-kb region, respectively. The distribution of each class revealed that repetitive sequences are a major component in this region, as expected, and that unique sequence regions were mostly no longer than 6 kb due to interruption by repetitive sequences. We discuss how the map constructed here might be a powerful tool for characterization and comparison of the genome structures and the genes around the waxy locus in the Oryza species.Key words: BAC library, genomic organization, physical map, rice (Oryza sativa), the waxy locus.
Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat
Authors: Lijavetzky D , Muzzi G , Wicker T , Keller B , Wing R , Dubcovsky J
Published: April 2011

A genomic bacterial artificial chromosome (BAC) library of the A genome of wheat has been constructed. Triticum monococcum accession DV92 was selected for this purpose because it is a cultivated diploid wheat and one of the parental lines used in the construction of a saturated genetic map. Leaves from this accession were used to isolate high-molecular-weight DNA from nuclei. This DNA was partially digested with restriction enzyme Hind III, subjected to double size selection, electroeluted and cloned into the pINDIGO451 BAC vector. The library consists of 276 480 clones with an average insert size of 115 kb. Excluding the 1.33% of empty clones and 0.14% of clones with chloroplast DNA, the coverage of this library is 5.6 genome equivalents. With this genome coverage the probability of having any DNA sequence represented in this library is higher than 99.6%. Clones were sorted in 720 384-well plates and blotted onto 15 high-density filters. High-density filters were screened with several single or low-copy clones and five positive BAC clones were selected for further analysis. Since most of the T. monococcum BAC ends included repetitive sequences, a modification was introduced into the classical end-isolation procedure to select low copy sequences for chromosome walking.Key words: bacterial artificial chromosome, BAC library, Triticum monococcum, wheat.
Sequential meiotic prophase development in the pubertal Indian pygmy field mouse: Synaptic progression of the XY chromosomes, autosomal heterochromatin, and pericentric inversions
Authors: Bardhan Amit , Sharma T
Published: April 2011

Sequential meiotic prophase development has been followed in the pubertal male pygmy mouse Mus terricolor, with the objective to identify early meiotic prophase stages. The pygmy mouse differs from the common mouse by having large heterochromatic blocks in the X and Y chromosomes. These mice also show various chromosomal mutations; for example, fixed variations of autosomal short arms heterochromatin among different chromosomal species and pericentric inversion polymorphism. Identification of prophase stages was crucial to analyzing effects of heterozygosity for these chromosomal changes on the process of homologous synapsis. Here we describe identification of the prophase stages in M. terricolor, especially the pachytene substages, on the basis of morphology of the XY bivalent. Based on this substaging, we show delayed pairing of the heterochromatic short arms, which may be the reason for their lack of chiasmata. The identification of precise pachytene substages also reveals an early occurrence of "synaptic adjustment" in the pericentric inversion heterobivalents, a mechanism that would prevent chiasma formation in the inverted segment and thereby would abate adverse effects of such heterozygosity. The identification of pachytene substages would serve as the basis to analyze the nature of synaptic anomalies met in M. terricolor hybrids (which will be the basis of a subsequent paper). Key words: Mus terricolor, meiotic synapsis, sex chromosomes, pericentric inversion, heterochromatin.
A genetic and molecular characterization of thegarnetgene ofDrosophila melanogaster
Authors: Lloyd Vett K , Sinclair D A , Wennberg R , Warner T S , Honda B M , Grigliatti T A
Published: April 2011

The garnet gene was one of the first genes to be identified in Drosophila melanogaster. Mutations in the garnet gene affect both of the biochemically distinct types of pigments in the eye and disrupt pigmentation of other organs. As an initial step in the analysis of this gene, we have analyzed the pigmentation defects in several of the garnet alleles. We have also cloned the gene and examined its expression in various tissues and at different stages of development. The garnet gene is expressed throughout development and in all tissues examined. Structurally related sequences can be detected in a variety of other eukaryotes. The predicted protein sequence of the garnet product resembles clathrin and nonclathrin adaptin proteins and is highly similar to the delta subunit of the newly isolated mammalian AP-3 adaptin complex, which is associated with the trans-Golgi network and endosomes. This suggests that garnet encodes a protein that acts in the intracellular sorting and trafficking of vesicles from the trans-Golgi network to endosomes, and related specialized organelles such as the pigment granule. This finding provides an explanation for the phenotype of garnet mutations and predicts that other Drosophila eye-colour genes will be a rich resource for the genetic dissection of intracellular vesicle transport.Key words: garnet, Drosophila melanogaster, AP-3, eye pigments.
Genomic in situ hybridization analysis of Thinopyrum chromatin in a wheat - Th. intermedium partial amphiploid and six derived chromosome addition lines
Authors: Chen Qin , Conner R L , Laroche A , Ji W Q , Armstrong K C , Fedak G
Published: April 2011

The genomic origin of alien chromosomes present in a wheat - Thinopyrum intermedium partial amphiploid TAF46 (2n = 8x = 56) and six derived chromosome addition lines were analyzed by genomic in situ hybridization (GISH) using S genomic DNA from Pseudoroegneria strigosa (2n = 2x = 14, SS) as a probe. The GISH analysis clearly showed that the chromosome complement of the partial amphiploid TAF46 consists of an entire wheat genome plus one synthetic genome consisting of a mixture of six S genome chromosomes and eight J (=E) genome chromosomes derived from Th. intermedium (2n = 6x = 42, JJJsJsSS). There were no Js genome chromosomes present in TAF46. The J genome chromosomes present in TAF46 displayed a unique GISH hybridization pattern with the S genomic DNA probe, in which S genome DNA strongly hybridized at the terminal regions and weakly hybridized over the remaining parts of the chromosomes. This provides a diagnostic marker for distinguishing J genome chromosomes from Js or S genome or wheat ABD genome chromosomes. The genomic origin of the alien chromosomes present in the six derived chromosome addition lines were identified by their characteristic GISH hybridization patterns with S genomic DNA probe. GISH analysis showed that addition lines L1, L2, L3, and L5 carried one pair of J genome chromosomes, while addition lines L4 and L7 each carried one pair of S genome chromosomes. GISH patterns detected by the S genome probe on addition line of L1 were identical to those of the J genome chromosomes present in the partial amphiploid TAF46, suggesting that these chromosomes were not structurally altered when they were transferred from TAF46 to addition lines.Key words: GISH, genomic composition, addition lines, Thinopyrum intermedium, partial amphiploid.
Microsatellite repeats are not randomly distributed within Norway spruce (Picea abies K.) expressed sequences
Authors: Scotti I , Magni F , Fink R , Powell W , Binelli G , Hedley P E
Published: April 2011

A Norway spruce (Picea abies K.) cDNA library obtained from vegetative bud tissue was screened for the presence of (AG)n and (AC)n microsatellite repeats. Ten (AG)n and six (AC)n microsatellites were found, with an average length of 25.5 repeat units. Most of the microsatellites are simple perfect repeats. The microsatellite distribution within the clones is clearly non-random, with different classes of repeats lying in different positions relative to the coding region and in a highly conserved orientation. An estimate of the frequency of dinucleotide microsatellites in expressed regions was obtained, showing that SSRs (simple sequence repeats) are found in genes about 20 times less frequently than in random genomic clones, with (AG)n repeats more frequent than (AC)n repeats. Potential applications of these sequences as expressed region-based molecular markers are shown by developing six SSR markers for the detection of natural variation in Norway spruce populations and testing two of them for the identification of illegitimate progenies from a mapping population. Key words: Picea abies, microsatellites, SSRs, ESTs, population genetics, trees.
A PCR product derived from female DNA with regional localization on the Y chromosome
Authors: Torre Joaquina de la , Martínez-Ramírez Angel , Fernández José Luis , Díez-Martín José Luis , Gómez-Pineda Alfonso , Gosálvez Jaime , López-Fernández Carmen
Published: April 2011

A 154-bp PCR product amplified from human female DNA mapped onto the Y chromosome under high-stringency in situ hybridization conditions. The female DNA sequence revealed an 89% homology with the HSDYZ1 sequence. When the same primers were used to amplify male DNA, a 154-bp DNA fragment was also obtained, showing a 98% homology with HSDYZ1. However, although the HSDYZ1 sequence is widely distributed along the long arm of the Y chromosome, both of these particular PCR products are di-regionally localized within this distal block of constitutive heterochromatin. In situ hybridization under lower stringency showed that these 154-bp sequences map both onto the autosomes and the Y chromosome. Overall, this paper shows (i) a new class of DNA sequences shared by the autosomes and the Y chromosome; and (ii) a substructured organization of some DNA repeats within the DYZ1 family that forms a large part of the constitutive heterochromatin of the Y chromosome.Key words: human satellite DNA, satellite 3, DYZ1, Y chromosome.
Repetitive A-T rich DNA sequences from the Y chromosome of the Mediterranean fruit fly,Ceratitis capitata
Authors: Zhou Qin , Untalan Pia M , Haymer David S
Published: April 2011

Copies of a repetitive DNA sequence distributed over 90% of the length of the long arm of the Y chromosome of the Mediterranean fruit fly, Ceratitis capitata (medfly), have been characterized. Sequencing reveals that these repeats, ranging in size from approximately 1.3 to 1.7 kb, are A-T rich overall (67%). In most cases the repeat units appear to occur in tandemly linked arrays. The repeat copies also all contain a highly similar internal region, approximately 200 bp in length, with a more extreme A-T content bias. This internal region, designated as the AT element, exhibits an A-T content of at least 83%. This exceeds what has been described for any comparable element among invertebrates. Using primers designed from the DNA sequence, PCR amplification of an internal region encompassing the AT element also reveals that these sequences are present only in the male genome in different strains of the medfly.Key words: Y chromosome, medfly, Ceratitis capitata, AT elements, A-T content.
Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA ofTaraxacum(Lactuceae: Asteraceae)
Authors: Mes T HM , Kuperus P , Kirschner J , Stepanek J , Oosterveld P , Storchova H , den Nijs J CM
Published: April 2011

Sequence variation in 2.2 kb of non-coding regions of the chloroplast genome of eight dandelions (Taraxacum: Lactuceae) from Asia and Europe is interpreted in the light of the phylogenetic signal of base substitutions vs. indels (insertions-deletions). The four non-coding regions displayed a total of approximately 30 structural mutations of which 9 are potentially phylogenetically informative. Insertions, deletions, and an inversion were found that involved consecutive stretches of up to 172 bases. When compared to phylogenetic relationships of the chloroplast genomes based on nucleotide substitutions only, many homoplasious indels (33%) were detected that differed considerably in length and did not comprise simple sequence repeats typically associated with replication slippage. Though many indels in the intergenic spacers were associated with direct repeats, frequently, the variable stretches participated in inverted repeat stabilized hairpins. In each intergenic spacer or intron examined, nucleotide stretches ranging from 30 to 60 bp were able to fold into stabilized secondary structures. When these indels were homoplasious, they always ranked among the most stabilized hairpins in the non-coding regions. The association of higher order structures that involve both classes of repeats and parallel structural mutations in hot spot regions of the chloroplast genome can be used to differentiate among mutations that differ in phylogenetic reliability.Key words: Taraxacum, indel, non-coding chloroplast DNA, hairpin, evolution.
Polyploidy in a natural population of mussel, Mytilus trossulus
Authors: González-Tizón A , Martínez-Lage A , Ausio J , Méndez J
Published: April 2011

We have analyzed natural polyploidy in a population of Mytilus trossulus from Vancouver Island (British Columbia, Canada) by means of cytogenetic techniques. Results obtained are the first reporting on this type of numerical chromosome aberrations in mussels.

Key words: mussel, Mytilus trossulus, polyploidy, chromosome.
Enumeration and identification of heterotrophic bacteria in groundwater and in a mountain stream
Authors: Buchanan-Mappin J. M. , Wallis P. M. , Buchanan A. G.
Published: April 2011

Populations of heterotrophic bacteria were enumerated from stream and groundwater samples taken from an undisturbed catchment basin in southwestern Alberta. Direct counts using epifluorescence microscopy were compared with total viable counts using standard plate count methods, the iodonitrotetrazolium formazan method (reduction of 2-(p-iodophenyl)-3-(p-nitro phenyl)-5-phenyl tetrazolium chloride to iodonitrotetrazolium formazan), the nalidixic acid method, and the slide culture method. The nalidixic acid method gave the highest results, with total viable counts as high as 34.6% of the total direct count. Attempts to enumerate bacteria on media made from decaying leaves and algal–bacterial slime gave lower values, approximately 10% of the numbers obtained on enriched media. Stream waters were found to be dominated by Pseudomonas spp. and groundwaters were dominated by Bacillus spp. No differences were found in either numbers or species identified between tryptone – glucose – yeast extract agar, brain–heart infusion agar, nutrient agar, or casein–peptone–starch agar.
Quantitative characterization of microbial biomass and community structure in subsurface material: a prokaryotic consortium responsive to organic contamination
Authors: Smith Glen A. , Nickels Janet S. , Kerger Brent D. , Davis John. D. , Collins Stephen P. , Wilson John T. , McNabb James F. , White David C.
Published: April 2011

Application of quantitative methods for microbial biomass, community structure, and nutritional status to the subsurface samples collected with careful attention to contamination reveals the presence of a group of microbes. The microbiota is sparse by several measures of biomass compared with that present in surface sediments and soils. The community structure, as characterized by the patterns of ester-linked fatty acids from the phospholipids, shows an absence of long-chain polyenoic fatty acids typical of microeukaryotes and high proportions of fatty acids typical of bacteria. Subsurface samples contain a higher proportion of glycerol teichoic acids than surface samples. Microbes in uncontaminated subsurface sediments show nutritional stress as evidenced by high levels of poly-β-hydroxybutyrate and extracellular polysaccharides. The proportions of ester-linked phospholipid fatty acids show distinctive differences between surface and subsurface, between subsurface sandy clay and limestone, and between two sites of subsurface sandy clay as shown using stepwise discriminant analysis. Contamination increased the microbial biomass, shifted the community to a more gram-negative bacterial consortium, and induced growth as evidenced by phospholipid fatty acid biosynthesis.
Germination of Bacillus cereus spores induced by purine ribosides and their analogs: effects of modification of base and sugar moieties of purine nucleosides on germination-inducing activity
Authors: Shibata Hirofumi , Ohnishi Noriaki , Takeda Keiko , Fukunaga Hideko , Shimamura Kanako , Yasunobu Emiko , Tani Isamu , Hashimoto Tadayo
Published: April 2011

Purine riboside and some of its analogs were tested for their ability to induce germination of Bacillus cereus T spores. Hypoxanthine and adenine showed no germination-inducing activity either in the present or absence of D-ribose or its phosphorylated derivatives. Purine riboside and 18 analogs with modified purine base were all able to induce germination of the spores to various extents. In contrast to this, the requirement for the sugar moiety in the purine riboside appeared to be more stringent. Only those nucleosides that contained either D-ribose or deoxy-D-ribose, and certain species of azole derivatives such as 5-aminoimidazole-4-carboxamide covalently linked to the C(1′) of the sugar actively induced germination.
Localization of phytase inSelenomonas ruminantiumandMitsuokella multiacidusby transmission electron microscopy
Authors: D'Silva C G , Bae H D , Yanke L J , Cheng K -J , Selinger L B
Published: April 2011

The localization of phytase (myo-inositol-hexaphosphate phosphohydrolase) in the ruminal bacteria, Selenomonas ruminantium JY35 and Mitsuokella multiacidus 46/5(2), was determined with transmission electron microscopy. Phosphate produced from the enzymatic dephosphorylation of the calcium salt of phytic acid is precipitated as calcium phosphate. The calcium is then replaced with lead to produce electron-dense lead phosphate. This deposition of lead phosphate localized phytase in S. ruminantium JY35 and M. multiacidus 46/5(2) to the outer membrane, and confirmed intracellular expression of the enzyme in Escherichia coli pSrP.2, the recombinant clone which possesses the gene (phyA) encoding phytase (phyA) in S. ruminantium.Key words: phytase, localization, ruminal bacteria, transmission electron microscopy.
The potential of soil microorganisms to mineralize atrazine as predicted by MCH-PCR followed by nested PCR
Authors: Shapir Nir , Goux Sebastien , Mandelbaum Raphi T , Pussemier Luc
Published: April 2011

The potential of soil microorganisms to mineralize atrazine was studied in soil samples collected from fields with various histories of atrazine application. In contrast to many previous studies, which showed no atrazine mineralization activity, all the tested soils mineralized atrazine regardless of their atrazine application history. However, the delay before mineralization and the variation in the subsequent mineralization rate were in agreement with the initial copy number of the atrazine dechlorinaze gene, and the proliferation rate of the degraders. Soils from corn fields, which had up to 100 copies of the atzA gene per gram of soil, had a lag period of 4-5 days before atrazine mineralization started, and final mineralization percentages ranged from 40% to 54%. However, soils from fields that were never amended with atrazine had much longer lag periods (more than 17 days), which decreased after enrichment of the degrader population with high concentrations of atrazine for 15 days. Generally the mineralization rate and the atzA gene copy number increased after the enrichment period. The atrazine mineralization potential was measured by PCR of genes from the atrazine mineralization pathway. Magnetic capture hybridization was the most efficient of the two tested methods for purifying target DNA of PCR inhibitors, without reducing the copy number of the required fragment. Nested PCR proved to be the most effective method for predicting the exact potential of the soil to mineralize the pollutant even without enrichment of a small population with the target genes. This method can complement microcosm studies and eliminate futile efforts when the potential to mineralize the pollutant does not exist in the soil.Key words: MCH-PCR, mineralization, atrazine.
Monitoring by laser-flow-cytometry of the polycyclic aromatic hydrocarbon-degradingSphingomonassp. strain 107 during biotreatment of a contaminated soil
Authors: Thomas Jean-Christophe , St-Pierre Yves , Beaudet Réjean , Villemur Richard
Published: April 2011

A flow cytometric method (FCM) was used to detect and accurately enumerate a polycyclic aromatic hydrocarbon-degrading bacterial strain, Sphingomonas sp. 107, inoculated into a soil sample artificially contaminated with pyrene. To compare the FCM method with colony forming unit (CFU) assays, a rifampicin-resistant Sphingomonas sp. 107 was obtained which could be distinguished from the indigenous microflora, since there was no organism resistant to rifampicin in the soil that could transform indole to indigo (naphthalene dioxygenase activity). By combining light-scattering profiles (i.e., morphological properties), ethidium bromide influx (i.e., cell wall permeability), and fluorescence in situ hybridization against the 16S rRNA (i.e., detection specificity), we could enumerate the bacterial population of interest from the indigenous microflora and soil debris during the biotreatment. The FCM technique revealed that the number of inoculated Sphingomonas cells decreased gradually for 15 days of incubation before reaching a steady level of 7 to 12 × 105cells·g-1of soil. Similar values were obtained with the CFU assay. During this period, pyrene concentration decreased from 632 to 26 mg·kg-1of dry soil. The FCM detection was improved by adding blocking reagent to the hybridization buffer to minimize the non-specific attachment of the fluorescent probe to soil particles. Combined with the improvements in probe technology, FCM detection was shown to be a good alternative to the conventional culture methods for the analysis of bacterial populations in environmental samples. This technique could be potentially useful for the detection of microorganisms that grow poorly in culture.Key words: polycyclic aromatic hydrocarbons, Sphingomonas, bioremediation, soil, laser flow cytometry.
Mushroom (Agaricus bisporus) compost quality factors for predicting potential yield of fruiting bodies
Authors: Sharma H S , Kilpatrick M
Published: April 2011

A quality model has been developed from parameters determining the interactions of physical, chemical, and biological factors during the preparation of mushroom compost for growing Agaricus bisporus. Our results show that a partial least square model based on the combination of pH, dry matter, ammonia, carbon, hydrogen, ash, Cu, Fe, and Na could explain nearly 90% of the variation in mushroom yield obtained from four compost comparative trials. The yields in the data base for generating the model ranged from 138 to 305 kg per tonne of compost. The validity of the yield model has been confirmed in a trial carried out in collaboration with experienced commercial growers. This has significant implications for compost producers, as production efficiencies can be maintained by targeting the important parameters.Key words: Agaricus bisporus, compost quality, partial least squares model, modelling, physiology.
Eight UCA codons differentially affect the expression of the lacZ gene in the divE42 mutant of Escherichia coli
Authors: Kubo Takashi , Aiso Toshiko , Ohki Reiko
Published: April 2011

In the divE mutant, which has a temperature-sensitive mutation in the tRNA1Ser gene, the synthesis of beta-galactosidase is dramatically decreased at the non-permissive temperature. In Escherichia coli, the UCA codon is only recognized by tRNA1Ser. Several genes containing UCA codons are normally expressed at 42°C in the divE mutant. Therefore, it is unlikely that the defect is due to the general translational deficiency of the mutant tRNA1Ser. In this study, we constructed mutant lacZ genes, in which one or several UCA codons at eight positions were replaced with other serine codons such as UCU or UCC, and we examined the expression of these mutant genes in the divE mutant. We found that a single UCA codon at position 6 or 462 was sufficient to cause the same level of reduced beta-galactosidase synthesis as that of the wild-type lacZ gene, and that the defect in beta-galactosidase synthesis was accompanied by a low level of lacZ mRNA. It was also found that introduction of an rne-1 pnp-7 double mutation restored the expression of mutant lacZ genes with only UCA codons at position 6 or 462. A polarity suppressor mutation in the rho gene had no effect on the defect in lacZ gene expression in the divE mutant. We propose a model to explain these results.Key words: divE gene, tRNA1Ser, lacZ gene expression, UCA codon.
Enzymatic degradation of nitriles by aCandida guilliermondiiUFMG-Y65
Authors: Dias João CT , Rezende Rachel P , Rosa Carlos A , Lachance Marc-André , Linardi Valter R
Published: April 2011

Candida guilliermondii UFMG-Y65, isolated from a gold mine, was able to utilize different nitriles and the corresponding amides as sole source of nitrogen, at concentrations up to 2 M. Resting cells cultivated on YCB-acetonitrile medium showed nitrile hydrolyzing enzyme activities against acrylonitrile and benzonitrile. These enzymes were inducible and intracellular; the optimum pH was 7.0-8.0, and the optimum temperature 25°C-30°C. Liquid chromatographic analysis indicated that C. guilliermondii UFMG-Y65 metabolized 12 mM benzonitrile to 11 mM benzoic acid and 10 mM acrylonitrile to 7.9 mM acrylic acid. The results suggest that C. guilliermondii UFMG-Y65 may be useful for the bioproduction of amides and acids, and for the bioremediation of environments contaminated with nitriles.Key words: Candida guilliermondii, nitrile hydrolyzing enzyme, amidase, nitriles, amides.
Changes in the metabolism of the microalga Chlorella vulgaris when coimmobilized in alginate with the nitrogen-fixing Phyllobacterium myrsinacearum
Authors: Gonzalez-Bashan Luz E , Lebsky Vladimir K , Hernandez Juan P , Bustillos Jose J , Bashan Yoav
Published: April 2011

In an agroindustrial wastewater pond, a naturally occurring unicellular microalga, Chlorella vulgaris, was closely associated with the terrestrial plant-associative N2-fixing bacterium Phyllobacterium myrsinacearum. When the two microorganisms were artificially coimmobilized in alginate beads, they shared the same internal bead cavities, and the production of five microalgal pigments increased, but there were no effects on the number of the cells or the biomass of the microalga. The association, however, reduces the ability of C. vulgaris to remove ammonium ions and phosphorus from water. The bacterium produced nitrate from ammonium in synthetic wastewater with or without the presence of the microalga, and fixed nitrogen in two culture media. Our results suggest that interactions between microalgae and associative bacteria should be considered when cultivating microalgae for wastewater treatment.Key words: alginate, bacterial immobilization, microalgae, nitrogen fixation, Phyllobacterium, wastewater treatment.